Rotamer decomposition and protein dynamics

Efficiently analyzing dihedral populations from molecular dynamics

Hiroshi Watanabe, Marcus Elstner, Thomas Steinbrecher

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Molecular mechanics methods have matured into powerful methods to understand the dynamics and flexibility of macromolecules and especially proteins. As multinanosecond to microsecond length molecular dynamics (MD) simulations become commonplace, advanced analysis tools are required to generate scientifically useful information from large amounts of data. Some of the key degrees of freedom to understand protein flexibility and dynamics are the amino acid residue side chain dihedral angles. In this work, we present an easily automated way to summarize and understand the relevant dihedral populations. A tremendous reduction in complexity is achieved by describing dihedral timeseries in terms of histograms decomposed into Gaussians. Using the familiar and widely studied protein lysozyme, it is demonstrated that our approach captures essential properties of protein structure and dynamics. A simple classification scheme is proposed that indicates the rotational state population for each dihedral angle of interest and allows a decision if a given side chain or peptide backbone fragment remains rigid during the course of an MD simulation, adopts a converged distribution between conformational substates or has not reached convergence yet.

Original languageEnglish
Pages (from-to)198-205
Number of pages8
JournalJournal of Computational Chemistry
Volume34
Issue number3
DOIs
Publication statusPublished - 2013 Jan 30
Externally publishedYes

Fingerprint

Molecular Dynamics
Molecular dynamics
Dihedral angle
Decomposition
Proteins
Protein
Decompose
Molecular Dynamics Simulation
Flexibility
Molecular Mechanics
Protein Structure
Backbone
Peptides
Histogram
Peptide Fragments
Molecular mechanics
Amino Acids
Computer simulation
Fragment
Degrees of freedom (mechanics)

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

Rotamer decomposition and protein dynamics : Efficiently analyzing dihedral populations from molecular dynamics. / Watanabe, Hiroshi; Elstner, Marcus; Steinbrecher, Thomas.

In: Journal of Computational Chemistry, Vol. 34, No. 3, 30.01.2013, p. 198-205.

Research output: Contribution to journalArticle

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