title: Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential.
abstract: A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER03(2D) force field with the implementation of a polarization scheme (AMBER03(2D)p). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER03(2D) without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures.
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 China.
authors.forename: Yongxiu
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institutes for Advanced Interdisciplinary Research, East China Normal University, Shanghai 200062 China.
authors.forename: Lirong
authors.initials: L
authors.lastname: Mou
authors.affiliation: State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 China.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Lin
authors.affiliation: 1] State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 China [2] NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai China 200062.
authors.forename: John Z H
authors.initials: JZ
authors.lastname: Zhang
authors.affiliation: 1] State Key Laboratory of Precision Spectroscopy, Department of Physics and Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 China [2] NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai China 200062.
authors.forename: Ye
authors.initials: Y
authors.lastname: Mei
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary