Role of Conformational Flexibility in Monte Carlo Simulations of Many-Protein Systems

Bibhab Bandhu Majumdar, Vera Prytkova, Eric K. Wong, J. Alfredo Freites, Douglas J. Tobias, Matthias Heyden

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Efficient computational modeling of biological systems characterized by high concentrations of macromolecules often relies on rigid-body Brownian Dynamics or Monte Carlo (MC) simulations. However, the accuracy of rigid-body models is limited by the fixed conformation of the simulated biomolecules. Multi-conformation Monte Carlo (mcMC) simulations of protein solutions incorporate conformational flexibility via a conformational swap trial move within a predetermined library of discrete protein structures, thereby alleviating artifacts arising from the use of a single protein conformation. Here, we investigate the impact of the number of distinct protein structures in the conformational library and the extent of conformational sampling used in its generation on structural observables computed from simulations of hen egg white lysozyme (HEWL), human D-Crystallin, and bovine B-Crystallin solutions. We find that the importance of specific protocols for the construction of the protein structure library is strongly dependent on the nature of the simulated system.

Original languageEnglish (US)
Pages (from-to)1399-1408
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume15
Issue number2
DOIs
StatePublished - Feb 12 2019

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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