Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent

Yongzhi Chen, Xin Chen, Yuefan Deng

Research output: Contribution to journalArticlepeer-review

Abstract

A new method was proposed by Mongan et al. for constant pH molecular dynamics simulation and was implemented in AMBER 8 package. Protonation states are modeled with different charge sets, and titrating residues are sampled from a Boltzmann distribution of protonation states. The simulation periodically adopts Monte Carlo sampling based on Generalized Born (GB) derived energies. However, when this approach was applied to a bio-toxin, Botulinum Neurotoxin Type A (BoNT/A) at pH 4.4, 4.7, 5.0, 6.8 and 7.2, the p Ka predictions yielded by the method were inconsistent with the experimental values. The systems being simulated were divergent. Furthermore, the system behaviors in a very weak acidic solution (pH 6.8) and in a very weak basic solution (pH 7.2) were significantly different from the neutral case (pH 7.0). Hence, we speculate this method may require further study for modeling large biomolecule.

Original languageEnglish (US)
Pages (from-to)210-213
Number of pages4
JournalComputer Physics Communications
Volume177
Issue number1-2 SPEC. ISS.
DOIs
StatePublished - Jul 2007

Keywords

  • Botulinum neurotoxin
  • Constant pH molecular dynamics
  • Generalized Born method

ASJC Scopus subject areas

  • Hardware and Architecture
  • Physics and Astronomy(all)

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