Coupled two-dimensional main-chain torsional potential for protein dynamics II: Performance and validation

Ya Gao, Yongxiu Li, Lirong Mou, Wenxin Hu, Jun Zheng, John Zhang, Ye Mei

Research output: Contribution to journalArticle

Abstract

The accuracy of force fields is of utmost importance in molecular modeling of proteins. Despite successful applications of force fields for about the past 30 years, some inherent flaws lying in force fields, such as biased secondary propensities and fixed atomic charges, have been observed in different aspects of biomolecular research; hence, a correction to current force fields is desirable. Because of the simplified functional form and the limited number of parameters for main chain torsion (MCT) in traditional force fields, it is not easy to propose an exquisite force field that is well-balanced among various conformations. Recently, AMBER-compatible force fields with coupled MCT term have been proposed, which show some improvement over AMBER03 and AMBER99SB force fields. In this work, further calibration of the torsional parameters has been conducted by changing the solvation model in quantum mechanical calculation and minimizing the deviation from the nuclear magnetic resonance experiments for some benchmark model systems and a folded protein. The results show that the revised force fields give excellent agreement with experiments in J coupling, chemical shifts, and secondary structure populations. In addition, the polarization effect is found to be crucial for the systems with ordered secondary structures.

Original languageEnglish (US)
Pages (from-to)4188-4193
Number of pages6
JournalJournal of Physical Chemistry B
Volume119
Issue number11
DOIs
StatePublished - Mar 19 2015

Fingerprint

Torsional stress
field theory (physics)
proteins
Proteins
Molecular modeling
Solvation
Chemical shift
Conformations
Experiments
Nuclear magnetic resonance
Calibration
Polarization
Defects
torsion
solvation
chemical equilibrium
deviation
nuclear magnetic resonance
defects
polarization

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Coupled two-dimensional main-chain torsional potential for protein dynamics II : Performance and validation. / Gao, Ya; Li, Yongxiu; Mou, Lirong; Hu, Wenxin; Zheng, Jun; Zhang, John; Mei, Ye.

In: Journal of Physical Chemistry B, Vol. 119, No. 11, 19.03.2015, p. 4188-4193.

Research output: Contribution to journalArticle

Gao, Ya ; Li, Yongxiu ; Mou, Lirong ; Hu, Wenxin ; Zheng, Jun ; Zhang, John ; Mei, Ye. / Coupled two-dimensional main-chain torsional potential for protein dynamics II : Performance and validation. In: Journal of Physical Chemistry B. 2015 ; Vol. 119, No. 11. pp. 4188-4193.
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