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Peptide Conformation (peptide + conformation)
Selected AbstractsSelf-assembling peptides: Sequence, secondary structure in solution and film formationBIOPOLYMERS, Issue 11 2008Roberta Gambaretto Abstract Peptides of alternating charge and hydrophobic amino acids have a tendency to adopt unusually stable ,-sheet structures that can form insoluble macroscopic aggregates under physiological conditions. In this study, analogues of a well-known self-assembling peptide, characterized by the same polar/nonpolar periodicity but with different residues, were designed to study the relationship between sequence, conformation in solution and film-forming capacity in saline solution. Peptide conformation, evaluated by circular dichroism, correlated with film forming capacity observed by inverted optical microscopy after addition of saline solution and subsequent drying. We found that polar/nonpolar periodicity of several analogues is not criterion enough to induce ,-sheet and thus film formation and that conformations different from ,-sheet also allow self-assemblage. Furthermore, addition of the short adhesive sequence RGD to a known self-assembling sequence was shown to not prevent the self-assembling process. This finding might prove useful for the design of biomimetic scaffolds. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 906,915, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] A short proregion of trialysin, a pore-forming protein of Triatoma infestans salivary glands, controls activity by folding the N-terminal lytic motifFEBS JOURNAL, Issue 5 2008Rafael M. Martins Triatoma infestans (Hemiptera: Reduviidae) is a hematophagous insect that transmits the protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas' disease. Its saliva contains trialysin, a protein that forms pores in membranes. Peptides based on the N-terminus of trialysin lyse cells and fold into ,-helical amphipathic segments resembling antimicrobial peptides. Using a specific antiserum against trialysin, we show here that trialysin is synthesized as a precursor that is less active than the protein released after saliva secretion. A synthetic peptide flanked by a fluorophore and a quencher including the acidic proregion and the lytic N-terminus of the protein is also less active against cells and liposomes, increasing activity upon proteolysis. Activation changes the peptide conformation as observed by fluorescence increase and CD spectroscopy. This mechanism of activation could provide a way to impair the toxic effects of trialysin inside the salivary glands, thus restricting damaging lytic activity to the bite site. [source] Study of peptide conformation in terms of the ABEEM/MM methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2006Zhong-Zhi Yang Abstract The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard,Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7°. The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 1,10, 2006 [source] Functional reconstruction and synthetic mimicry of a conformational epitope using CLIPSÔ technology,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2007Peter Timmerman Abstract This paper describes immunization studies with CLIPS-constrained peptides covering only the major part (,3-loop) of a structurally complex antigenic site on human Follicle Stimulating Hormone , -subunit (FSH- ,). In cases where linear and SS-constrained peptides fail, the CLIPS-constrained peptides generate polyclonal antibodies with high neutralizing activity for hFSH. The sera were shown to be specific for hFSH over human Luteinizing Hormone (hLH) and human Chorionic Gonadotropin (hCG). ELISA-competition studies and circular dichroism (CD)-measurements illustrate clearly that activity of the peptides in antibody binding and generation relates directly to precise and appropriate fixation of the peptide conformation. Design of the CLIPS-peptides was entirely based on epitope mapping studies with two neutralizing anti-hFSH mAbs. Both mAbs were shown to bind to a conformational epitope located at the top of the ,1,,3-loop covering the amino acid sequences Y58 -P77 (,3-loop). The results described in this paper show that CLIPS-constrained peptides covering the Y58 -P77 sequence provide the minimally required structural entity necessary to generate reproducibly sera with high hFSH-neutralizing activity. Copyright © 2007 John Wiley & Sons, Ltd. [source] Design and synthesis of new trehalose-conjugated pentapeptides as inhibitors of A,(1,42) fibrillogenesis and toxicity,JOURNAL OF PEPTIDE SCIENCE, Issue 3 2009Paolo De Bona Abstract Aggregation of the amyloid A, peptide and its accumulation into insoluble deposits (plaques) are believed to be the main cause of neuronal dysfunction associated with Alzheimer's disease (AD); small molecules that can interfere with the A, amyloid fibril formation are therefore of interest for a potential therapeutic strategy. Three new trehalose-conjugated peptides of the well known ,-sheet breaker peptide iA,5p, were synthesized. The disaccharide was covalently attached to different sites of the LPFFD peptide chain, i.e. at the N-terminus, C-terminus or at the Asp side chain. CD spectroscopy in different solvents was used to assess changes in the peptide conformation of these compounds. The effects of these glycopeptides on the self-assembly and morphology of A, aggregates were investigated by ThT fluorescence assay and dynamic Scanning Force Microscopy, respectively. All the synthesized compounds were tested as inhibitors of A, toxicity toward pure cultures of rat cortical neurons. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and study of a gramicidin B mutant possessing a ditryptophan crosslinkJOURNAL OF PEPTIDE SCIENCE, Issue 9 2002Alice L. Presley Bodnar Abstract Recent studies of peptide dimers linked by Trp-Trp (ditryptophan) crosslinks suggest that the crosslinks can reinforce antiparallel ,-structure. Depending on environment, gramicidins A, B and C form either helical ion channels with parallel ,-structure or non-functional pores with antiparallel ,-structure. In the channel conformation of the gramicidins Trp9 and Trp15 are close in space, but in the pore conformation Trp9 and Trp15 are far apart. We hypothesized that a ditryptophan crosslink between Trp9 and Trp15 could pre-organize gramicidin in an active conformation. To test the potential for pre-organization, an intramolecular ditryptophan crosslink was formed between Trp9 and Trp15 in a W13F mutant of gramicidin B. Photooxidative conditions were shown to generate ditryptophan crosslinks in low yields. While not preparatively useful, photooxidative tryptophan crosslinking may have implications for protein aging processes like cataract formation. The ditryptophan crosslink in the gramicidin B mutant substantially lowered the antibiotic activity of the gramicidin B mutant, unlike the ditryptophan crosslink in the antibiotic X-indolicidin. The biaryl chromophore generated diagnostic Cotton effects in the CD spectrum that revealed the absolute stereochemistry of the biaryl chromophore, but the biaryl chromophore obscured diagnostic features below 220 nm. However, changes in peptide conformation were reflected in changes in the biaryl region of the CD spectrum above 240 nm. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Modeling the electrophoresis of oligoglycinesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 16 2010Stuart A. Allison Abstract The electrophoretic mobility of low molecular mass oligoglycines is examined in this study using a "coarse-grained" bead modeling methodology [Pei, H., Allison, S. A., J. Chromatogr. A 2009, 1216, 1908,1916]. The advantage of focusing on these peptides is that their charge state is well known [Plasson, R., Cottet, H., Anal. Chem. 2006, 78, 5394,5402] and extensive electrophoretic mobility data are also available in different buffers [Survay, M. A., Goodall, D. M., Wren, S. A. C., Rowe, R. C., J. Chromatogr. A 1996, 741, 99,113] and over a broad range of temperatures [Plasson, R., Cottet, H., Anal Chem. 2005, 77, 6047,6054]. Except for assumptions about peptide secondary structure, the B model has no adjustable parameters. It is concluded that the oligoglycines adopt a random configuration at high temperature (50°C and higher), but more compact conformations at lower temperature. It is proposed that triglycine through pentaglycine adopt compact cyclic structures at low temperature (up to about 25°C) in aqueous solution. At 25°C, buffer interactions are also examined and may or may not influence peptide conformation depending on the buffer species. In a borate buffer at high pH, the mobility data are consistent with complex formation between the oligoglycine and borate anion. [source] Solution NMR evidence for a cis Tyr-Ala peptide group in the structure of [Pro93Ala] bovine pancreatic ribonuclease APROTEIN SCIENCE, Issue 2 2000Ying Xiong Abstract Proline peptide group isomerization can result in kinetic barriers in protein folding. In particular, the cis proline peptide conformation at Tyr92-Pro93 of bovine pancreatic ribonuclease A (RNase A) has been proposed to be crucial for chain folding initiation. Mutation of this proline-93 to alanine results in an RNase A molecule, P93A, that exhibits unfolding/refolding kinetics consistent with a cis Tyr92-Ala93 peptide group conformation in the folded structure (Dodge RW, Scheraga HA, 1996, Biochemistry 35:1548,1559). Here, we describe the analysis of backbone proton resonance assignments for P93 A together with nuclear Overhauser effect data that provide spectroscopic evidence for a type VI ,-bend conformation with a cis Tyr92-Ala93 peptide group in the folded structure. This is in contrast to the reported X-ray crystal structure of [Pro93Gly]-RNase A (Schultz LW, Hargraves SR, Klink TA, Raines RT, 1998, Protein Sci 7:1620,1625), in which Tyr92-Gly93 forms a type-II ,-bend with a trans peptide group conformation. While a glycine residue at position 93 accommodates a type-II bend (with a positive value of ø93), RNase A molecules with either proline or alanine residues at this position appear to require a cis peptide group with a type-VI ,-bend for proper folding. These results support the view that a cis Pro93 conformation is crucial for proper folding of wild-type RNase A. [source] Structures of dipeptides: the head-to-tail storyACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010Carl Henrik Görbitz The hydrogen-bonding patterns in crystal structures of unprotected, zwitterionic dipeptides are dominated by head-to-tail chains involving the N -terminal amino groups and the C -terminal carboxylate groups. Patterns that include two concomitant chains, thus generating a hydrogen-bonded layer, are of special interest. A comprehensive survey shows that dipeptide structures can conveniently be divided into only four distinct patterns, differing by definition in the symmetry of the head-to-tail chains and amide hydrogen-bonding type, but also in other properties such as peptide conformation and the propensity to include solvent water or various organic guest molecules. Upon crystallization, the choice of pattern for a specific dipeptide is not random, but follows from the amino acid sequence. [source] ,-Sheet aggregation of kisspeptin-10 is stimulated by heparin but inhibited by amphiphilesBIOPOLYMERS, Issue 8 2010Søren B. Nielsen Abstract The murine 10-residue neurohormone kisspeptin (YNWNSFGLRY) is an important regulator of reproductive behavior and gonadotrophin secretion. It is known to form a random coil in solution, but undergoes a structural change in the presence of membranes although the nature of this change is not fully determined. The peptide's conformational versatility raises the question whether it is also able to form ordered aggregates under physiological conditions, which might be relevant as a storage mechanism. Here we show that heparin induces kisspeptin to form ,-sheet rich amyloid aggregates both at neutral (pH 7.0) and slightly acidic (pH 5.2) conditions. Addition of heparin leads to aggregation after a certain lag phase, irrespective of the time of addition of heparin, indicating that heparin is needed to facilitate the formation of fibrillation nuclei. Aggregation is completely inhibited by submicellar concentrations of zwitterionic and anionic surfactants. Unlike previous reports, our NMR data do not indicate persistent structure in the presence of zwitterionic surfactant micelles. Thus kisspeptin can aggregate under physiologically relevant conditions provided heparin is present, but the process is highly sensitive to the presence of amphiphiles, highlighting the very dynamic nature of the peptide conformation and suggesting that kisspeptin aggregation is a biologically regulatable process. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 678,689, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] 4-Fluorophenylglycine as a Label for 19F NMR Structure Analysis of Membrane-Associated PeptidesCHEMBIOCHEM, Issue 11 2003Sergii Afonin Abstract The non-natural amino acid 4-fluorophenylglycine (4F-Phg) was incorporated into several representative membrane-associated peptides for dual purpose. The 19F-substituted ring is directly attached to the peptide backbone, so it not only provides a well-defined label for highly sensitive 19F NMR studies but, in addition, the D and L enantiomers of the stiff side chain may serve as reporter groups on the transient peptide conformation during the biological function. Besides peptide synthesis, which is accompanied by racemisation of 4F-Phg, we also describe separation of the epimers by HPLC and removal of trifluoroacetic acid. As a first example, 18 different analogues of the fusogenic peptide "B18" were prepared and tested for induction of vesicle fusion; the results confirmed that hydrophobic sites tolerated 4F-Phg labelling. Similar fusion activities within each pair of epimers suggest that the peptide is less structured in the fusogenic transition state than in the helical ground state. In a second example, five doubly labelled analogues of the antimicrobial peptide gramicidin S were compared by using bacterial growth inhibition assays. This cyclic ,-sheet peptide could accommodate both L and D substituents on its hydrophobic face. As a third example, we tested six analogues of the antimicrobial peptide PGLa. The presence of d- 4F-Phg reduced the biological activity of the peptide by interfering with its amphiphilic ,-helical fold. Finally, to illustrate the numerous uses of l- 4F-Phg in 19F NMR spectroscopy, we characterised the interaction of labelled PGLa with uncharged and negatively charged membranes. Observing the signal of the free peptide in an aqueous suspension of unilamellar vesicles, we found a linear saturation behaviour that was dominated by electrostatic attraction of the cationic PGLa. Once the peptide is bound to the membrane, however, solid-state 19F NMR spectroscopy of macroscopically oriented samples revealed that the charge density has virtually no further influence on the structure, alignment or mobility of the peptide. [source] Ion channel activity of transmembrane segment 6 of Escherichia coli proton-dependent manganese transporterBIOPOLYMERS, Issue 8 2010uková Abstract Synthetic peptides corresponding to the sixth transmembrane segment (TMS6) of secondary-active transporter MntH (Proton-dependent Manganese Transporter) from Escherichia coli and its two mutations in the functionally important conserved histidine residue were used as a model for structure,function study of MntH. The secondary structure of the peptides was estimated in different environments using circular dichroism spectroscopy. These peptides interacted with and adopted helical conformations in lipid membranes. Electrophysiological experiments demonstrated that TMS6 was able to form multi-state ion channels in model biological membranes. Electrophysiological properties of these weakly cation-selective ion channels were strongly dependent on the surrounding pH. Manganese ion, as a physiological substrate of MntH, enhanced the conductivity of TMS6 channels, influenced the transition between closed and open states, and affected the peptide conformations. Moreover, functional properties of peptides carrying two different mutations of His211 were analogous to in vivo functional characteristics of Nramp/MntH proteins mutated at homologous residues. Hence, a single functionally important TMS can retain some of the functional properties of the full-length protein. These findings could contribute to understanding the structure,function relationship at the molecular level. However it remains unclear to what extent the peptide-specific channel activity represents a functional aspect of the full-length membrane carrier protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 718,726, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||