A coupled two-dimensional main chain torsional potential for protein dynamics: Generation and implementation

Yongxiu Li, Ya Gao, Xuqiang Zhang, Xingyu Wang, Lirong Mou, Lili Duan, Xiao He, Ye Mei, John Zhang

Research output: Contribution to journalArticle

Abstract

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G**level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models. [Figure not available: see fulltext.]

Original languageEnglish (US)
Pages (from-to)3647-3657
Number of pages11
JournalJournal of Molecular Modeling
Volume19
Issue number9
DOIs
StatePublished - Sep 2013

Fingerprint

Torsional stress
proteins
Proteins
torsion
Solvation
field theory (physics)
Molecular mechanics
Dipeptides
Parameterization
solvation
parameterization
Potential energy surfaces
Molecular modeling
Quantum theory
Dihedral angle
grids
Alanine
Peptides
Conformations
expansion

Keywords

  • Alanine oligopeptide
  • Density functional theory
  • Force field
  • Free energy landscape
  • J coupling
  • Solvation effect

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Catalysis
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

A coupled two-dimensional main chain torsional potential for protein dynamics : Generation and implementation. / Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John.

In: Journal of Molecular Modeling, Vol. 19, No. 9, 09.2013, p. 3647-3657.

Research output: Contribution to journalArticle

Li, Yongxiu ; Gao, Ya ; Zhang, Xuqiang ; Wang, Xingyu ; Mou, Lirong ; Duan, Lili ; He, Xiao ; Mei, Ye ; Zhang, John. / A coupled two-dimensional main chain torsional potential for protein dynamics : Generation and implementation. In: Journal of Molecular Modeling. 2013 ; Vol. 19, No. 9. pp. 3647-3657.
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