The mineralization process of the fibrils results in a rigid, porous silica network that retains the microscale and nanoscale structure of the peptide fibril network. Though less sensitive than fluorescence, the Toac electron spin resonance ESR isotropic hyperfine splitting parameter can also monitor the titration of side-chain residues located relatively far from the probe. PNAs are nucleotide analogs that make use of a polymer of ethylenediamine monoacetic acid EDMA or 2-amninoethyl glycine with the bases attached by an acetic acid.
The three-dimensional structures of PhoE and OmpF have been determined [2]. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. A3APO- and Alyteserin-containing supernatants from these recombinant L.
The certified value of C- peptide The catalytic synthesis of peptides is a major challenge in the modern organic chemistry hindered by the well-established use of stoichiometric coupling reagents. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides.
The reaction was efficient in phosphate buffered saline and a wide range of biological buffers. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls.
Molecular dynamics MD simulation for ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.
For tissue regeneration and drug delivery applications, various architectures are explored to serve as biomaterial tools. The thermochemical characteristics of a wide range of amino acids and their derivatives were calculated. This mini-review discusses all the surprising twists of heterochiral self-assembled peptide hydrogels, and delineates emerging key findings to exploit all the benefits of D-amino acids in this novel medicinal area.
Furthermore, N-Boc-proline residue was successfully conjugated with oxindole derivatives using similar procedures. Reconstitution of porins into planar lipid bilayers revealed that the pores could be closed by application of a potential above a certain threshold value [8, 9].
Local softness, softness dipole, and polarizabilities of functional groups: Application to the side chains of the 20 amino acids. NASA Astrophysics Data System ADS. The values of molecular polarizabilities and softnesses of the 20 amino acids were computed ab initio MP2. By using the iterative Hirshfeld scheme to partition the molecular electronic properties, we demonstrate that the values of the softness of the side chain of the 20 amino acids are clustered in groups reflecting their biochemical classification, namely: The present findings are in agreement with previous results using different approximations and partitioning schemes [P.
In addition, we show that the polarizability of the side chain of an amino acid depends mainly on its number of electrons reflecting its size and consequently cannot be used to cluster the amino acids in different biochemical groups, in contrast to the local softness. Our results also demonstrate that the global softness is not simply proportional to the global polarizability in disagreement with the intuition that "a softer moiety is also more polarizable.
This discrepancy can be understood from first principles as we show that the molecular polarizability depends on a "softness dipole vector" and not simply on the global softness. The profiles of the utilization of 20 protein amino acids in Klebsiella pneumoniae sub- sp.
The utilization of amino acids was determined on minimal saline agar containing amino acid as the only source of nitrogen and carbon; the results were evaluated after hour incubation at 37 degrees C. The full coincidence of amino- acid utilization profiles in bacteria of K.
Borinic acid catalysed peptide synthesis. The catalytic synthesis of peptides is a major challenge in the modern organic chemistry hindered by the well-established use of stoichiometric coupling reagents. Herein, we describe for the first time that borinic acid is able to catalyse this reaction under mild conditions with an improved activity compared to our recently developed thiophene-based boronic acid. This catalyst is particularly efficient for peptide bond synthesis affording dipeptides in good yields without detectable racemization.
Nanotechnology for delivery of peptide nucleic acids PNAs. Over the past three decades, peptide nucleic acids have been employed in numerous chemical and biological applications. Peptide nucleic acids possess enormous potential because of their superior biophysical properties, compared to other oligonucleotide chemistries.
However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge. In this review, we summarize the progress that has been made in delivering peptide nucleic acids to intracellular targets.
In addition, we emphasize recent nanoparticle-based strategies for efficient delivery of conventional and chemically-modified peptides nucleic acids. An active twenty-amino- acid -residue peptide derived from the inhibitor protein of the cyclic AMP-dependent protein kinase. Digestion with Staphylococcus aureus V8 proteinase of the inhibitor protein of the cyclic AMP-dependent protein kinase results in the sequential formation of three active inhibitory peptides.
The smallest active peptide has the sequence Thr-Thr-Tyr-Ala-Asp-Phe-Ile-Ala-Ser-Gly-Arg-Thr-Gly-Arg-Arg-Asn-Ala-Ile- His-Asp. Inhibition, as a minimum, appears to be based upon the inhibitor protein containing the recognition sequences that dictate protein-substrate-specificity.
This inhibitory peptide also has sequence homology with the phosphorylation site for a protein kinase other than the cyclic AMP-dependent enzyme.
Glutamic Acid Selective Chemical Cleavage of Peptide Bonds. Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl pGlu imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.
Peptide and amino acid separation with nanofiltration membranes. Several nanofiltration membranes [UTC, 60 Toray IndustriesNF Film-Tech CorporationDesal-5, G Desalination Systemsand NTR Nitto Electric Industrial Co. Nanofiltration membranes having a molecular weight cutoff MWCO below UTC, 60, NF and Desal-5 were not suitable for separation of amino acids.
On the other hand, separation of amino acids and peptides with nanofiltration membranes having a MWCO around NTR and G was satisfactory based on a charge effect mechanism; charged amino acids and peptides were rejected while neutral amino acids and peptides permeated through the membranes. Separation of peptides having different isoelectric points with nanofiltration membranes was possible by adjusting the pH. BIOACTIVE PROTEINS, PEPTIDESAND AMINO ACIDS FROM MACROALGAE 1.
Macroalgae are a diverse group of marine organisms that have developed complex and unique metabolic pathways to ensure survival in highly competitive marine environments. As a result, these organisms have been targeted for mining of natural biologically active components.
The exploration of marine organisms has revealed numerous bioactive compounds that are proteinaceous in nature. These include proteins, linear peptidescyclic peptides and depsipeptides, peptide derivatives, amino acidsand amino acid -like components. Furthermore, some species of macroalgae have been shown to contain significant levels of protein. While some protein-derived bioactive peptides have been characterized from macroalgae, macroalgal proteins currently still represent good candidate raw materials for biofunctional peptide mining.
This review will provide an overview of the important bioactive amino- acid -containing compounds that have been identified in macroalgae. Moreover, the potential of macroalgal proteins as substrates for the generation of biofunctional peptides for utilization as functional foods to provide specific health benefits will be discussed.
Fatty acid conjugation enhances the activities of antimicrobial peptides. Antimicrobial peptides are small molecules that play a crucial role in innate immunity in multi-cellular organisms, and usually expressed and secreted constantly at basal levels to prevent infection, but local production can be augmented upon an infection. The clock is ticking as rising antibiotic abuse has led to the emergence of many drug resistance bacteria, kaspar k18c.
Due to their broad spectrum antibiotic and antifungal activities as well as anti-viral and anti-tumor activities, efforts are being made to develop antimicrobial peptides into future microbial agents. This article describes some of the recent patents on antimicrobial peptides with fatty acid conjugation.
Potency and selectivity of antimicrobial peptide can be modulated with fatty acid tails of variable length. Interaction between membranes and antimicrobial peptides was affected by fatty acid conjugation. At concentrations above the critical miscelle concentration CMCpropensity of solution selfassembly hampered binding of the peptide to cell membranes. Overall, fatty acid conjugation has enhanced the activities of antimicrobial peptidesand occasionally it rendered inactive antimicrobial peptides to be bioactive.
Antimicrobial peptides can not only be used as medicine but also as food additives. Amino Acid and Peptide Immobilization on Oxidized Nanocellulose: In this work, oxidized nanocellulose ONC was synthesized and chemically coupled with amino acids and peptides using a two step coupling method at room temperature.
Second, the active ester was reacted with the amino group of the amino acid or peptideforming an amide bond between ONC and the grafted molecule. Using this method, the intermolecular interaction of amino acids and peptides was avoided and uniform coupling of these molecules on ONC was achieved.
The coupling reaction was very fast in mild conditions and without alteration of the polysaccharide. The coupling products ONC-amino acids and ONC- peptides were characterized by transmission electron microscopy and by the absorption, emission, Fourier transform infrared spectroscopy FTIR and X-ray photoelectron spectroscopy XPS spectroscopic techniques. Peptide nucleic acid probes with charged photocleavable mass markers.
Halogen-labelled peptide organic acid HPOA monomers have been synthesised and incorporated into sequence-specific peptide nucleic acid PNA probes. Three different types of probe have been prepared; the unmodified PNA probe, the PNA probe with a mass marker, and the PNA probe with photocleavable mass marker. All three types of probe have been used in model studies to develop a mass spectrometry-based hybridisation assay for detection of point mutations in DNA.
Fragmentation reactions of deprotonated peptides containing aspartic acid. The fragmentation reactions of deprotonated peptides containing aspartic acid have been elucidated using MS2 and MS3 experiments and accurate mass measurements where necessary. The disposition of labile N and O bonded hydrogens in the fragmentation products has been studied by exchanging the labile hydrogens for deuterium whereby the [MD]- ion is formed on electrospray ionization.
Dipeptides of sequence HXxxAspOH give characteristic spectra different from the [alpha]- and [beta]-isomers. For larger peptides containing aspartic acid a common fragmentation reaction involves nominal cleavage of the NC bond N-terminal to the aspartic acid residue to form a c ion deprotonated amino acid amide c1 or peptide amide cn and the complimentary product involving elimination of a neutral amino acid amide or peptide amide.
When aspartic acid is in the C-terminal position this fragmentation reaction occurs from the [MH]- ion while when the aspartic acid is not in the C-terminal position the fragmentation reaction occurs mainly from the [MHH2O]- ion. The products of this NC bond cleavage reaction serve to identify the position of the aspartic acid residue in the peptide. A cumulative experience examining the effect of natural and synthetic antimicrobial peptides vs.
We tested the activity of 48 structurally diverse antimicrobial peptides against Chlamydia trachomatis, serovar L2. Peptides of 20 amino acids were more active than larger peptidessuch as defensins. Beta-sheet protegrins, as well as alpha-helical peptides such as novispirin G were equally active.
Enantiomers were as active as native structures. Moderate-sized circular mini-defensins were less effective against C. Moderate-sized cationic peptides may be useful in microbicide preparations designed to prevent chlamydial infection.
Method of identity analyte-binding peptides. A method for affinity chromatography or adsorption of a designated analyte utilizes a paralog as the affinity partner. The immobilized paralog can be used in purification or analysis of the analyte; the paralog can also be used as a substitute for antibody in an immunoassay. The paralog is identified by screening candidate peptide sequences of 20 amino acids for specific affinity to the analyte.
The paralog is identified by screening candidate peptide sequences of 4- 20 amino acids for specific affinity to the analyte. Histidine-lysine peptides as carriers of nucleic acids. Leng, Qixin; Goldgeier, Lisa; Zhu, Jingsong; Cambell, Patricia; Ambulos, Nicholas; Mixson, A James.
With their biodegradability and diversity of permutations, peptides have significant potential as carriers of nucleic acids. This review will focus on the sequence and branching patterns of peptide carriers composed primarily of histidines and lysines. While lysines within peptides are important for binding to the negatively charged phosphates, histidines are critical for endosomal lysis enabling nucleic acids to reach the cytosol.
Histidine-lysine HK polymers by either covalent or ionic bonds with liposomes augment transfection compared to liposome carriers alone. With a protocol change and addition of a histidine-rich tail, HK peptides as sole carriers were more effective than liposomes alone in several cell lines. While four-branched polymers with a primary repeating sequence pattern of -HHK- were more effective as carriers of plasmids, eight-branched polymers with a sequence pattern of -HHHK- were more effective as carriers of siRNA.
Compared to polyethylenimine, HK carriers of siRNA and plasmids had reduced toxicity. When injected intravenously, HK polymers in complex with plasmids encoding antiangiogenic proteins significantly decreased tumor growth.
Furthermore, modification of HK polymers with polyethylene glycol and vascular-specific ligands increased specificity of the polyplex to the tumor by more than fold. Together with further development and insight on the structure of HK polyplexes, HK peptides may prove to be useful as carriers of different forms of nucleic acids both in vitro and in vivo. Chiral separation of amino acids and peptides by capillary electrophoresis.
Chiral separation of amino acids and peptides by capillary electrophoresis CE is reviewed regarding the separation principles of different approaches, advantages and limitations, chiral recognition mechanisms and applications. The direct approach details various chiral selectors with an emphasis on cyclodextrins and their derivatives, antibiotics and chiral surfactants as the chiral selectors.
The indirect approach deals with various chiral reagents applied for diastereomer formation and types of separation media such as micelles and polymeric pseudo-stationary phases. Many derivatization reagents used for high sensitivity detection of amino acids and peptides are also discussed and their characteristics are summarized in tables.
A large number of relevant examples is presented illustrating the current status of enantiomeric and diastereomeric separation of amino acids and peptides. Strategies to enhance the selectivity and optimize separation parameters by the application of experimental designs are described.
The reversal of enantiomeric elution order and the effects of organic modifiers on the selectivity are illustrated in both direct and indirect methods. Some applications of chiral amino acid and peptide analysis, in particular, regarding the determination of trace enantiomeric impurities, are given. This review selects more than articles published between and How Amino Acids and Peptides Shaped the RNA World. Relatively small RNAs have catalytic power, RNA is everywhere in present-day life, the ribosome is seen as a ribozyme, and rRNA and tRNA are crucial for modern protein synthesis.
However, this view is incomplete at best. Very small RNAs versatile and stable due to basepairing and amino acidsas well as dipeptides, coevolved. Remember, it is the amino group of aminoacylated tRNA that attacks peptidyl-tRNA, destroying the bond between peptide and tRNA. This activity of the amino acid part of aminoacyl-tRNA illustrates the centrality of amino acids in life. The necessary presence and activity of amino acids and peptides is in need of highlighting. In this article, we try to bring the role of the peptide component of early life back into focus.
We argue that an RNA world completely independent of amino acids never existed. The bioactive acidic serine- and aspartate-rich motif peptide. The small integrin-binding ligand N-linked glycoprotein SIBLING family, a NCP, is considered to play a key role in bone mineralization. SIBLING family of proteins share common structural features and includes the arginine-glycine-aspartic acid RGD motif and acidic serine- and aspartic acid -rich motif ASARM.
ASARM peptides might not be primary responsible for the functional diversity of SIBLINGs, but this motif is suggested to be a key domain of SIBLINGs. However, the exact function of ASARM peptides is poorly understood. In this article, we discuss the considerable progress made in understanding the role of ASARM as a bioactive peptide.
A New Compound with Anti-Tyrosinase Potential. Singh, Birendra Kumar; Park, Seok Hoon; Lee, Hyang-Bok; Goo, Young-Aae; Kim, Hyoung Shik; Cho, Seung Hee; Lee, Jeong Hun; Ahn, Ghe Whan; Kim, Jin Pyo; Kang, Su Myoung. Background Kojic acid was used for decades in the cosmetic industry as an antimelanogenic agent.
However, there are two major drawbacks of Kojic acidone is cytotoxicity and second are instability on storage. These limitations led the scientist to synthesize the active Kojic acid peptides. Objective In the present study, we synthesize and investigate the effect of five Kojic acid peptides to overcome the limitation of Kojic acid. Methods The peptide was analyzed and purified by high-performance liquid chromatography and matrix-assisted laser desorption ionization time of flight mass spectroscopy.
Further, the tyrosinase activities of the Kojic acid and Kojic acid peptides were compared. The toxicity was measured and the melanin content is recorded in B16F10 mouse melanoma cells. Results Maximum tyrosinase activity was measured by Kojic acid peptides. Therefore, Kojic acid peptides were subjected to melanin assay and cytotoxicity assay and finally the stability of the Kojic acid peptide was measured. Conclusion It was observed that this newly synthesized Kojic acid peptide is stable and potent to inhibit the tyrosinase activity and melanin content of B16F10 mouse melanoma cells without exhibiting cell toxicity.
Together, these preliminary results suggest that a further exploration is being needed to establish Kojic acid peptide as antimelanogenic agent. Towards the improved discovery and design of functional peptides: The conventional wisdom is that certain classes of bioactive peptides have specific structural features that endow their particular functions.
Accordingly, predictions of bioactivity have focused on particular subgroups, such as antimicrobial peptides. We hypothesized that bioactive peptides may share more general features, and assessed this by contrasting the predictive power of existing antimicrobial predictors as well as a novel general predictor, Peptide Ranker, across different classes of peptides.
We observed that existing antimicrobial predictors had reasonable predictive power to identify peptides of certain other classes i.
These general predictors had performance that was typically as good as, or better than, that of specific predictors. We noted some striking differences in the features of short peptide and long peptide predictions, in particular, high scoring short peptides favour phenylalanine.
This is consistent with the hypothesis that short and long peptides have different functional constraints, perhaps reflecting the difficulty for typical short peptides in supporting independent tertiary structure. We conclude that there are general shared features of bioactive peptides across different functional classes, indicating that computational prediction may accelerate the discovery of novel bioactive peptides and aid in the improved design of existing peptidesacross many functional classes.
An implementation of the predictive method, Peptide Ranker, may be used to identify among a set of peptides those that may be more likely to be bioactive. The nature of peptide interactions with acid end-group PLGAs and facile aqueous-based microencapsulation of therapeutic peptides.
Maxwell; Tong, Ling; Cheng, Ji-Xin; Olsen, Karl F. An important poorly understood phenomenon in controlled-release depots involves the strong interaction between common cationic peptides and low Mw free acid end-group poly lactic-co-glycolic acids PLGAs used to achieve continuous peptide release kinetics. The kinetics of peptide sorption to PLGA was examined by incubating peptide solutions of 0.
Confocal Raman microspectroscopy and stimulated Raman scattering SRS and laser scanning confocal imaging techniques were used to examine peptide penetration in the polymer phase. We found that when the PLGA-COOH chains are sufficiently mobilized, therapeutic peptides not only bind at the surface, a common belief to date, but can also internalized and distributed throughout the polymer phase at physiological temperature forming a salt with low-molecular weight PLGA-COOH.
This new approach, which bypasses the traditional encapsulation method and associated production cost, opens up the potential for facile production of low-cost controlled-release injectable depots for leuprolide and related peptides.
Molecular self-assembly using peptide nucleic acids. Peptide nucleic acids PNAs are extensively studied for the control of genetic expression since their design in the s. However, the application of PNAs in nanotechnology is much more recent.
PNAs share the specific base-pair recognition characteristic of DNA together with material-like properties of polyamides, both proteins and synthetic polymers, such as Kevlar and Nylon. The first application of PNA was in the form of PNA-amphiphiles, resulting in the formation of either lipid integrated structures, hydrogels or fibrillary assemblies.
Heteroduplex DNA-PNA assemblies allow the formation of hybrid structures with higher stability as compared with pure DNA. A systematic screen for minimal PNA building blocks resulted in the identification of guanine-containing di-PNA assemblies and protected guanine-PNA monomer spheres showing unique optical properties.
Finally, the co-assembly of PNA with thymine-like three-faced cyanuric acid allowed the assembly of poly-adenine PNA into fibers. In summary, we believe that PNAs represent a new and important family of building blocks which converges the advantages of both DNA- and peptide -nanotechnologies. Amino acid sequence of atrial natriuretic peptides in human coronary sinus plasma. Two atrial natriuretic peptides were purified from pooled human coronary sinus plasma by Sep-Pak extraction, immunoaffinity chromatography and reverse phase HPLC.
The amino acid sequences of the two peptides were homologous with human atrial natriuretic peptide hANP and hANP, the latter being most probably linked to ANP by the disulphide bond. The molar ratio of the peptides in plasma, as assessed by radioimmunoassay was Microcin 25, a novel antimicrobial peptide produced by Escherichia coli. Microcin 25, a peptide antibiotic excreted by an Escherichia coli strain isolated from human feces, was purified to homogeneity and characterized.
Composition analysis and data from gel filtration indicated that microcin 25 may contain 20 amino acid residues. It has a blocked amino-terminal end. Microcin synthesis and immunity are plasmid determined, and the antibiotic was produced in minimal medium when the cultures entered the stationary phase of growth.
The peptide appears to interfere with cell division, since susceptible cells filamented when exposed to it. This response does not seem to be mediated by the SOS system.
Di-heterometalation of thiol-functionalized peptide nucleic acids. As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium II polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru II -polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone H-a-a-g-t-c-t-g-c-linker-cys-NH2 has been performed by standard peptide coupling method.
As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 H-gly-a-a-g-t-c-t-g-c-linker-cys-NH2 and PNA2 C1-a-a-g-t-c-t-g-c-linker-cys-NH2 to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed.
The synthesized ruthenium II -cymantrenyl PNA oligomers have been characterized by mass spectrometry ESI-MS and IR spectroscopy. Synthesis of hybrid hydrazino peptides: However, the lack of straightforward method for the synthesis of optically pure hydrazino acids and efficient incorporation of hydrazino building blocks into peptide sequence hamper wider exploitation of hydrazino peptidomimetics.
Pyrrolidinyl peptide nucleic acid homologues: The cyclobutane derivatives acbcPNA show the highest T m and excellent specificity with cDNA and RNA.
New mechanisms that regulate Saccharomyces cerevisiae short peptide transporter achieve balanced intracellular amino acid concentrations. The budding yeast Saccharomyces cerevisiae is able to take up large quantities of amino acids in the form of di- and tripeptides via a short peptide transporter, Ptr2p.
It is known that PTR2 can be induced by certain peptides and amino acidsand the mechanisms governing this upregulation are understood at the molecular level. We describe two new opposing mechanisms of regulation that emphasize potential toxicity of amino acids: Our findings emphasize the importance of proper amino acid balance in the cell and extend understanding of peptide import regulation in yeast.
Desalted duck egg white peptides promote calcium uptake by counteracting the adverse effects of phytic acid. The structure of the desalted duck egg white peptides -calcium chelate was characterized by fluorescence spectroscopy, fourier transform infrared spectroscopy, and dynamic light scattering.
Characterization results showed structural folding and aggregation of amino acids or oligopeptides during the chelation process. Desalted duck egg white peptides enhanced the calcium uptake in the presence of oxalate, phosphate and zinc ions in Caco-2 monolayers.
Animal model indicated that desalted duck egg white peptides effectively enhanced the mineral absorption and counteracted the deleterious effects of phytic acid. These findings suggested that desalted duck egg white peptides might promote calcium uptake in three pathways: Comparative studies of adhesion peptides based on l- or d-amino acids. Detailed studies comparing solid-supported l- or d-amino acid adhesion peptides based on the sequence KLHRIRA were performed.
Stability towards proteases and levels of cellular adhesion to the otherwise inert surface of PEGA resin were compared by using fluorescently labelled peptides. A clear difference in the peptide stability towards cleavage by subtilisin, trypsin, or papain was observed. However, all of the on-bead peptides provided an optimal surface for cell adhesion and proliferation.
In long-term experiments, these properties were still found to be similar on the resins modified either with l- or with d-amino acids and unaffected by the nature of their fluorescence labelling at either terminus. These results support that the more accessible l-amino acids can be utilized for cell adhesion experiments and confirm the nonspecific interaction mechanism of cell binding to these peptides on the bead surface.
Peptide -- Silica Hybrid Networks. In this study, a bio-inspired route was used to fabricate scaffolds that display hierarchical organization of an inorganic layer around an organic self-assembled peptide fibril template. The 20 amino acid peptide used in this study intramolecular folds into a beta-hairpin conformation on addition of a desired solution stimulus. This intramolecular folding is followed by intermolecular self-assembly of the peptides into a three dimensional network of entangled fibrils rich in beta-sheet with a high density of lysine groups exposed on the fibril-surfaces.
The lysine-rich surface chemistry was utilized to create a silica shell around the fibrils. The mineralization process of the fibrils results in a rigid, porous silica network that retains the microscale and nanoscale structure of the peptide fibril network.
Structural characterization via Transmission Electron Microscopy, cryogenic-Scanning Electron Microscopy, mechanical characterization via oscillatory rheology, Small Angle X-ray and Neutron Scattering of the silicified hydrogels will be presented.
The condensation of Val, Leu and Lys to form their homodipeptides can occur to a considerable extent due to catalytic effects of other amino acids and related compounds, among which glycine, histidine, diglycine and diketopiperazine exhibit the most remarkable activity.
These findings also lead to a modification of the table of amino acid sequences preferentially formed by the salt-induced peptide formation SIPF reaction, previously used for a comparison with the sequence preferences in membrane proteins of primitive organisms. Isolation and nature of intracellular alpha-aminoadipic acid -containing peptides from Paecilomyces persicinus P Small intracellular peptides containing alpha-aminoadipic acidcysteine, and a valine moiety were obtained from mycelia of Paecilomyces persicinus P by ethanol or trichloroacetic acid extraction.
After performic acid oxidation and ion-exchange chromatography, analysis of the peptide fractions by two-dimensional thin-layer electrophoresis and chromatography revealed the presence of three related peptidesas sulfonic acid derivatives, each containing alpha-aminoadipic acid. Each peptide was isolated in chromatographically pure form by semipreparative thin-layer electrophoresis and chromatography. The purified peptides were subjected to differential hydrolysis, dansylation, and combined dansylation-phenylisothiocyanate sequence analysis.
Based on these studies, the structures of the isolated peptides were determined to be i glycl-delta- alpha-aminoadipyl -cysteinyl-beta-hydroxyvaline, ii glycyl-delta- alpha-aminoadipyl -cysteinylvaline, and iii delta- alpha-aminoadipyl -cysteinylvaline. The peptides isolated from Paecilomyces are similar to the alpha-aminoadipic acid -cysteine-valine moiety complex peptides isolated from Cephalosporium. Phospholipid conjugate for intracellular delivery of peptide nucleic acids.
Shen, Gang; Fang, Huafeng; Song, Yinyin; Bielska, Agata A. Peptide nucleic acids PNAs have a number of attractive features that have made them an ideal choice for antisense and antigene-based tools, probes and drugs, but their poor membrane permeability has limited their application as therapeutic or diagnostic agents.
Herein we report a general method for the synthesis of phospholipid-PNAs LP-PNAsand compare the effect of non-cleavable lipids and bioreductively cleavable lipids L and LSS and phospholipid LP on the splice-correcting bioactivity of a PNA bearing the cell penetrating Arg9 group PNA-R9. The activity of both LP-PNA-R9 and L-PNA-R9 were found to dramatically increase with chloroquine, as expected for an endocytotic entry mechanism. Both constructs were also found to have CMC values of 1.
Supramolecular control of self-assembling terthiophene- peptide conjugates through the amino acid side chain. The self-assembly of oligothiophene— peptide conjugates can be directed through the systematic variation of the peptide sequence into different nanostructures, including flat spicules, nanotubes, spiral sheets, and giant, flat sheets. Furthermore, the assembly of these molecules is not controlled by steric interactions between the amino acid side chains.
Cyclic Sulfamidate Enabled Syntheses of Amino AcidsPeptidesCarbohydrates, and Natural Products. This article reviews the emergence of cyclic sulfamidates as versatile intermediatesfor the synthesis of unnatural amino acidschalcogen peptidesmodified sugars, drugs and drug candidates, and important natural products.
Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization. We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval.
Conventional reagents place both the selectively reacting group the "warhead" and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid PNAsynthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases, kaspar k18c.
As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand carrying the tagged protein and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat.
Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA: PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. Systematic studies of the mass spectrometric properties of alkaline earth metal cationized amino acids and peptides.
Furthermore, a model for the cationization with calcium at the C-terminal amino acid arginine in rotaviral polypeptides is presented. Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides. Li, Zhiyu; Dilger, Jonathan M. Cross sections for 61 palmitoylated peptides and 73 cysteine-unmodified peptides are determined and used together with a previously obtained tryptic peptide library to derive a set of intrinsic size parameters ISPs for the palmitoyl Pal group 1.
These values highlight the influence of the intrinsic hydrophobic and hydrophilic nature of these modifications on the overall cross sections. As a part of this analysis, we find that ISPs derived from a database of a modifier on one amino acid residue CysPal can be applied on the same modification group on different amino acid residues SerPal and TyrPal. We propose that modification groups should be treated as individual contribution factors, kaspar k18c, instead of treating the combination of the particular group and the amino acid residue they are on as a whole when considering their effects on the peptide ion mobility features.
Efficacy of peptide nucleic acid and selected conjugates against specific cellular pathologies of amyotrophic lateral sclerosis. Browne, Elisse C; Parakh, Sonam; Duncan, Luke F; Langford, Steven J; Atkin, Julie D; Abbott, Belinda M.
Cellular studies have been undertaken on a nonamer peptide nucleic acid PNA sequence, which binds to mRNA encoding superoxide dismutase 1, and a series of peptide nucleic acids conjugated to synthetic lipophilic vitamin analogs including a recently prepared menadione vitamin K analog.
Reduction of both mutant superoxide dismutase 1 inclusion formation and endoplasmic reticulum stress, two of the key cellular pathological hallmarks in amyotrophic lateral sclerosis, by two of the prepared PNA oligomers is reported for the first time. Antimicrobial Peptides Containing Unnatural Amino Acid Exhibit Potent Bactericidal Activity against ESKAPE Pathogens.
Antimicrobial peptides containing unnatural amino acid exhibit potent bactericidal activity against ESKAPE pathogens R. DATES COVERED - 4. TITLE AND SUBTITLE Antimicrobial Peptides Containing Unnatural Amino Acid Exhibit Potent Bactericidal Activity Against. Simultaneous separation of acid and basic bioactive peptides by electrodialysis with ultrafiltration membrane.
However, these protein hydrolysates have to be fractionated to obtain peptides in a more purified form. Electrodialysis with ultrafiltration membrane EDUF appeared to be a selective method of separation since amongst a total of 40 peptides in the raw hydrolysate, only 13 were recovered in the separated adjacent solutions KCl 1 and KCl 2.
Furthermore, the highest migration was obtained for the ACE-inhibitory peptide beta-lgwith a value of The integrity of the UF membrane was kept and EDUF would minimize the fouling of UF membrane. We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening.
The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, kaspar k18c, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments.
The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptideare available at http: Installing amino acids and peptides on N-heterocycles under visible-light assistance. Peptides and N-heterocycles exhibit various biological and pharmaceutical functions.
Conjugation of amino acids or peptides with N-heterocycles provides boundless potentiality for screening and discovery of diverse biologically active molecules.
However, it is a great challenge to install amino acids or peptides on N-heterocycles through formation of carbon-carbon bonds under mild conditions. Furthermore, N-Boc-proline residue was successfully conjugated with oxindole derivatives using similar procedures. The simple protocol, mild reaction conditions, fast reaction, and high efficiency of this method make it an important strategy for synthesis of diverse molecules containing amino acid and peptide fragments.
Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products. NASA Technical Reports Server NTRS. The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products.
In our search for this prebiotic process that yielded catalytic takeover products such as polypeptideswe have been investigating a reaction system that generates peptide -forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes.
Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: Recently, we discovered that amino acidssuch as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid. Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides.
Molecular modelling approaches have been used to understand the interaction of collagen-like peptides with gallic acidwhich mimic vegetable tanning processes involved in protein stabilization. Several interaction sites have been identified and the binding energies of the complexes have been calculated. It is found that some complexes exhibit hydrogen bonding, and electrostatic interaction plays a dominant role in the stabilization of the peptide by gallic acid. Molecular dynamics MD simulation for ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.
Noninvasive molecular imaging of MYC mRNA expression in human breast cancer xenografts with a [99mTc] peptide-peptide nucleic acid-peptide chimera. Tian, Xiaobing; Aruva, Mohan R; Qin, Wenyi; Zhu, Weizhu; Sauter, Edward R; Thakur, Mathew L; Wickstrom, Eric.
Human estrogen receptor-positive breast cancer cells typically display elevated levels of Myc protein due to overexpression of MYC mRNA, and elevated insulin-like growth factor 1 receptor IGF1R due to overexpression of IGF1R mRNA. We hypothesized that scintigraphic detection of MYC peptide nucleic acid PNA probes with an IGF1 peptide loop on the C-terminus, and a [99mTc]chelator peptide on the N-terminus, could measure levels of MYC mRNA noninvasively in human IGF1R-overexpressing MCF7 breast cancer xenografts in nude mice.
We prepared the chelator-MYC PNA-IGF1 peptideas well as a 4-nt mismatch PNA control, by solid-phase synthesis. We imaged MCF7 xenografts scintigraphically and measured the distribution of [99mTc]probes by scintillation counting of dissected tissues. MCF7 xenografts in nude mice were visualized at 4 and 24 h after tail vein administration of the [99mTc]PNA probe specific for MYC mRNA, but not with the mismatch control.
The [99mTc]probes distributed normally to the kidneys, livers, tumors, and other tissues. Molecular imaging of oncogene mRNAs in solid tumors with radiolabel-PNA- peptide chimeras might provide additional genetic characterization of preinvasive and invasive breast cancers. Activation of carboxyl group with cyanate: The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth.
The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the 1H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution pH 2. The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution.
The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.
Amino Acid - vs. Responses of Individual Olfactory Receptor Neurons in an Aquatic Species. Amino acids are widely used waterborne olfactory stimuli proposed to serve as cues in the search for food.
In natural waters the main source of amino acids is the decomposition of proteins. But this process also produces a variety of small peptides as intermediate cleavage products. In the present study we tested whether amino acids actually are the natural and adequate stimuli for the olfactory receptors they bind to. Alternatively, these olfactory receptors could be peptide receptors which also bind amino acids though at lower affinity.
Employing calcium imaging in acute slices of the main olfactory epithelium of the fully aquatic larvae of Xenopus laevis we show that amino acidsand not peptidesare more effective waterborne odorants. Synthesis and biological properties of amino acids and peptides containing a tetrazolyl moiety.
Literature data published mainly in the last 15 years on the synthesis and biological properties of amino acid analogues and derivatives containing tetrazolyl moieties are analyzed.
Tetrazolyl analogues and derivatives of amino acids and peptides are shown to be promising for medicinal chemistry. Being polynitrogen heterocyclic systems comprising four endocyclic nitrogen atoms, tetrazoles can behave as acids and bases and form strong hydrogen bonds with proton donors more rarely, with acceptors. They have high metabolic stability and are able to penetrate biological membranes. The review also considers the synthesis and properties of linear and cyclic peptides based on modified amino acids incorporating a tetrazolyl moiety.
A special issue is the discussion of the biological properties of tetrazole-containing amino acids and peptideswhich exhibit high biological activity and can be used to design new drugs. The bibliography includes references. A toy model of prebiotic peptide evolution: This paper presents a mathematical-computational toy model based on the assumed dynamic principles of prebiotic peptide evolution.
Starting from a pool of amino acid monomers, the model describes in a generalized manner the generation of peptides and their sequential information. The model integrates the intrinsic and dynamic key elements of the initiation of biopolymerization, such as the relative amino acid abundances and polarities, as well as the oligomer reversibility, i.
Our modeling results suggest that the relative amino acid abundances, as indicated by Miller-Urey type electric discharge experiments, played a principal role in the early sequential information of peptide profiles. Moreover, the computed profiles display an astonishing similarity to peptide profiles observed in so-called biological common ancestors found in the following three microorganisms; E.
The prebiotic peptide fingerprint was obtained by the so-called polarity index method that was earlier reported as a tool for the identification of cationic amphipathic antibacterial short peptides. Analysis of Endogenous D-Amino Acid -Containing Peptides in Metazoa. Peptides are chiral molecules with their structure determined by the composition and configuration of their amino acid building blocks.
The naturally occurring amino acidsexcept glycine, possess two chiral forms. This allows the formation of multiple peptide diastereomers that have the same sequence. Although living organisms use L-amino acids to make proteins, a group of D-amino acid -containing peptides DAACPs has been discovered in animals that have at least one of their residues isomerized to the D-form via an enzyme-catalyzed process. In many cases, the biological functions of these peptides are enhanced due to this structural conversion.
These DAACPs are different from those known to occur in bacterial cell wall and antibiotic peptidesthe latter of which are synthesized in a ribosome-independent manner. DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. Their serendipitous discovery has often resulted from discrepancies observed in bioassays or in chromatographic behavior between natural peptide fractions and peptides synthesized according to a presumed all-L sequence.
Because this L-to-D post-translational modification is subtle and not detectable by most sequence determination approaches, it is reasonable to suspect that many studies have overlooked this change; accordingly, DAACPs may be more prevalent than currently thought. Although diastereomer separation techniques developed with synthetic peptides in recent years have greatly aided in the discovery of natural DAACPs, there is a need for new, more robust methods for naturally complex samples.
In this review, a brief history of DAACPs in animals is presented, followed by discussion of a variety of analytical methods that have been used for diastereomeric separation and detection of peptides. The Prebiotic Synthesis of Ethylenediamine Monoacetic AcidThe Repeating Unit of Peptide Nucleic Acids. The polymerization of ribonucleic acids or their precursors constitutes an important event in prebiotic chemistry. The various problems using ribonucleotides to make RNA suggest that there may have been a precursor.
An attractive possibility are the peptide nucleic acids PNA. PNAs are nucleotide analogs that make use of a polymer of ethylenediamine monoacetic acid EDMA or 2-amninoethyl glycine with the bases attached by an acetic acid. EDMA is an especially attractive alternative to the ribose phosphate or deoxyribose phosphate backbone because it contains no chiral centers and is potentially prebiotic, but there is no reported prebiotic synthesis.
We have synthesized both EDMA and ethylenediamine diacetic acid EDDA from the prebiotic compounds ethylenediamine, formaldehyde, and hydrogen cyanide. These reactions work with concentrations of 10 exp -1 M and as low as 10 exp -4 M, and the reaction is likely to be effective at even lower concentrations. Ethylenediamine is a likely prebiotic compound, but it has not yet been demonstrated, although compounds such as ethanolamine and cysteamine have been proven to be prebiotic.
Under neutral pH and heating at l00 C, EDMA is converted to the lactam, monoketopiperazine MKP. We have measured the solubilities of EDMA center dot H20 as 6. These syntheses together with the high solubility of EDMA suggest that EDMA would concentrate in drying lagoons and might efficiently form polymers.
Given the instability of ribose and the poor polymerizability of nucleotides, the prebiotic presence of EDMA and the possibility of its polymerization raises the possibility that PNAs are the progenitors of present day nucleic acids.
A pre-RNA world may have existed in which PNAs or. Trifluoroethanol effects on helix propensity and electrostatic interactions in the helical peptide from ribonuclease T1. Trifluoroethanol TFE is often used to increase the helicity of peptides to make them usable as models of helices in proteins.
There are three main conclusions from our studies. A method for the 32P labeling of peptides or peptide nucleic acid oligomers. A novel approach to the radioactive labeling of peptides and PNA oligomers is described. Peptide nucleic acid PNA: It is proposed that the primordial genetic material could have been peptide nucleic acidsi.
PNA monomers based on the amino acidalpha, gamma-diaminobutyric acid or ornithine are suggested as compounds that could have been formed in the prebiotic soup. Bacterial expression of self-assembling peptide hydrogelators. For tissue regeneration and drug delivery applications, various architectures are explored to serve as biomaterial tools.
Via de novo design, functional peptide hydrogel materials have been developed as scaffolds for biomedical applications. The objective of this study is to investigate bacterial expression as an alternative method to chemical synthesis for the recombinant production of self-assembling peptides that can form rigid hydrogels under physiological conditions.
The Schneider and Pochan Labs have designed and characterized a 20 amino acid beta-hairpin forming amphiphilic peptide containing a D-residue in its turn region MAX1. As a result, this peptide must be prepared chemically. Peptide engineering, using the sequence of MAX1 as a template, afforded a small family of peptides for expression EX peptides that have different turn sequences consisting of natural amino acids and amenable to bacterial expression.
Each sequence was initially chemically synthesized to quickly assess the material properties of its corresponding gel. One model peptide EX1, was chosen to start the bacterial expression studies. DNA constructs facilitating the expression of EX1 were designed in such that the peptide could be expressed with different fusion partners and subsequently cleaved by enzymatic or chemical means to afford the free peptide.
Optimization studies were performed to increase the yield of pure peptide that ultimately allowed 50 mg of pure peptide to be harvested from one liter of culture, providing an alternate means to produce this hydrogel-forming peptide.
Recombinant production of other self-assembling hairpins with different turn sequences was also successful using this optimized protocol. The studies demonstrate that new beta-hairpin self-assembling peptides that are amenable to bacterial production and form rigid hydrogels at physiological conditions can be designed and produced by fermentation in good yield at significantly reduced cost when compared to.
The enthalpies of formation and sublimation of amino acids and peptides. The experimental enthalpies of formation of L-amino acids and peptides were analyzed using the additive scheme and group contributions.
Group contributions to the enthalpies of formation were calculated increment denotations corresponded to the Benson-Buss symbols. The thermochemical characteristics of a wide range of amino acids and their derivatives were calculated.
Site-Specific Characterization of d-Amino Acid Containing Peptide Epimers by Ion Mobility Spectrometry. Traditionally, the d-amino acid containing peptide DAACP candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates.
Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry IMS analysis of mass spectrometry MS -generated epimeric fragment ions.
The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones CHHs, 8. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus.
Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues. Predicting three-dimensional conformations of peptides constructed of only glycine, alanine, aspartic acidand valine. The GADV hypothesis is a form of the protein world hypothesis, which suggests that life originated from proteins Lacey et al. In the GADV hypothesis, life is thought to have originated from primitive proteins constructed of only glycine, alanine, aspartic acidand valine [GADV]-proteins.
In this study, the three-dimensional 3D conformations of randomly generated short [GADV]- peptides were computationally investigated using replica-exchange molecular dynamics REMD simulations Sugita and Okamoto Because the peptides used in this study consisted of only 20 residues each, they could not form certain 3D structures. However, the conformational tendencies of the peptides were elucidated by analyzing the conformational ensembles generated by REMD simulations.
The results indicate that secondary structures can be formed in several randomly generated [GADV]- peptides. A long helical structure was found in one of the hydrophobic peptidessupporting the conjecture of the GADV hypothesis that many peptides aggregated to form peptide multimers with enzymatic activity in the primordial soup.
In addition, these results indicate that REMD simulations can be used for the structural investigation of short peptides. Predicting Three-Dimensional Conformations of Peptides Constructed of Only Glycine, Alanine, Aspartic Acidand Valine. REACTION OF AMINO- ACIDS AND PEPTIDE BONDS WITH FORMALDEHYDE AS MEASURED BY CHANGES IN THE ULTRA-VIOLET SPECTRA. Peptide modules for overcoming barriers of nucleic acids transport to cells.
Absence of safe and efficient methods of nucleic acids delivery is one of the major issues which limits the development of human gene therapy. Highly efficient viral vectors raise questions due to safety reasons. Among non-viral vectors peptide -based carriers can be considered as good candidates for the development of "artificial viruses"--multifunctional polyplexes that mimic viruses. Suggested strategy to obtain multifunctionality is to combine several peptide modules into one modular carrier.
Different kinds of peptide modules are needed for successful overcoming barriers of nucleic acids transport into the cells. Design of such modules and establishment of structure-function relationships are issues of importance to researchers working in the field of nucleic acids delivery. Effect of Fatty Acid Conjugation on Antimicrobial Peptide Activity. Since amphipathicity is requisite for antimicrobial action KAK is not Antimicrobial evaluation of N-alkyl betaines and N-alkyl-N,N-dimethylamine oxides with variations in chain length.
Targeting pre-miRNA by Peptide Nucleic Acids. PNAs conjugated to carrier peptides have been employed for the targeting of miRNA precursor, with the aim to develop molecules able to interfere in the pre-miRNA processing.
The capability of the molecules to bind pre-miRNA has been tested in vitro by fluorescence assayes on Thiazole Orange labeled molecules and in vivo, in K cells, evaluating the amount of miRNA produced after treatment of cells with two amounts of PNAs. Effects of Acidic Peptide Size and Sequence on Trivalent Praseodymium Adduction and Electron Transfer Dissociation Mass Spectrometry.
Using the lanthanide ion praseodymium, Pr IIImetallated ion formation and electron transfer dissociation ETD were studied for 25 biological and model acidic peptides. For chain lengths of seven or more residues, even highly acidic peptides that can be difficult to protonate by electrospray ionization will metallate and undergo abundant ETD fragmentation. Primarily metallated and non-metallated c- and z-ions form for all peptides investigated.
Metal adducted product ions are only present when at least half of the peptide sequence can be incorporated into the ion; this suggests that the metal ion simultaneously attaches to more than one acidic site.
The only site consistently lacking dissociation is at the N-terminal side of a proline residue. Increasing peptide chain length generates more backbone cleavage for metal- peptide complexes with the same charge state. The results of this study indicate that highly acidic peptides can be sequenced by ETD of complexes formed with Pr III.
Calcium Binding to Amino Acids and Small Glycine Peptides in Aqueous Solution: Toward Peptide Design for Better Calcium Bioavailability. Deprotonation of amino acids as occurs during transfer from stomach to intestines during food digestion was found by comparison of complex formation constants as determined electrochemically for increasing pH to increase calcium binding i by a factor of around 6 for the neutral amino acidsii by a factor of around 4 for anions of the acidic amino acids aspartic and glutamic acidand iii by a factor of around 5.
Optimized structures of the 1: For binary amino acid mixtures, the calcium-binding constant was close to the predicted geometric mean of the individual amino acid binding constants indicating separate binding of calcium to two amino acids when present together in solution. Hajisharifi, Zohre; Piryaiee, Moien; Mohammad Beigi, Majid; Behbahani, Mandana; Mohabatkar, Hassan. Cancer is an important reason of death worldwide. Traditional cytotoxic therapies, such as radiation and chemotherapy, are expensive and cause severe side effects.
Currently, design of anticancer peptides is a more effective way for cancer treatment. So there is a need to develop a computational method for predicting the anticancer peptides. In the present study, two methods have been developed to predict these peptides using support vector machine SVM as a powerful machine learning algorithm.
Since a number of HIV-1 proteins have cytotoxic effect, therefore we predicted the anticancer effect of HIV-1 p24 protein with these methods. After the prediction, mutagenicity of 2 anticancer peptides and 2 non-anticancer peptides was investigated by Ames test.
Our results show that, the accuracy and the specificity of local alignment kernel based method are The accuracy and specificity of PseAAC-based method are By computational analysis, out of 22 peptides of p24 protein, 4 peptides are anticancer and 18 are non-anticancer. In the Ames test results, it is clear that anticancer peptides ARP Therefore the results demonstrate that the described computation methods are useful to identify potential anticancer peptideswhich are worthy of further experimental validation and 2 peptides ARP A model structure for the primordial genetic material?
It is proposed that the primordial genetic material could have been peptide nucleic aicds,i. The influence two original derivatives of a therapeutically important peptidebearing arachidonic acid residue with semax and proglyprol, upon platelet aggregation have been studied in vitro.
It is established that both derivatives, in contrast to the parent peptidepossess moderate anti-aggregant properties and produce a dose-dependent decrease in the interplatelet interaction induced by ADP, epinephrine, and arachidonic acid within the concentration range of 0. This activity was more pronounced for arachidonoylsemax in comparison with arachidonoylproglyprol.
Peptide interfacial biomaterials improve endothelial cell adhesion and spreading on synthetic polyglycolic acid materials. Huang, Xin; Zauscher, Stefan; Klitzman, Bruce; Truskey, George A; Reichert, William M; Kenan, Daniel J; Grinstaff, Mark W.
Resorbable scaffolds such as polyglycolic acid PGA are employed in a number of clinical and tissue engineering applications owing to their desirable property of allowing remodeling to form native tissue over time. However, native PGA does not promote endothelial cell adhesion. Here we describe a novel treatment with hetero-bifunctional peptide linkers, termed "interfacial biomaterials" IFBMswhich are used to alter the surface of PGA to provide appropriate biological cues.
IFBMs couple an affinity peptide for the material with a biologically active peptide that promotes desired cellular responses. One such PGA affinity peptide was coupled to the integrin binding domain, Arg-Gly-Asp RGDto build a chemically synthesized bimodular 27 amino acid peptide that mediated interactions between PGA and integrin receptors on endothelial cells.
Cell binding studies indicated that IFBM efficiently mediated adhesion, spreading, and cytoskeletal organization of endothelial cells on PGA in an integrin-dependent manner. Synthesis of lipoic acid-peptide conjugates and their effect on collagen and melanogenesis.
Lu, Chichong; Kim, Bo Mi; Lee, Duckhee; Lee, Min Hee; Kim, Jin Hwa; Pyo, Hyeong-Bae; Chai, Kyu Yun. We report new examples of lipoic acid LA - peptide conjugates, their potential as codrugs having anti-melanogenic and anti-aging properties was evaluated. These multifunctional molecules were prepared by linking lipophilic moiety LA to the pentapeptide KTTKS.
The inhibitory effect of LA- peptide conjugates on melanin synthesis and tyrosinase activity is stronger than that of LA or the pentapeptide alone. Importantly, the conjugates display no cytotoxicity at a high concentration. LA-KTTKS and LA-PEG-KTTKS also inhibit UV-induced matrix metalloproteinase-1 expression up to LA- peptide conjugates stimulate collagen biosynthesis in fibroblasts more efficiently than their parent molecules do. These data suggest that LA- peptide conjugates may have cosmeceutical application as anti-melanogenic and anti-aging agents.
Surface Functionalization of Piezoelectric Aluminum Nitride with Selected Amino Acid and Peptides. In the present contribution, we elaborate on the covalent attachment of the amino acid cysteine and selected cysteine-bearing peptidesin aqueous buffered media, onto AlN surfaces modified with adlayers of one of our homemade bifunctional alkyltrichlorosilane cross-linking molecules bearing the benzenethiosulfonate head group.
Oxidative diversification of amino acids and peptides by small-molecule iron catalysis. Secondary metabolites synthesized by non-ribosomal peptide synthetases display diverse and complex topologies and possess a range of biological activities. Much of this diversity derives from a synthetic strategy that entails pre- and post-assembly oxidation of both the chiral amino acid building blocks and the assembled peptide scaffolds.
The vancomycin biosynthetic pathway is an excellent example of the range of oxidative transformations that can be performed by the iron-containing enzymes involved in its biosynthesis. However, because of the challenges associated with using such oxidative enzymes to carry out chemical transformations in vitro, chemical syntheses guided by these principles have not been fully realized in the laboratory. Oxidation of proline to 5-hydroxyproline furnishes a versatile intermediate that can be transformed to rigid arylated derivatives or flexible linear carboxylic acidsalcohols, olefins and amines in both monomer and peptide settings.
The value of this C-H oxidation strategy is demonstrated in its capacity for generating diversity: Additionally, a macrocyclic peptide containing a proline turn element is transformed via late-stage C-H oxidation to one containing a linear unnatural amino acid.
Characterization of bioactive RGD peptide immobilized onto poly acrylic acid thin films by plasma polymerization. Seo, Hyun Suk; Ko, Yeong Mu; Shim, Jae Won; Lim, Yun Kyong; Kook, Joong-Ki; Cho, Dong-Lyun; Kim, Byung Hoon. Plasma surface modification can be used to improve the surface properties of commercial pure Ti by creating functional groups to produce bioactive materials with different surface topography.
In this study, a titanium surface was modified with acrylic acid AA using a plasma treatment and immobilized with bioactive arginine-glycine-aspartic acid RGD peptidewhich may accelerate the tissue integration of bone implants. Both terminals containing the -NH2 of RGD peptide sequence and -COOH of poly acrylic acid PAA thin film were combined with a covalent bond in the presence of 1-ethyldimethylaminopropyl carbodiimide EDC.
The chemical structure and morphology of AA film and RGD immobilized surface were investigated by X-ray photoelectron spectroscopy XPSFourier transform infrared FT-IRatomic force microscopy AFMand scanning electron microscopy SEM.
All chemical analysis showed full coverage of the Ti substrate with the PAA thin film containing COOH groups and the RGD peptide. The MC3T3-E1 cells were cultured on each specimen, and the cell alkaline phosphatase ALP activity were examined. The surface-immobilized RGD peptide has a significantly increased the ALP activity of MC3T3-E1 cells.
These results suggest that the RGD peptide immobilization on the titanium surface has an effect on osteoblastic differentiation of MC3T3-E1 cells and potential use in osteo-conductive bone implants. Lactobacillus gasseri requires peptidesnot proteins or free amino acidsfor growth in milk. Lactobacillus gasseri is a widespread commensal lactic acid bacterium inhabiting human mucosal niches and has many beneficial effects as a probiotic.
It had been previously reported that supplementation with yeast extract or proteose peptone, including peptidesenables L. In this study, our objective was to confirm peptide requirement of L. Three strains of L. In contrast, little effect was observed after adding casein or a casein-derived amino acid mixture, casamino acids. These results indicate that L. Lactobacillus gasseri JCM T hardly had growth capacity in 6 kinds of milk-based media: Moreover, treatment with digestive proteases, particularly pepsin, to release peptides made it grow well in each milk-based medium.
As well as strain JCM T, pepsinolysis of milk improved growth of other L. These results suggest that some relatives of L. Synthesis of peptides from amino acids and ATP with lysine-rich proteinoid. The paper examines the synthesis of peptides from aminoacids and ATP with a lysine-rich protenoid. The latter in aqueous solution catalyzes the formation of peptides from free amino acids and ATP; this catalytic activity is not found in acidic protenoids, even though the latter contain a basic aminoacid.
The pH optimum for the synthesis is about 11, but it is appreciable below 8 and above Temperature data indicate an optimum at 20 C or above, with little increase in rate up to 60 C. Pyrophosphate can be used instead of ATP, but the yields are lower. The ATP-aided syntheses of peptides in aqueous solution occur with several types of proteinous aminoacids. Antimicrobial peptides incorporating non-natural amino acids as agents for plant protection.
The control of plant pathogens is mainly based on copper compounds and antibiotics. However, the use of these compounds has some limitations. They have a high environmental impact and the use of antibiotics is not allowed in several countries. Moreover, resistance has been developed to these pathogens. The identification of new agents able to fight plant pathogenic bacteria and fungi will represent an alternative to currently used antibiotics or pesticides.
Antimicrobial peptides are widely recognized as promising candidates, however naturally occurring sequences present drawbacks that limit their development. These include susceptibility to protease degradation and low bioavailability.
To overcome these problems, research has focused on the introduction of unnatural amino acids into lead peptide sequences. In particular, we have improved the biological profile of antimicrobial peptides active against plant pathogenic bacteria and fungi by incorporating triazolyl, biaryl and D-amino acids into their sequence.
These modifications and their influence on the biological activity are summarized. Release of free amino acids upon oxidation of peptides and proteins by hydroxyl radicals.
Hydroxyl radical-induced oxidation of proteins and peptides can lead to the cleavage of the peptideleading to a release of fragments. Bovine serum albumin BSAovalbumin OVA as model proteins, and synthetic tripeptides comprised of varying compositions of the amino acids Gly, Ala, Ser, and Met were used for reactions with hydroxyl radicals, which were generated by the Fenton reaction of iron ions and hydrogen peroxide.
Upon oxidation of tripeptides with Gly in C-terminal, mid-chain, or N-terminal positions, Gly was preferentially released when it was located at the C-terminal site. Overall, we observe evidence for a site-selective formation of free amino acids in the OH radical-induced oxidation of peptides and proteins, which may be due to a reaction pathway involving nitrogen-centered radicals.
Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods. Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acidwere compared. MALDI post-source decay PSDMALDI nm photodissociation, tris 2,4,6-trimethoxyphenyl phosphonium bromide TMPP charge tagging in PSD and photodissociation, ESI collision-induced dissociation CIDelectron transfer dissociation ETDand free-radical initiated peptide sequencing FRIPS with CID were applied to peptides containing either aspartic or isoaspartic acid.
For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.
Studies on anchoring of Fmoc-amino acids and peptide cleavage. The esterification of 2-chlorotrityl chloride resin with Fmoc-amino acids in the presence of DIEA is studied under various conditions.
High esterification yields are obtained using 0. The reaction proceeds without by product formation even in the case of Fmoc-Asn and Fmoc-Gln. Under these exceptionally mild conditions 2-chlorotrityl cations generated during the cleavage of amino acids and peptides from resin do not attack the nucleophilic side chains of Trp, Met, and Tyr.
Eight biological acidic peptidesranging in size from 11 to 33 residues, were studied by negative ion mode ISD nISD. The matrices 2,5-dihydroxybenzoic acid2-aminobenzoic acid2-aminobenzamide, 1,5-diaminonaphthalene, 5-aminonaphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene DANand extensive sequence informative fragmentation was observed for every peptide except hirudin The formation of c and z ions is also found in electron transfer dissociation ETDelectron capture dissociation ECDand positive ion mode ISD, which are considered to be radical-driven techniques.
Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues.
In addition, spectra were obtained by positive ion mode ISD for each protonated peptide ; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides. Selected Lactic Acid Bacteria Synthesize Antioxidant Peptides during Sourdough Fermentation of Cereal Flours.
A pool of selected lactic acid bacteria was used for the sourdough fermentation of various cereal flours with the aim of synthesizing antioxidant peptides.
WSE were subjected to reverse-phase fast protein liquid chromatography. Thirty-seven fractions were collected and assayed in vitro. The most active fractions were resistant to further hydrolysis by digestive enzymes.
Twenty-five peptides of 8 to 57 amino acid residues were identified by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry. Almost all of the sequences shared compositional features which are typical of antioxidant peptides. All of the purified fractions showed ex vivo antioxidant activity on mouse fibroblasts artificially subjected to oxidative stress.
This study demonstrates the capacity of sourdough lactic acid bacteria to release peptides with antioxidant activity through the proteolysis of native cereal proteins. Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor. CD4 T cells recognize peptides bound to major histocompatibility complex MHC class II molecules.
Most MHC class II molecules have four binding pockets occupied by amino acids 1, 4, 6, and 9 of the minimal peptide epitope, while the residues at positions 2, 3, 5, 7, and 8 are available to interact with the T cell receptor TCR.
In addition MHC class II bound peptides have flanking residues situated outside of this peptide core. Here we demonstrate that the flanking residues of the conalbumin peptide bound to I-A k have no effect on recognition by the D10 TCR. To study the role of peptide flanks for recognition by a second TCR, we determined the MHC and TCR contacting amino acids of the I-A b bound Ealpha peptide. The Ealpha peptide is shown to bind I-A b using four alanines as anchor residues.
TCR recognition of Ealpha peptides with altered flanking residues again suggested that, in general, no specific interactions occurred with the peptide flanks. However, using an HLA-DM-mediated technique to measure peptide binding to MHC class II molecules, we found that the peptide flanking residues contribute substantially to MHC binding.
Laser ion beam photodissociation studies of model amino acids and peptides. Photoexcitation of the DNP peptides by a visible proton results in fragmentation of the peptide chain with little fragmentation within the chromophore.
These results are rationalized with particular emphasis on energy-selective dissociation channels of large ionic systems. The rate of dissociation of photoexcited ions of DNP peptides is shown to decrease with increasing molecular weight degrees of freedom.
Lastly, comparisons between photodissociation and collision-induced dissociation as a structural probe are presented. Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases.
If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides.
Next, we synthesize identified peptides in the array format and rescreen the serum used for phage panning to validate antibody binding peptides. Finally, we systematically vary the sequence of validated antibody binding peptides to identify those amino acids within the peptides that are crucial for binding "their" antibody species. The resulting immune fingerprints can then be used to trace them back to potential antigens. We investigated the serum of an individual in this pipeline, which led to the identification of 73 antibody fingerprints.
Some fingerprints could be traced back to their most likely antigen, for example the immunodominant capsid protein VP1 of enteroviruses, most likely elicited by the ubiquitous poliovirus vaccination. Thus, with our approach, it is possible, to pinpoint those antibody species that correlate with a certain antigen, without any pre-information. This can help to unravel hitherto enigmatic diseases. Antimicrobial Peptides Targeting Gram-negative Pathogens, Produced and Delivered by Lactic Acid Bacteria.
We present results of tests with recombinant Lactococcus lactis that produce and secrete heterologous antimicrobial peptides with activity against Gram-negative pathogenic Escherichia coli and Salmonella.
In an initial screening, the activities of numerous candidate antimicrobial peptidesmade by solid state synthesis, were assessed against several indicator pathogenic E.
Peptides A3APO and Alyteserin were selected as top performers based on high antimicrobial activity against the pathogens tested and on significantly lower antimicrobial activity against L. Expression cassettes containing the signal peptide of the protein Usp45 fused to the codon optimized sequence of mature A3APO and Alyteserin were cloned under the control of a nisin-inducible promoter nisA and transformed into L. The resulting recombinant strains were induced to express and secrete both peptides.
A3APO- and Alyteserin-containing supernatants from these recombinant L. This system may serve as a model for the production and delivery of antimicrobial peptides by lactic acid bacteria to target Gram-negative pathogenic bacteria populations. HIV-1 enhancing effect of prostatic acid phosphatase peptides is reduced in human seminal plasma. We recently reported that HIV-1 infection can be inhibited by innate antimicrobial components of human seminal plasma SP. Conversely, naturally occurring peptidic fragments from the SP-derived prostatic acid phosphatase PAP have been reported to form amyloid fibrils called "SEVI" and enhance HIV-1 infection in vitro.
In order to understand the biological consequence of this proviral effect, we extended these studies in the presence of human SP. PAP-derived peptides were agitated to form SEVI and incubated in the presence or absence of SP. The anti-HIV-1 activity of SP was concentration dependent and was reduced following filtration. Supraphysiological concentrations of PAP peptides and SEVI incubated with diluted SP were degraded within hours, with SP exhibiting proteolytic activity at dilutions as high as 1: Sub-physiological concentrations of two prominent proteases of SP, prostate-specific antigen PSA and matriptase, could degrade physiological and supraphysiological concentrations of PAP peptides and SEVI.
While human SP is a complex biological fluid, containing both antiviral and proviral factors, our results suggest that PAP peptides and SEVI may be subject to naturally occurring proteolytic components capable of reducing their proviral activity.
Aromatic amino acids providing characteristic motifs in the Raman and SERS spectroscopy of peptides. Raman and surface-enhanced Raman spectroscopies SERS are potentially important tools in the characterization of biomolecules such as proteins and DNA. In this work, SERS spectra of three cysteine-containing aromatic peptides: From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present.
It follows that the Raman modes of these three small constructed peptides may likely apply to the assignment of Raman and SERS features in the spectra of other peptides and proteins. Secondary metabolites synthesized by nonribosomal peptide synthetases NRPSs display diverse and complex topologies and possess an impressive range of biological activities1,2 Much of this diversity derives from a synthetic strategy that entails the oxidation of both the chiral amino acid building blocks and the assembled peptide scaffolds pre-3 and post-assembly2.
Oxidation of proline to 5-hydroxyproline furnishes a versatile intermediate that can be transformed to rigid arylated derivatives or flexible linear carboxylic acidsalcohols, olefins, and amines in both monomer and peptide settings. The value of this C—H oxidation strategy is demonstrated in its capacity for generating diversity: Additionally, a macrocyclic peptide containing a proline turn element is transformed via late-stage C—H oxidation to one containing a linear UAA.
Interaction of cationic peptides with lipoteichoic acid and gram-positive bacteria. Compounds with antiendotoxin properties have been extensively studied for their potential as therapeutic agents for sepsis attributable to gram-negative bacteria. However, with the increasing incidence of gram-positive sepsis, there is interest in identifying compounds with a broad spectrum of action against both gram-positive and gram-negative bacteria.
A series of synthetic alpha-helical cationic peptides related to bee melittin and silk moth cecropin have previously been shown to bind lipopolysaccharide LPS with high affinity, inhibit LPS-induced tumor necrosis factor alpha TNF-alpha production in vitro and in vivo, and kill gram-negative bacteria.
In this study, we analyzed whether these peptides were active against gram-positive bacteria; whether they could bind to lipoteichoic acid LTAthe major proinflammatory structure on gram-positive bacteria; and whether they could block the ability of LTA to promote the release of cytokines by the RAW We found that the cationic peptides demonstrated moderate growth-inhibitory activity toward gram-positive bacteria.
In addition, the peptides bound LTA with high affinity. This correlated with the ability of the peptides to block LTA-induced production of TNF and interleukin-6 by RAW The peptides also effectively inhibited LTA-induced TNF production in a whole human blood assay. The peptides were also able to partly block the ability of heat-killed Staphylococcus aureus, as well as soluble products of live S.
Our results indicate that these cationic peptides may be useful to prevent sepsis and inflammation caused by both gram-negative and gram-positive bacteria. Stable Isotope Peptide Mass Spectrometry To Decipher Amino Acid Metabolism in Dehalococcoides Strain CBDB1. Dehalococcoides species are key players in the anaerobic transformation of halogenated solvents at contaminated sites.
Here, we analyze isotopologue distributions in amino acid pools from peptides of Dehalococcoides strain CBDB1 after incubation with 13C-labeled acetate or bicarbonate as a carbon source. The resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. With this method, we identify isotope incorporation patterns for 17 proteinaceous amino acidsincluding proline, cysteine, lysine, and arginine, which escaped previous analyses in Dehalococcoides.
Similarly, the isotopologue pattern obtained for arginine provided biochemical evidence of its synthesis from glutamate. By addition of unlabeled free amino acids to labeled cells, we show that in strain CBDB1 none of the 17 tested amino acids was incorporated into cell mass, indicating that they are all synthesized de novo.
Our approach is widely applicable and provides a means to analyze amino acid metabolism by studying specific proteins even in mixed consortia. Entropy reduction in unfolded peptides and proteins due to conformational preferences of amino acid residues. As established by several groups over the last 20 years, amino acid residues in unfolded peptides and proteins do not exhibit the unspecific random distribution as assumed by the classical random coil model. Individual amino acid residues in small peptides were found to exhibit different conformational preferences.
Here, we utilize recently obtained conformational distributions of guest amino acid residues in GxG peptides to estimate their conformational entropy, which we find to be significantly lower than the entropy of an assumed random coil like distribution. Only at high temperature do backbone entropies approach random coil like values. Calculated and experimentally derived entropic losses were found to be in good agreement. For most of the amino acid residues investigated entropic losses derived from our GxG distributions correlate very well with corresponding values recently obtained from MD simulations biased by conformational propensities derived from truncated coil libraries.
Both, conformational entropy and the entropy of solvation exhibit a strong, residue specific temperature dependence, which can be expected to substantially affect the stability of unfolded states. Altogether, our results provide strong evidence for the notion that conformational preferences of amino acid residues matter with regard to the thermodynamics of peptide and protein folding.
The Unexpected Advantages of Using D-Amino Acids for Peptide Self-Assembly into Nanostructured Hydrogels for Medicine. Self-assembled peptide hydrogels have brought innovation to the medicinal field, not only as responsive biomaterials but also as nanostructured therapeutic agents or as smart drug delivery systems.
D-amino acids are typically introduced to increase the peptide enzymatic stability. However, there are several reports of unexpected effects on peptide conformation, self-assembly behavior, cytotoxicity and even therapeutic activity. This mini-review discusses all the surprising twists of heterochiral self-assembled peptide hydrogels, and delineates emerging key findings to exploit all the benefits of D-amino acids in this novel medicinal area.
Peptide nucleic acids and the origin and homochirality of life. The possibilities of pseudo peptide DNA mimics like PNA peptide nucleic acid having a role for the prebiotic origin of life prior to an RNA world is discussed. In particular a scenario is proposed in which protocells with an achiral genetic material through several generations stepwise is converted into a chiral genetic material, e.
Provided that a sufficiently large sequence space is occupied, a selection process based on catalytic function in which a single cell first common ancestor has a definite evolutionary advantage, selection of this cell would by contingency also lock it into homochirality. Applications of hydrophilic interaction chromatography to amino acidspeptidesand proteins.
This review summarizes the recent advances in the analysis of amino acidspeptidesand proteins using hydrophilic interaction chromatography. Various reports demonstrate the successful analysis of amino acids under such conditions. However, a baseline resolution of the 20 natural amino acids has not yet been published and for this reason, there is often a need to use mass spectrometry for detection to further improve selectivity.
Hydrophilic interaction chromatography is also recognized as a powerful technique for peptide analysis, and there are a lot of papers showing its applicability for proteomic applications peptide mapping. It is expected that its use for peptide mapping will continue to grow in the future, particularly because this analytical strategy can be combined with reversed-phase liquid chromatography, in a two-dimensional setup, to reach very high resolving power. Finally, the interest in hydrophilic interaction chromatography for intact proteins analysis is less evident due to possible solubility issues and a lack of suitable hydrophilic interaction chromatography stationary phases.
To date, it has been successfully employed only for the characterization of membrane proteins, histones, and the separation of glycosylated isoforms of an intact glycoprotein. From our point of view, the number of hydrophilic interaction chromatography columns compatible with intact proteins higher upper temperature limit, large pore size, etc.
Stabilization Effect of Amino Acid Side Chains in Peptide Assemblies on Graphite Studied by Scanning Tunneling Microscopy. An analysis is presented of the effects of amino acid side chains on peptide assemblies in ambient conditions on a graphite surface. The molecularly resolved assemblies of binary peptides are examined with scanning tunneling microscopy. A comparative analysis of the assembly structures reveals that the lamellae width has an appreciable dependence on the peptide sequence, which could be considered as a manifestation of a stabilizing effect of side-chain moieties of amino acids with high phenylalanine and low alanine, asparagine, histidine and aspartic acid propensities for aggregation.
These amino acids are representative for the chemical structures involving the side chains of charged histidine and aspartic acidaromatic phenylalaninehydrophobic alanineand hydrophilic asparagine amino acids. These results might provide useful insight for understanding the effects of sequence on the assembly of surface-bound peptides.
Enhancement of acid tolerance in Zymomonas mobilis by a proton-buffering peptide. Baumler, David J; Hung, Kai F; Bose, Jeffrey L; Vykhodets, Boris M; Cheng, Chorng M; Jeong, Kwang-Cheol; Kaspar, Charles W. A portion of the cbpA gene from Escherichia coli K encoding a 24 amino acid proton-buffering peptide Pbp was cloned via the shuttle vector pJB99 into E.
Expression of Pbp was confirmed in both JM and CP4 by HPLC. Although the expression of Pbp influenced survival at a low pH, the minimum growth pH was unaffected. Results from this study demonstrate that the production of a peptide with a high proportion of basic amino acids can contribute to protection from low pH and weak organic acids such as acetic acid.
Mass spectral study of hybrid peptides derived from R -aminoxy ester and [beta]-amino acids: The influence of aminoxy peptide bond CO-NH-O on peptide fragmentation under electrospray ionization conditions. MS3 CID of protonated aminoxy peptides of [beta]-hAla- R -Ama- yield intense [beta]-amino acid characteristic retro-Mannich fragmentation. Intense cationized cn and zn ions are formed due to the cleavage of N-O bond. All these results clearly indicate the influence of aminoxy peptide bond on fragmentation of these hybrid peptides.
Sumbatian, N V; Kuznetsova, I V; Karpenko, V V; Fedorova, N V; Chertkov, V A; Korshunova, G A; Bogdanov, A A. Fourteen new functionally active amino acid and peptide derivatives of the antibiotics tylosin, desmycosin, and 5-O-mycaminosyltylonolide were synthesized in order to study the interaction of the growing polypeptide chain with the ribosomal tunnel. The conjugation of various amino acids and peptides with a macrolide aldehyde group was carried out by two methods: Properties of synthetic ferrihydrite as an amino acid adsorbent and a promoter of peptide bond formation.
Ferrihydrite, an iron oxide hydroxide, is found in all kinds of environments, from hydrothermal hot springs to extraterrestrial materials. It has been shown that this material is nanoporous, and because of its high surface area, it has outstanding adsorption properties and in some cases catalysis properties.
In this work we studied the adsorption properties of ferrihydrite with respect to amino acids. Samples of pure ferrihydrite were synthesised and exposed to solutions of amino acids including both proteinaceous and non-proteinaceous species. These experiments revealed important characteristics of this mineral as both an adsorbent of amino acids and a promoter of peptide bond formation.
Tritium labeling of amino acids and peptides with liquid and solid tritium. Amino acids and peptides were labeled with liquid and solid tritium at 21 K and 9 K. At these low temperatures radiation degradation is minimal, and tritium incorporation increases with tritium concentration and exposure time. Ring saturation in L-phenyl-alanine does not occur. Peptide linkage in oligopeptides is stable toward tritium.
Deiodination in 3-iodotyrosine and 3,5-diiodotyrosine occurs readily and proceeds in steps by losing one iodine atom at a time. Nickel and noble metal supported catalysts when used as supports for dispersion of the substrate promote tritium labeling at 21 K. Our study shows that both liquid and solid tritium are potentially useful agents for labeling peptides and proteins.
Ring saturation in L-phenylalanine does not occur. Our study shows that both liquid and solid tritiums are potentially useful agents for labeling peptides and proteins. Biological Activity of Aminophosphonic Acids and Their Short Peptides.
The biological activity and natural occurrence of the aminophosphonic acids were described half a century ago. Since then the chemistry and biology of this class of compounds have developed into the separate field of phosphorus chemistry.
Today it is well acknowledged that these compounds possess a wide variety of promising, and in some cases commercially useful, physiological activities. Thus, they have found applications ranging from agrochemical with the herbicides glyphosate and bialaphos being the most prominent examples to medicinal with the potent antihypertensive fosinopril and antiosteoporetic bisphosphonates being examples.
Role of Amino Acid Insertions on Intermolecular Forces between Arginine Peptide Condensed DNA Helices. In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines.
We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide.
Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted.
Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads.
Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads. Lactic Acid Bacteria as Cell Factories for the Generation of Bioactive Peptides.
Brown, Lucia; Pingitore, Esteban Vera; Mozzi, Fernanda; Saavedra, Lucila; Villegas, Josefina M; Hebert, Elvira M. There is a growing interest in the incorporation of functional foods in the daily diet to achieve health promotion and disease risk reduction. Numerous studies have focused on the production of biologically active peptides as nutraceuticals and functional food ingredients due to their health benefits.
These short peptidesdisplaying antihypertensive, antioxidant, mineral binding, immunomodulatory and antimicrobial activities are hidden in a latent state within the primary sequences of food proteins requiring enzymatic proteolysis for their release. While microbial fermentation is one of the major and economically most convenient processes used to generate bioactive peptideslactic acid bacteria LAB are widely used as starter cultures for the production of diverse fermented foods.
This article reviews the current knowledge on LAB as cell factories for the production of bioactive peptides from a variety of food protein sources. These microorganisms depend on a complex proteolytic system to ensure successful fermentation processes. In the dairy industry, LAB containing cell envelope-associated proteinases CEPs are employed as biocatalysts for the first step of casein breakdown releasing bioactive peptides during milk fermentation.
A better understanding of the functionality and regulation of the proteolytic system of LAB opens up future opportunities for the production of novel food-derived compounds with potential health-promoting properties.
Transporters for ammonium, amino acids and peptides are expressed in pitchers of the carnivorous plant Nepenthes. Insect capture and digestion contribute substantially to the nitrogen budget of carnivorous plants. In Nepenthes, insect-derived nitrogenous compounds are imported from the pitcher fluid and transported throughout the plant via the vascular tissue to support growth.
Import and distribution of nutrients may require transmembrane nitrogen transporters. Representatives of three classes of genes encoding transporters for the nitrogenous compounds ammonium, amino acids and peptides were identified in Nepenthes pitchers. The expression at the cellular level of an ammonium transporter gene, three amino acid transporter genes, and one peptide transporter gene were investigated in the insect trapping organs of Nepenthes. Expression of the ammonium transporter gene NaAMT1 was detected in the head cells of digestive glands in the lower part of the pitcher where NaAMT1 may function in ammonium uptake from the pitcher fluid.
One amino acid transporter gene, NaAAP1, was expressed in bundle sheath cells surrounding the vascular tissue. To understand the locations where transmembrane transport could be required within the pitcher, symplasmic and apoplasmic continuity was probed using fluorescent dyes.
Symplasmic connections were not found between cortical cells and vascular bundles. Therefore, the amino acid transporter encoded by NaAAP1 may be involved in transport of amino acids into the vascular tissue. In contrast, expression of the peptide transporter gene NaNTR1 was detected in phloem cells of the vascular tissue within pitchers. NaNTR1 may function in the export of nitrogen from the pitcher by loading peptides into the phloem.
Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization. When polyanions and polycations are mixed, counterion release drives formation of polymer-rich complexes that can either be solid precipitates or liquid coacervates depending on the properties of the polyelectrolytes. These complexes are important in many fields, from encapsulation of industrial polymers to membrane-free segregation of biomolecules such as nucleic acids and proteins. Condensation of long double-stranded DNA has been studied for several decades, but comparatively little attention has been paid to the polyelectrolyte behavior of oligonucleotides.
We report here studies of DNA oligonucleotides 10 - 88 nt complexed with polylysine 10 - aa. Unexpectedly, we find that the phase of the resulting complexes is controlled by the hybridization state of the nucleic acidwith double-stranded DNA forming precipitates and single-stranded DNA forming coacervates.
Mixing coacervates formed by complementary single-stranded oligonucleotides results in precipitate formation, raising the possibility of stimulus-responsive material design. Characterisation of neuroprotective efficacy of modified poly-arginine-9 R9 peptides using a neuronal glutamic acid excitotoxicity model.
In a recent study, we highlighted the importance of cationic charge and arginine residues for the neuroprotective properties of poly-arginine and arginine-rich peptides. In this study, using cortical neuronal cultures and an in vitro glutamic acid excitotoxicity model, we examined the neuroprotective efficacy of different modifications to the poly-arginine-9 peptide R9.
We compared an unmodified R9 peptide with R9 peptides containing the following modifications: The three C-terminal amidated peptides R9-NH2, Ac-R9-NH2, and R9D-NH2 displayed neuroprotective effects greater than the unmodified R9 peptidewhile the N-terminal acetylated peptide Ac-R9 had reduced efficacy.
In addition, all peptides were capable of reducing glutamic acid -mediated neuronal intracellular calcium influx, in a manner that reflected their neuroprotective efficacy. This study further highlights the neuroprotective properties of poly-arginine peptides and provides insight into peptide modifications that affect efficacy.
Systematic amino acid substitutions improved efficiency of GD2- peptide mimotope vaccination against neuroblastoma. Bleeke, Matthias; Fest, Stefan; Huebener, Nicole; Landgraf, Christiane; Schraven, Burkhart; Gaedicke, Gerhard; Volkmer, Rudolf; Lode, Holger N. The likelihood of identifying peptides of sufficient quality for the development of effective cancer vaccines by screening of phage display libraries is low. Here, we introduce the sequential application of systematic amino acid substitution by SPOT synthesis.
After the substitution of two amino acids within the sequence of a phage display-derived mimotope of disialoganglioside GD2 mimotope MAthe novel mimotope C3 showed improved GD2 mimicry in vitro. Peptide vaccination with the C3 mimotope induced an fold increased anti-GD2 serum response associated with reduction of primary tumour growth and spontaneous metastasis in contrast to MA mimotope controls in a syngeneic neuroblastoma model.
In summary, SPOT provides an ideal optimisation tool for the development of phage display-derived cancer vaccines. Peptide -based identification of functional motifs and their binding partners. Shelton, Martin N; Huang, Ming Bo; Ali, Syed; Johnson, Kateena; Roth, William; Powell, Michael; Bond, Vincent.
Specific short peptides derived from motifs found in full-length proteins, in our case HIV-1 Nef, not only retain their biological function, but can also competitively inhibit the function of the full-length protein. A set of 20 Nef scanning peptides20 amino acids in length with each overlapping 10 amino acids of its neighbor, were used to identify motifs in Nef responsible for its induction of apoptosis. Peptides containing these apoptotic motifs induced apoptosis at levels comparable to the full-length Nef protein.
Protein transfection and antibody inhibition was used to physically disrupt the interaction between Nef and mortalin, one of the isolated SMR-binding proteins, and the effect was measured with a fluorescent-based exNef secretion assay.
Thus, by employing the techniques described here, which utilize the unique properties of specific short peptides derived from motifs found in full-length proteins, one may accelerate the identification of functional motifs in proteins and the development of peptide -based inhibitors of pathogenic functions.
Spontaneous intermolecular amide bond formation between side chains for irreversible peptide targeting. Peptides and synthetic peptide -like molecules are powerful tools for analysis and control of biological function. One major limitation of peptides is the instability of their interactions with biomolecules, because of the limited accessible surface area for noncovalent interactions and the intrinsic flexibility of peptides. Peptide tags are nonetheless fundamental for protein detection and purification, because their small size minimizes the perturbation to protein function.
Here we have designed a 16 amino acid peptide that spontaneously forms an amide bond to a protein partner, via reaction between lysine and asparagine side chains.
This depended upon splitting a pilin subunit from a human pathogen, Streptococcus pyogenes, which usually undergoes intramolecular amide bond formation to impart mechanical and proteolytic stability to pili. The amide bond formation was independent of redox state and occurred at pH The reaction was efficient in phosphate buffered saline and a wide range of biological buffers. Surprisingly, amide bond formation occurred at a similar rate at 4 and 37 degrees C. Both peptide and protein partners are composed of the regular 20 amino acids and reconstituted efficiently inside living E.
Labeling also showed high specificity on the surface of mammalian cells. Irreversible targeting of a peptide tag may have application in bioassembly, in cellular imaging, and to lock together proteins subject to high biological forces. Exploring the sequence space for tri- peptide self-assembly to design and discover new hydrogels. Peptides that self-assemble into nanostructures are of tremendous interest for biological, medical, photonic and nanotechnological applications. The enormous sequence space that is available from 20 amino acids probably harbours many interesting candidates, but it is currently not possible to predict supramolecular behaviour from sequence alone.
Here, we demonstrate computational tools to screen for the aqueous self-assembly propensity in all of the 8, possible tripeptides and evaluate these by comparison with known examples. We applied filters to select for candidates that simultaneously optimize the apparently contradicting requirements of aggregation propensity and hydrophilicity, which resulted in a set of design rules for self-assembling sequences. A number of peptides were subsequently synthesized and characterized, including the first reported tripeptides that are able to form a hydrogel at neutral pH.
These tools, which enable the peptide sequence space to be searched for supramolecular properties, enable minimalistic peptide nanotechnology to deliver on its promise. The paper shows it promising to use peptide bioregulators--fractions obtained from the cattle immune system thymus, spleen, and lymph nodes during immunotherapy for intoxication experimentally caused by the herbicide 2,4-dichlorophenoxyacetic acid.
Oral administration of the fractions in a dose of 0. Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity. Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution.
The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0. The exchange prediction errors modestly correlate with the crystallographic resolution.
The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange.
However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. Development of SI-traceable C- peptide certified reference material NMIJ CRM a using isotope-dilution mass spectrometry-based amino acid analyses. A certified reference material CRM is a higher-order calibration material used to enable a traceable analysis. This paper describes the development of a C- peptide CRM NMIJ CRM a by the National Metrology Institute of Japan using two independent methods for amino acid analysis based on isotope-dilution mass spectrometry.
This CRM is a lyophilized synthetic peptide having the human C- peptide sequence, and contains deamidated and pyroglutamylated forms of C- peptide. By adding water 1. We assigned two certified values that represent the concentrations of total C- peptide mixture of C- peptidedeamidated C- peptideand pyroglutamylated C- peptide and C- peptide.
The certified concentration of total C- peptide was determined by two amino acid analyses using pre-column derivatization liquid chromatography-mass spectrometry and hydrophilic chromatography-mass spectrometry following acid hydrolysis.
The certified concentration of C- peptide was determined by multiplying the concentration of total C- peptide by the ratio of the relative area of C- peptide to that of the total C- peptide measured by liquid chromatography.
The certified value of C- peptide Investigating the inclusion properties of aromatic amino acids complexing beta-cyclodextrins in model peptides. Caso, Jolanda Valentina; Russo, Luigi; Palmieri, Maddalena; Malgieri, Gaetano; Galdiero, Stefania; Falanga, Annarita; Isernia, Carla; Iacovino, Rosa.
Cyclodextrins are commonly used as complexing agents in biological, pharmaceutical, and industrial applications since they have an effect on protein thermal and proteolytic stability, refolding yields, solubility, and taste masking. In the case of peptide -cyclodextrin and protein-cyclodextrin host-guest complexes the aromatic amino acids are reported to be the principal responsible of the interaction. For these reasons, we have investigated the inclusion properties of nine designed tripeptides, obtained permuting the position of two L-alanines Ala, A with that of one L-tryptophan Trp, WL-phenylalanine Phe, For L-tyrosine Tyr, Yrespectively.
The tripeptides containing a tyrosine showed the highest binding constants, with the central position in the Ac-AYA-NH2 peptide becoming the most favorite for the interaction. Acid -base titration of melanocortin peptides: Tryptophantime-resolved fluorescence was used to monitor acid -base titration properties of alpha-melanocyte stimulating hormone alpha-MSH and the biologically more potent analog [Nle4, D-Phe7]alpha -MSH NDP-MSHlabeled or not with the paramagnetic amino acid probe 2,2,6,6-tetramthylpiperidine-N-oxylaminocarboxylic acid Toac.
Global analysis of fluorescence decay profiles measured in the pH range between 2. The long and intermediate lifetime preexponential factors interconverted along that pH interval and the result was interpreted as due to interconversion between Trp g- and trans chi1 rotamers, driven by conformational changes promoted by modifications in the ionization state of side-chain residues.
The differences in the extent of interconversion in alpha-MSH and NDP-MSH are indicative of structural differences between the peptideswhile titration curves suggest structural similarities between each peptide and its Toac-labeled species, in aqueous solution. Though less sensitive than fluorescence, the Toac electron spin resonance ESR isotropic hyperfine splitting parameter can also monitor the titration of side-chain residues located relatively far from the probe.
Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition.
It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.
Hence, it would be very hard to get started with a homochiral mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality.
It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system.
Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.
Application of hydrophilic interaction chromatography retention coefficients for predicting peptide elution with TFA and methanesulfonic acid ion-pairing reagents. Hydrophilic retention coefficients for 17 peptides were calculated based on retention coefficients previously published for TSKgel silica and were compared with the experimental elution profile on a Waters Atlantis HILIC silica column using TFA and methanesulfonic acid MSA as ion-pairing reagents.
Relative peptide retention could be accurately determined with both counter-ions. Peptide retention and chromatographic behavior were influenced by the percent acid modifier used with increases in both retention and peak symmetry observed at increasing modifier concentrations. The enhancement of net peptide polarity through MSA pairing shifted retention out by nearly five-fold for the earliest eluting peptidecompared with TFA. Despite improvements in retention and efficiency N eff for MSA over TFA, a consistent reduction in calculated selectivity alpha was observed.
This result is believed to be attributed to the stronger polar contribution of MSA masking and diminishing the underlying influence of the amino acid residues of each associated peptide.
Finally, post-column infusion of propionic acid and acetic acid was evaluated for their potential to recover signal intensity for TFA and MSA counter-ions for LC-ESI-MS applications.
Acetic acid generally yielded more substantial signal improvements over propionic acid on the TFA system while minimal benefits and some further reductions were noted with MSA. Formation pathways and opioid activity data for 3-hydroxypyridinium compounds derived from glucuronic acid and opioid peptides by Maillard processes. The kinetics of formation and identity of the reaction products of the glucuronic acid with three representative opioid peptides were investigated in vitro.
Peptides were conjugated with glucuronic acid either in solution or under dry-heating conditions. From the incubations performed in solution N- 1-deoxy-D-fructofuranosyluronic acid -peptide derivatives Amadori compounds were isolated, whereas from the dry-heated reactions products containing the 3-hydroxypyridinium moiety at the N-terminal of the peptide chain were obtained.
The mechanism of 3-hydroxypyridinium formation is discussed. In comparison with their respective parent peptidesthe N- 1-deoxy-D-fructofuranosyl-uronic acid derivatives of the opioid peptides showed three- to fold lower mu- and delta-receptor-binding affinities and agonist potencies in the functional assays, likely as a consequence of the steric bulk introduced at the N-terminal amino group.
The further decrease in opioid activity observed with the 3-hydroxypyridinium-containing peptides may be due to the lower pK a of the 3-hydroxypyridinium moiety and to delocalization of the positive charge in the pyridinium ring system. Anticoagulant Effects of Heparin Complexes with Prolyl-Glycine Peptide and Glycine and Proline Amino Acids.
The study demonstrates the formation of heparin complexes with prolyl-glycine peptide and proline and glycine amino acids. The method was developed for in vitro production of these complexes at 1: These complexes, unlike the constituents, proline and glycine, exhibited significant anticoagulant, antiplatelet, and fibrin-depolymerization activities of varying degree in vitro and in vivo.
The heparin-dipeptide complex produced maximum effect. The dipeptide by itself also showed anticoagulant properties, but less pronounced than in the complex with heparin. Synthesis and characterization of a peptide nucleic acid conjugated to a D- peptide analog of insulin-like growth factor 1 for increased cellular uptake.
DNA therapeutics show great potential for gene-specific, nontoxic therapy of a wide variety of diseases. The deoxyribose phosphate backbone of DNA has been modified in a number of ways to improve nuclease stability and cell membrane permeability. Recently, a new DNA derivative with an amide backbone instead of a deoxyribose phosphate backbone, peptide nucleic acid PNAhas shown tremendous potential as an antisense agent. Although PNAs hybridize very strongly and specifically to RNA and DNA, they are taken up by cells very poorly, limiting their potential as nucleic acid binding agents.
To improve cellular uptake of a PNA sequence, it was conjugated to a D-amino acid analog of insulin-like growth factor 1 IGF1which binds selectively to the cell surface receptor for insulin-like growth factor 1 IGF1R. The IGF1 D- peptide analog was assembled on 4-methylbenzhydryl amine resin, and then the PNA was extended as a continuation of the peptide.
The conjugate and control sequences were radiolabeled with 14C or fluorescently labeled with fluorescein isothiocyanate. The specific PNA- peptide conjugate displayed much higher uptake than the control PNA, but only in cells expressing IGF1R. This approach may allow cell-specific and tissue-specific application of PNAs as gene-regulating agents in vivo.
Amino acid sequence of homologous rat atrial peptides: A substance called atrial natriuretic factor ANFlocalized in secretory granules of atrial cardiocytes, was isolated as four homologous natriuretic peptides from homogenates of rat atria. The complete sequence of the longest form showed that it is composed of 33 amino acids. The three other shorter forms, and represent amino-terminally truncated versions of the 33 amino acid parent molecule as shown by analysis of sequence, amino acid composition, or both.
The proposed primary structure agrees entirely with the amino acid composition and reveals no significant sequence homology with any known protein or segment of protein. The short form ANF- was synthesized by a multi-fragment condensation approach and the synthetic product was shown to exhibit specific activity comparable to that of the natural ANF- Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Amino-Thiol Unnatural Amino Acids.
A versatile method for orchestrating the formation of side-chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro, or directly in living bacterial cells.
This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. Acetylation dictates the morphology of nanophase biosilica precipitated by a amino acid leucine-lysine peptide. N-terminal acetylation is a commonly used modification technique for synthetic peptidesmostly applied for reasons of enhanced stability, and in many cases regarded as inconsequential.
In engineered biosilification - the controlled deposition of silica for nanotechnology applications by designed peptides - charged groups often play a deciding role. Here we report that changing the charge by acetylation of a amino acid leucine-lysine LK peptide dramatically changes the morphology of precipitated biosilica; acetylated LK peptides produce nano-spheres, whereas nano-wires are precipitated by the same peptide in a non-acetylated form.
By using interface-specific vibrational spectroscopy and coarse-grained molecular simulations, we show that this change in morphology is not the result of modified peptide -silica interactions, but rather caused by the stabilization of the hydrophobic core of peptide aggregates created by the removal of a peptide charge upon acetylation.
These results should raise awareness of the potential impact of N-terminal modifications in peptide applications. The Perseus Exobiology mission on MIR: Leucine, alpha-methyl leucine and two peptides were exposed to space conditions on board the MIR station during the Perseus-Exobiology mission. This long duration space mission was aimed at testing the delivery of prebiotic building blocks.
During this mission, two amino acids leucine and alpha-methyl leucine and two peptides leucine-diketopiperazine and trileucine thioethylester were exposed in Earth orbit for three months.
Basalt, clay and meteorite powder were also mixed with the samples in order to simulate the effects of potential meteorite protection. Analysis of the material after the flight did not reveal any racemization or polymerisation but did provide information regarding photochemical pathways for the degradation of leucine and of the tripeptide.
Amino acids appeared to be more sensitive to UV radiation than peptidesthe cyclic dipeptide being found to be as particularly resistant. Meteorite powder which exhibits the highest absorption in Vacuum UltraViolet VUV afforded the best protection to the organic molecules whereas montmorillonite clay, almost transparent in VUV, was the least efficient.
By varying the thickness of the meteorite, we found that the threshold for efficient protection against radiation was about 5 microm. The possible exogenous origin of biological building blocks is discussed with respect to the stability to the molecules and the nature of the associated minerals. Programmable Multivalent Display of Receptor Ligands using Peptide Nucleic Acid Nanoscaffolds.
Multivalent effects dictate the binding affinity of multiple ligands on one molecular entity to receptors. Integrins are receptors that mediate cell attachment through multivalent binding to peptide sequences within the extracellular matrix, and overexpression promotes the metastasis of some cancers.
Multivalent display of integrin antagonists enhances their efficacy, but current scaffolds have limited ranges and precision for the display of ligands. Here we present an approach to study multivalent effects across wide ranges of ligand number, density, and three-dimensional arrangement.
The optimal construct improves the inhibitory activity of the antagonist by two orders of magnitude against the binding of melanoma cells to the extracellular matrix in both in vitro and in vivo models. A descriptor of amino acids: SVRG and its application to peptide quantitative structure-activity relationship. In this work, a descriptor, SVRG principal component scores vector of radial distribution function descriptors and geometrical descriptorswas derived from principal component analysis PCA of a matrix of two structural variables of coded amino acidsincluding radial distribution function index RDF and geometrical index.
SVRG scales were then applied in three panels of peptide quantitative structure-activity relationships QSARs which were modelled by partial least squares regression PLS. Satisfactory results showed that SVRG contained much chemical information relating to bioactivities. The approach may be a useful structural expression methodology for studies on peptide QSAR. Design, synthesis and biological evaluation of novel non- peptide boronic acid derivatives as proteasome inhibitors. Ge, Ying; Li, Aibo; Wu, Jianwei; Feng, Haiwei; Wang, Letian; Liu, Hongwu; Xu, Yungen; Xu, Qingxiang; Zhao, Li; Li, Yuyan.
A novel series of non- peptide proteasome inhibitors bearing the 1, 4-naphthoquinone scaffold and boronic acid warhead was developed. In the biological evaluation on the chymotrypsin-like activity of human 20S proteasome, five compounds showed IC50 values in the nanomolar range. Docking experiments into the yeast 20S proteasome rationalized their biological activities and allowed further optimization of this interesting class of inhibitors.
Within the cellular proliferation inhibition assay and western blot analysis, compound 3e demonstrated excellent anti-proliferative activity against solid tumor cells and clear accumulation of ubiquitinated cellular proteins.
Furthermore, in the microsomal stability assay compound 3e demonstrated much improved metabolic stability compared to bortezomib, emerging as a promising lead compound for further design of non- peptide proteasome inhibitors. Site-Specific Pyrolysis Induced Cleavage at Aspartic Acid Residue in Peptides and Proteins.
A simple and site-specific non-enzymatic method based on pyrolysis has been developed to cleave peptides and proteins. This suggests that pyrolysis-induced cleavage at aspartyl residues can be used as a rapid protein digestion procedure for the generation of sequence specific protein biomarkers.
Formation of peptides from amino acids by single or multiple additions of ATP to suspensions of nucleoproteinoid microparticles. The synthesis of peptides from individual amino acids or pairs of amino acids and ATP in the presence of catalysis by nucleoproteinoid microparticles is investigated. Experiments were performed with suspensions formed from the condensation of lysine-rich and acidic proteinoids with polyadenylic acidto which were added glycine, phenylalanine, proline, lysine or glycine-phenylalanine mixtures, and ATP either at once or serially.
Peptide yields are found to be greatest for equal amounts of acidic and basic proteinoids. The addition of imidazole is found to alter the preference of glycine-phenylalanine mixtures to form mixed heteropeptides rather than homopeptides.
A rapid ATP decay in the peptide synthesis reaction is observed, and a greater yield is obtained for repeated small additions than for a single addition of ATP. The experimental system has properties similar to modern cells, and represents an organizational unit ready for the evolution of associated biochemical pathways.
Synthesis of stable C-linked ferrocenyl amino acids and their use in solution-phase peptide synthesis. Incorporation of ferrocenyl group to peptides is an efficient method to alter their hydrophobicity.
Ferrocenyl group can also act as an electrochemical probe when incorporated onto functional peptides. Most often, ferrocene is incorporated onto peptides post-synthesis via amide, ester or triazole linkages. Stable amino acids containing ferrocene as a C-linked side chain are potentially useful building units for the synthesis of ferrocene-containing peptides. We report here an efficient route to synthesize ferrocene-containing amino acids that are stable and can be used in peptide synthesis.
The reduction or hydrolysis of the dithiane group yields an alkyl or an oxo derivative. The usability of the synthesized amino acids is demonstrated by incorporating one of the amino acids in both C-terminus and N-terminus of tripeptides in solution phase.
Peptides released from acid goat whey by a yeast-lactobacillus association isolated from cheese microflora. Didelot, Sandrine; Bordenave-Juchereau, Stephanie; Rosenfeld, Eric; Piot, Jean-Marie; Sannier, Frederic. Seven lactobacilli and a variety of microflora extracted from twenty five commercial cheeses were grown on unsupplemented acid goat whey and screened for their capacity to hydrolyse whey proteins [alpha-lactalbumin alpha-la and beta-lactoglobulin beta-lg ] and to generate peptides.
Fermentations were performed aerobically or anaerobically at 37 degrees C using crude or pre-heated whey 10 min at 65, 75 or 85 degrees C. Under aerobic conditions, growth of lactobacilli was poor and protein hydrolysis did not occur. Anaerobic conditions slightly increased lactobacilli growth but neither beta-lg hydrolysis nor peptide generation were observed. Twenty-five microflora extracted from raw milk cheeses were screened for their proteolytic activities on acid goat whey under the conditions previously described.
The corresponding hydrolysates were enriched in peptides. Fermentation kinetic profiles suggested that peptides were released from alpha-la hydrolysis. The co-culture of both microorganisms was required for alpha-la hydrolysis that occurred concomitantly with the pH decrease. During whey fermentation, Cand. Solvation thermodynamics of amino acid side chains on a short peptide backbone. The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment.
A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone.
To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone.
The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone.
We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected.
This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution.
We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side. Expression pattern of peptide and amino acid genes in digestive tract of transporter juvenile turbot Scophthalmus maximus L.
Turbot Scophthalmus maximus L. The results showed that the expression of two peptide and eleven amino acid transporters genes exhibited distinct patterns. Peptide transporter 1 PepT1 was rich in proximal intestine while peptide transporter 2 PepT2 was abundant in distal intestine. These findings comprehensively characterized the distribution of solute carrier family proteins, which revealed the relative importance of peptide and amino acid absorption through luminal membrane.
Our findings are helpful to understand the mechanism of the utilization of dietary protein in fish with a short digestive tract. Quantitative Analysis of Single Amino Acid Variant Peptides Associated with Pancreatic Cancer in Serum by an Isobaric Labeling Quantitative Method. Single amino acid variations are highly associated with many human diseases.
The direct detection of peptides containing single amino acid variants SAAVs derived from nonsynonymous single nucleotide polymorphisms SNPs in serum can provide unique opportunities for SAAV associated biomarker discovery.
In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls p-value peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring SRM analysis.
These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. Highly efficient peptide formation from N-acetylaminoacyl-AMP anhydride and free amino acid. Under similar conditions, the corresponding unblocked aminoacyl adenylate anhydrides are considerably more unstable, and undergo appreciable hydrlysis in the presence of free amino acid.
Because N-blocked aminoacyl adenylate anhydrides serve as model compounds of peptidyl adenylate anhydrides, these results suggest that primitive amino acid polymerization systems may have operated by cyclic reactivation of the peptidyl carboxyl group, rather than that of the incoming amino acid. Stereochemical Sequence Ion Selectivity: Proline versus Pipecolic- acid -containing Protonated Peptides. Substitution of proline by pipecolic acidthe six-membered ring congener of proline, results in vastly different tandem mass spectra.
The well-known proline effect is eliminated and amide bond cleavage C-terminal to pipecolic acid dominates instead. Why do these two ostensibly similar residues produce dramatically differing spectra? Recent evidence indicates that the proton affinities of these residues are similar, so are unlikely to explain the result [Raulfs et al.
An additional hypothesis based on increased flexibility was also advocated. Here, we provide a computational investigation of the "pipecolic acid effect," to test this and other hypotheses to determine if theory can shed additional light on this fascinating result. Our calculations provide evidence for both the increased flexibility of pipecolic- acid -containing peptidesand structural changes in the transition structures necessary to produce the sequence ions. R proline to S pipecolic acid.
Additionally, our calculations predict substantial stabilization of the amide bond cleavage barriers for the pipecolic acid congeners by reduction in deleterious steric interactions and provide evidence for the importance of experimental energy regime in rationalizing the spectra.
ResearchGate
Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. Peptides A3APO and Alyteserin were selected as top performers based on high antimicrobial activity against the pathogens tested and on significantly lower antimicrobial activity against L.
Fermentations were performed aerobically or anaerobically at 37 degrees C using crude or pre-heated whey 10 min at 65, 75 or 85 degrees C. Peptide -- Silica Hybrid Networks. The direct approach details various chiral selectors with an emphasis on cyclodextrins and their derivatives, antibiotics and chiral surfactants as the chiral selectors.
The residues E and F in the tip of loop L3 of PhoE are located in close proximity to residues K18 and D in the barrel wall Fig. Each sequence was initially chemically synthesized to quickly assess the material properties of its corresponding gel. The further decrease in opioid activity observed with the 3-hydroxypyridinium-containing peptides may be due to the lower pK a of the 3-hydroxypyridinium moiety and to delocalization of the positive charge in the pyridinium ring system.
Such a structural heterogeneity was previously also observed in an OmpF mutant [6]. Absence of safe and efficient methods of nucleic acids delivery is one of the major issues which limits the development of human gene therapy. Structure and functions, Biochemistry Moscow Supplement Series A: The results of this study indicate that highly acidic peptides can be sequenced by ETD of complexes formed with Pr III.
DAACPs have now also been identified in a number of distinct groups throughout the Metazoa. The third loop L3 is folded into the barrel, thereby forming a constriction at half the height of the membrane. Macroalgae are a diverse group of marine organisms that have developed complex and unique metabolic pathways to ensure survival in highly competitive marine environments.
Peptides containing these apoptotic motifs induced apoptosis at levels comparable to the full-length Nef protein. These experiments revealed important characteristics of this mineral as both an adsorbent of amino acids and a promoter of peptide bond formation.
amino acid peptide: Topics by q96522ur.beget.tech
We have measured the solubilities of EDMA center dot H20 as 6. Group contributions to the enthalpies of formation were calculated increment denotations corresponded to the Benson-Buss symbols. Peptide interfacial biomaterials improve endothelial cell adhesion and spreading on synthetic polyglycolic acid materials. All chemical analysis showed full coverage of the Ti substrate with the PAA thin film containing COOH groups and the RGD peptide. The uptake of the neutrally charged cephaloridine was increased but that of the negatively charged cefsulodin was decreased in cells expressing the mutant protein K18C, suggesting that the anion selectivity of the pores is reduced by this mutation.
In this study, the role in voltage gating of a loop that forms a constriction within the pore was studied. Properties of synthetic ferrihydrite as an amino acid adsorbent and a promoter of peptide bond formation. Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides. These reactions work with concentrations of 10 exp -1 M and as low as 10 exp -4 M, and the reaction is likely to be effective at even lower concentrations. Animal model indicated that desalted duck egg white peptides effectively enhanced the mineral absorption and counteracted the deleterious effects of phytic acid.
While some protein-derived bioactive peptides have been characterized from macroalgae, macroalgal proteins currently still represent good candidate raw materials for biofunctional peptide mining. Synthesis and biological properties of amino acids and peptides containing a tetrazolyl moiety. However, for therapeutic applications, intracellular delivery of peptide nucleic acids remains a challenge.
From this study we conclude that, together with protein backbone groups, aromatic amino acid residues provide the overwhelmingly dominant features in the Raman and SERS spectra of peptides and proteins when present. While microbial fermentation is one of the major and economically most convenient processes used to generate bioactive peptides , lactic acid bacteria LAB are widely used as starter cultures for the production of diverse fermented foods.
Accordingly, predictions of bioactivity have focused on particular subgroups, such as antimicrobial peptides.
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