title: Effects of solvents on the intrinsic propensity of peptide backbone conformations.
abstract: We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.
authors.affiliation: National Laboratory of Solid State Microstructure, and Department of Physics, Nanjing University, Nanjing 210093, China.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Li
authors.forename: Meng
authors.initials: M
authors.lastname: Qin
authors.forename: Zuoxiu
authors.initials: Z
authors.lastname: Tie
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D012997:Solvents / Q000737:chemistry*
chemical_list: D010455:Peptides; D012997:Solvents