Publication detail

Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins

HADDAD, Y. ADAM, V. HEGER, Z.

Original Title

Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins

Type

journal article in Web of Science

Language

English

Original Abstract

Given by chi torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.

Keywords

rotamer; molecular dynamics; proteins

Authors

HADDAD, Y.; ADAM, V.; HEGER, Z.

Released

4. 6. 2019

Publisher

Elsevier

ISBN

0006-3495

Periodical

BIOPHYSICAL JOURNAL

Year of study

116

Number

11

State

United States of America

Pages from

2062

Pages to

2072

Pages count

11

URL

https://www.sciencedirect.com/science/article/abs/pii/S0006349519303352

Full text in the Digital Library

http://hdl.handle.net/11012/195616

BibTex

@article{BUT157616,
  author="Yazan Abdulmajeed Eyadh {Haddad} and Vojtěch {Adam} and Zbyněk {Heger}",
  title="Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins",
  journal="BIOPHYSICAL JOURNAL",
  year="2019",
  volume="116",
  number="11",
  pages="2062--2072",
  doi="10.1016/j.bpj.2019.04.017",
  issn="0006-3495",
  url="https://www.sciencedirect.com/science/article/abs/pii/S0006349519303352"
}