Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations

Suresh Gorle, Lela Vuković

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The present article describes techniques for classical simulations of proteins and protein-nucleic acid complexes, revealing their dynamics and protein-substrate binding energies. The approach is based on classical atomistic molecular dynamics (MD) simulations of the experimentally determined structures of the complexes. MD simulations can provide dynamics of complexes in realistic solvents on microsecond timescales, and the free energy methods are able to provide Gibbs free energies of binding of substrates, such as nucleic acids, to proteins. The chapter describes methodologies for the preparation of computer models of biomolecular complexes and free energy perturbation methodology for evaluating Gibbs free energies of binding. The applications are illustrated with examples of snapshots of proteins and their complexes with nucleic acids, as well as the precise Gibbs free energies of binding.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages579-592
Number of pages14
DOIs
StatePublished - Jan 1 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1814
ISSN (Print)1064-3745

Fingerprint

Molecular Dynamics Simulation
Nucleic Acids
Proteins
Protein Binding
Computer Simulation

Keywords

  • Atomistic simulations
  • Binding free energies
  • Free energy calculations
  • Molecular dynamics simulations
  • Protein-nucleic acid complexes

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Gorle, S., & Vuković, L. (2018). Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations. In Methods in Molecular Biology (pp. 579-592). (Methods in Molecular Biology; Vol. 1814). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-8591-3_34

Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations. / Gorle, Suresh; Vuković, Lela.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 579-592 (Methods in Molecular Biology; Vol. 1814).

Research output: Chapter in Book/Report/Conference proceedingChapter

Gorle, S & Vuković, L 2018, Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1814, Humana Press Inc., pp. 579-592. https://doi.org/10.1007/978-1-4939-8591-3_34
Gorle S, Vuković L. Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 579-592. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8591-3_34
Gorle, Suresh ; Vuković, Lela. / Nanoscale dynamics and energetics of proteins and protein-nucleic acid complexes in classical molecular dynamics simulations. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 579-592 (Methods in Molecular Biology).
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