Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates

Weihong Zhang; Steven C Howell; David W Wright; Andrew Heindel; Xiangyun Qiu; Jianhan Chen; Joseph E Curtis

doi:10.1016/j.jmgm.2017.02.010

Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates

J Mol Graph Model. 2017 May:73:179-190. doi: 10.1016/j.jmgm.2017.02.010. Epub 2017 Feb 23.

Authors

Weihong Zhang¹, Steven C Howell², David W Wright³, Andrew Heindel⁴, Xiangyun Qiu⁵, Jianhan Chen⁶, Joseph E Curtis⁷

Affiliations

¹ Kansas State University, Manhattan, KS, USA.
² NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA.
³ Centre for Computational Science, Department of Chemistry, University College London, 10 Gordon St., London, UK.
⁴ James Madison University, Department of Chemistry & Biochemistry, Harrisonburg, VA, USA.
⁵ Department of Physics, The George Washington University, Washington, DC, USA.
⁶ Kansas State University, Manhattan, KS, USA. Electronic address: jianhanc@ksu.edu.
⁷ NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA. Electronic address: joseph.curtis@nist.gov.

PMID: 28292714
DOI: 10.1016/j.jmgm.2017.02.010

Abstract

We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data.

Keywords: Monte Carlo; SANS; SAXS; Small-angle scattering; Structural biology; Torsion angle molecular dynamics.

Published by Elsevier Inc.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Carbohydrates / chemistry*
DNA / chemistry
Molecular Dynamics Simulation*
Monte Carlo Method*
Nucleic Acids / chemistry*
Peptides / chemistry
Proteins / chemistry*
Solvents / chemistry

Substances

Carbohydrates
Nucleic Acids
Peptides
Proteins
Solvents
DNA