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Padmanabhan Balaram - One of the best experts on this subject based on the ideXlab platform.
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Solvent-induced beta-hairpin to helix conformational transition in a designed peptide.
Biopolymers, 2001Co-Authors: Satish Kumar Awasthi, Srinivasarao Raghothama, Sasalu C Shankaramma, Padmanabhan BalaramAbstract:An octapeptide containing a central Aib-Gly- segment capable of adopting -turn conformations compatible with both hairpin ( II or I ) and helical ( I) structures has been designed. The effect of solvent on the conformation of the peptide Boc-Leu-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VIII; Boc: t-butyloxycarbonyl; OMe: methyl ester) has been investigated by NMR and CD spectroscopy. Peptide VIII adopts a well-defined -hairpin conformation in solvents capable of hydrogen bonding like (CD3)2SO and CD3OH. In solvents that have a lower tendency to interact with backbone peptide groups, like CDCl3 and CD3CN, helical conformations predominate. Nuclear Overhauser effects between the backbone protons and solvent shielding of NH groups involved in cross-strand hydrogen bonding, backbone chemical shifts, and vicinal coupling constants provide further support for the conformational assignments in different solvents. Truncated peptides Boc-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VII), Boc-Val-Val-Aib-Gly-Leu-Val-OMe (VI), and Boc-Val-Aib-Gly-Leu-OMe (IV) were studied in CDCl3 and (CD3)2SO by 500 MHz 1H-NMR spectroscopy. Peptides IV and VI show no evidence for hairpin conformation in both the solvents. The three truncated peptides show a well-defined helical conformation in CDCl3. In (CD3)2SO, peptide VII adopts a -hairpin conformation. The results establish that peptides may be designed, which are poised to undergo a dramatic conformational transition
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Vibrational Circular Dichroism of beta-Hairpin Peptides
2000Co-Authors: Chunxia Zhao, Prasad L Polavarapu, Padmanabhan BalaramAbstract:Analysis of vibrational absorption and vibrational circular dichroism (VCD) for synthetic peptides designed to adopt beta-hairpin conformations reveals characteristic well-resolved amide I absorption and VCD bands. All beta-hairpins with a type II’ beta-turn segment yield an intense negative VCD band in the _1643-1659 cm-1 region, and a weak positive VCD band at _1693 cm-1. These spectral features are diagnostic of beta-hairpins and distinct from those observed for other secondary structures. Comparison of the electronic CD spectra of the beta-hairpin peptides Boc-Leu-Val-Val-DPro-Gly-Leu-Val-Val-OMe (1) and Boc-Leu-Phe-Val-DPro-Gly-Leu-Phe-Val-OMe (2) reveals that cross-strand aromatic interactions result in anomalous CD spectra in the region 200-240 nm for peptide 2. Similar anomalous electronic CD are observed in the three-stranded beta-sheet peptide Boc-Leu-Phe-Val-DPro-Gly-Leu-Val-Leu-Ala-DPro-Gly-Phe-Val-Leu-OMe (3), while the VCD spectrum is characteristic of beta-hairpin conformations. The identical VCD spectra obtained for the peptides 1 and 2 emphasize the utility of VCD, as compared to electronic CD, in the conformational analysis of peptides containing aromatic residues.
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insertion of methylene units into the turn segment of designed beta hairpin peptides
Journal of the American Chemical Society, 1999Co-Authors: Sasalu C Shankaramma, Kumar S Singh, And Aruna Sathyamurthy, Padmanabhan BalaramAbstract:The effect of insertion of methylene groups into the turn segment of beta-hairpin peptides has been investigated in the model sequence Boc-Leu-Val-Val-Dpro-delta-Ava-Leu-Val-Val-OMe. This sequence is related to the previously well-characterized model beta-hairpin octapeptide, Boc-Leu-Val-Val-DPro-Gly-Leu-Val-Val-OMe. Replacement of Gly by delta-Ava (delta-aminovaleric acid) formally corresponds to expansion of the turn segment from a two-residue loop to a three-residue loop. Backbone proton chemical shifts, vicinal coupling constants, and circular dichroism spectra for the two peptides are virtually indistinguishable. Nuclear Overhauser effects corresponding to short cross-strand interproton distances confirm that the registry of the beta-hairpin structure is maintained in the delta-Ava peptide. Restrained molecular dynamics simulations, using experimental constraints, yield two structural families that are consistent with the NOE data. Both families correspond to beta-hairpin conformations and differ only in the backbone torsion angles at the delta-Ava residue.
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beta hairpin nucleation by pro gly beta turns comparison of d pro gly and l pro gly sequences in an apolar octapeptide
Journal of The Chemical Society-perkin Transactions 1, 1998Co-Authors: Srinivasarao Raghothama, Satish Kumar Awasthi, Padmanabhan BalaramAbstract:The solution conformation of the synthetic octapeptide Boc-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe 1 and Boc-Leu-Val-Val-Pro-Gly-Leu-Val-Val-OMe 2 have been investigated in organic solvents by NMR spectroscopy. Peptide 1 adopts well-defined β-hairpin conformations in CDCl3, C6D6 and (CD3)2SO, nucleated by a D-Pro-Gly Type II′ β-turn, as demonstrated by the observation of characteristic nuclear Overhauser effects (NOEs) between backbone protons and solvent shielding of NH groups involved in cross-strand hydrogen bonding. Chemical shifts and coupling constants provide further support for the β-hairpin conformation, which is consistent with the observation of a single negative circular dichroism band at 216 nm in methanol. In peptide 2, there is no characteristic interstrand NOE observed in (CD3)2SO, while in CDCl3 pronounced aggregation results in line broadening. The observation of a low temperature coefficient for the Leu(6)NH proton favours a population of Pro-Gly Type II β-turn conformations. These results suggest that in short peptide sequences, the precise nature of the β-turn is critical for hairpin formation, with Type II′ β-turns being particularly effective.
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a designed beta hairpin peptide in crystals
Proceedings of the National Academy of Sciences of the United States of America, 1996Co-Authors: Isabella L Karle, Satish Kumar Awasthi, Padmanabhan BalaramAbstract:Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin, t-butoxycarbonyl-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe in crystals is described. The two independent molecules of the octapeptide fold into almost ideal beta-hairpin conformations with the central D-Pro-Gly segment adopting a Type II' beta-turn conformation. The definitive characterization of a beta-hairpin has implications for de novo peptide and protein design, particularly for the development of three- and four-stranded beta-sheets.
Satish Kumar Awasthi - One of the best experts on this subject based on the ideXlab platform.
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Solvent-induced beta-hairpin to helix conformational transition in a designed peptide.
Biopolymers, 2001Co-Authors: Satish Kumar Awasthi, Srinivasarao Raghothama, Sasalu C Shankaramma, Padmanabhan BalaramAbstract:An octapeptide containing a central Aib-Gly- segment capable of adopting -turn conformations compatible with both hairpin ( II or I ) and helical ( I) structures has been designed. The effect of solvent on the conformation of the peptide Boc-Leu-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VIII; Boc: t-butyloxycarbonyl; OMe: methyl ester) has been investigated by NMR and CD spectroscopy. Peptide VIII adopts a well-defined -hairpin conformation in solvents capable of hydrogen bonding like (CD3)2SO and CD3OH. In solvents that have a lower tendency to interact with backbone peptide groups, like CDCl3 and CD3CN, helical conformations predominate. Nuclear Overhauser effects between the backbone protons and solvent shielding of NH groups involved in cross-strand hydrogen bonding, backbone chemical shifts, and vicinal coupling constants provide further support for the conformational assignments in different solvents. Truncated peptides Boc-Val-Val-Aib-Gly-Leu-Val-Val-OMe (VII), Boc-Val-Val-Aib-Gly-Leu-Val-OMe (VI), and Boc-Val-Aib-Gly-Leu-OMe (IV) were studied in CDCl3 and (CD3)2SO by 500 MHz 1H-NMR spectroscopy. Peptides IV and VI show no evidence for hairpin conformation in both the solvents. The three truncated peptides show a well-defined helical conformation in CDCl3. In (CD3)2SO, peptide VII adopts a -hairpin conformation. The results establish that peptides may be designed, which are poised to undergo a dramatic conformational transition
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beta hairpin nucleation by pro gly beta turns comparison of d pro gly and l pro gly sequences in an apolar octapeptide
Journal of The Chemical Society-perkin Transactions 1, 1998Co-Authors: Srinivasarao Raghothama, Satish Kumar Awasthi, Padmanabhan BalaramAbstract:The solution conformation of the synthetic octapeptide Boc-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe 1 and Boc-Leu-Val-Val-Pro-Gly-Leu-Val-Val-OMe 2 have been investigated in organic solvents by NMR spectroscopy. Peptide 1 adopts well-defined β-hairpin conformations in CDCl3, C6D6 and (CD3)2SO, nucleated by a D-Pro-Gly Type II′ β-turn, as demonstrated by the observation of characteristic nuclear Overhauser effects (NOEs) between backbone protons and solvent shielding of NH groups involved in cross-strand hydrogen bonding. Chemical shifts and coupling constants provide further support for the β-hairpin conformation, which is consistent with the observation of a single negative circular dichroism band at 216 nm in methanol. In peptide 2, there is no characteristic interstrand NOE observed in (CD3)2SO, while in CDCl3 pronounced aggregation results in line broadening. The observation of a low temperature coefficient for the Leu(6)NH proton favours a population of Pro-Gly Type II β-turn conformations. These results suggest that in short peptide sequences, the precise nature of the β-turn is critical for hairpin formation, with Type II′ β-turns being particularly effective.
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a designed beta hairpin peptide in crystals
Proceedings of the National Academy of Sciences of the United States of America, 1996Co-Authors: Isabella L Karle, Satish Kumar Awasthi, Padmanabhan BalaramAbstract:Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin, t-butoxycarbonyl-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe in crystals is described. The two independent molecules of the octapeptide fold into almost ideal beta-hairpin conformations with the central D-Pro-Gly segment adopting a Type II' beta-turn conformation. The definitive characterization of a beta-hairpin has implications for de novo peptide and protein design, particularly for the development of three- and four-stranded beta-sheets.
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a designed beta hairpin peptide
Biochemical and Biophysical Research Communications, 1995Co-Authors: Satish Kumar Awasthi, Srinivasarao Raghothama, Padmanabhan BalaramAbstract:A synthetic octapeptide, Boc-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe (1) has been designed as a model for a beta-hairpin conformation. Circular dichroism spectra in various organic solvents reveal a single negative band at 214-217 nm consistent with beta-sheet structures. NMR studies in CDCl3 and C6D6 establish the solvent shielded nature of the Leu(1), Val(3), Leu(6) and Val (8) NH groups. Nuclear Overhauser effects are observed between Val(7) CalphaH and Val(2) (CalphaH) protons providing strong support for a beta-hairpin conformation. Several important diagnostic interresidue NOEs establish a Type II′ beta-turn conformation for the D-Pro-Gly segment and extended conformations for the amino and carboxyl terminal tripeptide arms. The high solubility of the beta-hairpin peptide in organic solvents holds promise for the development of models for three and four stranded beta-sheets.
Dan W. Urry - One of the best experts on this subject based on the ideXlab platform.
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Coacervation properties in sequential polypeptide models of elastin. Synthesis of H-(Ala-Pro-Gly-Gly)n-Val-OMe and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe.
International journal of peptide and protein research, 2009Co-Authors: Rao S. Rapaka, K. Okamoto, Dan W. UrryAbstract:Syntheses of two sequential polypeptides H-(Ala-Pro-Gly-Gly)n-Val-OMe and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe via the p-nitrophenyl active ester procedure are reported. The two polymers were obtained in good yields and the polymers were shown to be of large molecular weights, n greater than 40. These two polypeptides were synthesized as analogs of the two coacervating sequential polypeptides H-(Val-Pro-Gly-Gly)n-Val-OMe, and H-(Val-Pro-Gly-Val-Gly)n-Val-OMe, in which the Val-l residue is replaced by an Ala-l residue. H-(Ala-Pro-Gly-Gly)n-Val-OMe did not coacervate even at as high a temperature as 100 degrees, and H-(Ala-Pro-Gly-Val-Gly)n-Val-OMe did not coacervate; however, it precipitated irreversibly around 65--70 degrees C. This suggests the critical role of the Val-Pro hydrophobic side chain interaction in coacervation.
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Crystal structure of cyclic (APGVGV)2, an analog of elastin, and a suggested mechanism for elongation/contraction of the molecule.
Biopolymers, 2005Co-Authors: Isabella L Karle, Dan W. UrryAbstract:Tropoelastin is a complex polymeric protein composed primarily of repeating segments of Val-Pro-Gly-Gly, Val-Pro-Gly-Val-Gly, and Ala-Pro-Gly-Val-Gly-Val that occurs in connective tissue and arteries. It has rubber-like extensible properties. A synthetic cyclic dodecapeptide, with a double repeat of the hexapeptide sequence, has been shown to undergo a reversible inverse temperature transition; that is, crystals grow at 60°C and dissolve in the mother liquor upon cooling. An x-ray crystal structure analysis established that the cyclic backbone formed an elongated loop with a Pro-Gly, type II beta turn at both ends. Six internal cross strand NH···OC hydrogen bonds form between six NH donors and four OC acceptors where two of the carbonyl O atoms are bifurcated acceptors. As a result, the molecule is pulled up into a corrugated profile. The corrugated loops form extended β-sheets by additional intermolecular hydrogen bonds. An analysis of the dome region in a corrugated sheet suggests a reversible mechanism for extending and contracting the length of the whole molecule, akin to the motion of opening and closing an umbrella, caused by the motion of a water molecule with its associated hydrogen bonds acting as spokes. Crystal parameters: C44H72N12O12˙3H2O, sp. gr. P212121, a = 9.212 A, b = 19.055 A, c = 32.247 A, d = 1.157 g/cm3. © 2005 Wiley Periodicals, Inc. Biopolymers, 2005
Masao Tanihara - One of the best experts on this subject based on the ideXlab platform.
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Thermosensitive gel formation of novel polypeptides containing a collagen-derived Pro-Hyp-Gly sequence and an elastin-derived Val-Pro-Gly-Val-Gly sequence
Journal of Polymer Science Part A: Polymer Chemistry, 2005Co-Authors: Yasushi Morihara, Shin-ichi Ogata, Masanobu Kamitakahara, Chikara Ohtsuki, Masao TaniharaAbstract:A triple-helix-forming collagen model peptide, (prolyl-trans-4-hydroxyprolyl-glycyl)10 [(Pro-Hyp-Gly)10], and a thermosensitive elastin-derived pentapeptide, valyl-prolyl-glycyl-valyl-glycyl (Val-Pro-Gly-Val-Gly), were copolymerized in various mole ratios using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride and 1-hydroxybenzotriazole in dimethyl sulfoxide at 20 °C. All of the obtained polypeptides have molecular weight higher than 103 and contain a triple-helical structure, and showed an inverse phase transition from transparent solution to turbid suspension in response to a rise in temperature. The lower critical solution temperature of the polypeptide solution decreased upon increasing the content of Val-Pro-Gly-Val-Gly. Furthermore, polypeptides containing 82–86 mol % of Val-Pro-Gly-Val-Gly in composition showed reversible gel formation, suggesting that (Pro-Hyp-Gly)10 acts as a hydrated unit and Val-Pro-Gly-Val-Gly acts as a thermosensitive crosslinking point. These biodegradable thermosensitive polypeptides may be useful for biomedical applications, including, as a scaffold for tissue regeneration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6048–6056, 2005
Stephen B. H. Kent - One of the best experts on this subject based on the ideXlab platform.
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Enhanced Solvation of Peptides Attached to “Solid-Phase” Resins: Straightforward Syntheses of the Elastin Sequence Pro-Gly-Val-Gly-Val-Pro-Gly-Val-Gly-Val
Organic letters, 2015Co-Authors: Bobo Dang, Balamurugan Dhayalan, Stephen B. H. KentAbstract:The solubility-enhancing power of covalent attachment to solvent-swollen cross-linked resin supports was illustrated by syntheses of the highly aggregating elastin-derived 10-residue peptide sequence Pro-Gly-Val-Gly-Val-Pro-Gly-Val-Gly-Val using standard protocols for both Boc and Fmoc chemistry SPPS.