title: Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide.
abstract: We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of alpha helices at both low and high temperatures but stabilizes beta structures only at high temperatures at which alpha helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes beta structures under all conditions, especially in the low temperature region where alpha helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.
authors.affiliation: Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
authors.forename: Yan
authors.initials: Y
authors.lastname: Mu
authors.forename: Yi Qin
authors.initials: YQ
authors.lastname: Gao
mesh_terms: D000577:Amides / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D000577:Amides; D010455:Peptides; D012313:RNA; D004247:DNA