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51.
Athanassios Stavrakoudis 《Molecular simulation》2013,39(2):127-137
A peptide mimotope of the CD52 antigen with the sequence T1SSPSAD7 has been co-crystallised with the CAMPATH-1H antibody. Molecular dynamics (MD) simulations in explicit water of the T1SSPSAD7 peptide in both antibody free and bound states showed that the peptide's β-turn remained stable in the bound state but it was eliminated in the free state. Based on the observation that Thr1 and Ala6 residues made close contacts through their side chain, a new peptide mimotope is proposed: (S,S)-C1SSPSCD7. Thr1 and Ala6 residues have been mutated in Cys residues and a disulphide bond has been imposed. The new analogue has been simulated in both antibody bound and free states with MD in explicit water. It was found that the peptide remained in the stable β-turn conformation, both in complexed and free states. The difference in configurational entropy was estimated to be 0.15 kJ/K/mol. However, despite the structural similarity, the cyclic analogue lost more than 25% of its buried surface area contact with the antibody and a couple of critical hydrogen bond interactions were broken. It is concluded that design of cyclic analogues that mimic the bound conformation of peptides should be carefully performed and conformational ‘freezing’ does not necessarily guarantee better binding. 相似文献
52.
Protein conformational stability is an important concern in many fields. Here, we describe a strategy for significantly increasing conformational stability by optimizing beta-turn sequence. Proline and glycine residues are statistically preferred at several beta-turn positions, presumably because their unique side-chains contribute favorably to conformational stability in certain beta-turn positions. However, beta-turn sequences often deviate from preferred proline or preferred glycine. Therefore, our strategy involves replacing non-proline and non-glycine beta-turn residues with preferred proline or preferred glycine residues. Here, we develop guidelines for selecting appropriate mutations, and present results for five mutations (S31P, S42G, S48P, T76P, and Q77G) that significantly increase the conformational stability of RNase Sa. The increases in stability ranged from 0.7 kcal/mol to 1.3 kcal/mol. The strategy was successful in overlapping or isolated beta-turns, at buried (up to 50%) or completely exposed sites, and at relatively flexible or inflexible sites. Considering the significant number of beta-turn residues in every globular protein and the frequent deviation of beta-turn sequences from preferred proline and preferred glycine residues, this simple, efficient strategy will be useful for increasing the conformational stability of proteins. 相似文献
53.
Poly(X-Gly-Gly), simple structural models for the hydrophobic, proline-devoid, regions of elastin, have been synthesized and studied by circular dichroism and NMR spectroscopies. The results gave evidence of type II beta-turns as the only ordered structure present in the polymers. The stability of the turns has been shown to decrease on hydration and to increase in the series Leu less than Ala less than Val less than Ile. 相似文献
54.
Ramesha Baba A. Channe Gowda D. 《International journal of peptide research and therapeutics》2001,8(6):309-318
Summary The commonly used coupling reagents in peptide syntheses such as dicyclohexylcabodiimide, diisopropyl-carbodiimide and 3-ethyl-1(N,N-dimethyl)aminopropylcarbodiimide
with or without 1-hydroxybenzotriazole or N-hydroxysuccinimide have been used as polymerizing agents in the synthesis of elastic/plastic
protein-based polymers. It was found that 3-ethyl-1(N,N-dimethyl)aminopropylcarbodiimide with 1-hydroxybenzotriazole gave
equally good polymers comparable to conventionalp-nitrophenol approach. Further, we present here the polymerization and characterization of structural and functional properties
of poly(Val-Pro-Gly-Val-Gly), which is the most striking repeating sequence in the bovine and porcine elastins. The polymers
obtained by bothp-nitrophenol and 3-ethyl-1(N,N-dimethyl)aminopropylcarbodiimide approach were characterized by carbon-13 and proton nuclear
magnetic resonance spectroscopy, differential scanning calorimetry, circular dichroism and fourier transform infrared spectroscopy.
These results conclude that poly(Val-Pro-Gly-Val-Gly) obtained by both methods were identical in all respects of physical
and chemical properties indicates that 3-ethyl-1(N,N-dimethyl)aminopropylcarbodiimide with 1-hydroxybenzotriazole method can
be conveniently employed to synthesize these polymers. 相似文献
55.
A Castiglione-Morelli A Scopa A M Tamburro V Guantieri 《International journal of biological macromolecules》1990,12(6):363-368
Spectroscopic studies on synthetic polypeptides containing the unit X-G-G (X = V or L) are reported. The sequences, constituting either fragments or model of elastin, were shown to adopt type II β-turns together with an ensemble of unordered conformations. Furthermore, it was found that the stability of the β-turns was depending on the nature of the X residue, on the hydration of the chain and, in the case of the sequence G-V-G-G-L, was decreasing by increasing the length of the chain. 相似文献
56.