Molecular dynamics simulation of protein crystal with polarized protein-specific force field

Yongxiu Li, John Zhang, Ye Mei

Research output: Contribution to journalArticle

Abstract

Two 250 ns molecular simulations have been carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing the polarized protein-specific charge (PPC), as well as the standard AMBER99SB force field, to investigate the electrostatic polarization on the simulated crystal stability. Results show that under PPC, the monomers in unit cell as well as the lattice in supercell are more stable with smaller root-mean-square deviations and more accurate lattice atomic fluctuations compared with the crystallographic B-factors than under AMBER99SB force field. Most of the interactions at interfaces in the X-ray structure are quite well-preserved, underscoring the important effect of polarization on maintaining the crystal stability. However, the results also show that the hydrogen bond between Asp53 and Gln37 and the cation-π interaction between Arg56 and His64 are not stable, indicating that further optimization of force field, especially the van der Waals interaction parameters, is desired.

Original languageEnglish (US)
Pages (from-to)12326-12335
Number of pages10
JournalJournal of Physical Chemistry B
Volume118
Issue number43
DOIs
StatePublished - Oct 30 2014

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field theory (physics)
Molecular dynamics
molecular dynamics
proteins
Proteins
Crystals
Computer simulation
Polarization
crystals
simulation
interactions
polarization
Cations
Electrostatics
Hydrogen bonds
monomers
Monomers
Positive ions
electrostatics
hydrogen bonds

ASJC Scopus subject areas

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

Cite this

Molecular dynamics simulation of protein crystal with polarized protein-specific force field. / Li, Yongxiu; Zhang, John; Mei, Ye.

In: Journal of Physical Chemistry B, Vol. 118, No. 43, 30.10.2014, p. 12326-12335.

Research output: Contribution to journalArticle

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