title: Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.
abstract: Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.
authors.affiliation: Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Yu
authors.forename: Zhiqing
authors.initials: Z
authors.lastname: Wu
authors.forename: Huibin
authors.initials: H
authors.lastname: Chen
authors.forename: Xu
authors.initials: X
authors.lastname: Liu
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
authors.forename: Zijing
authors.initials: Z
authors.lastname: Lin
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009842:Oligopeptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D000596:Amino Acids; D004151:Dipeptides; D009842:Oligopeptides