Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.

TitleCoarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.
Publication TypeJournal Article
Year of Publication2011
AuthorsOrozco, Modesto, Orellana Laura, Hospital Adam, Naganathan Athi N., Emperador Agustí, Carrillo Oliver, and Gelpí J L.
JournalAdv Protein Chem Struct Biol
Volume85
Pagination183-215
Date Published2011
ISSN1876-1631
KeywordsDatabases, Humans, Molecular Dynamics Simulation, Monte Carlo Method, Protein, Proteins
Abstract

Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition of the structure. Theoretical approaches have become then the alternative but face serious timescale problems, since many biologically relevant deformation movements happen in a timescale that is far beyond the possibility of current atomistic models. In this complex scenario, coarse-grained simulation methods have emerged as a powerful and inexpensive alternative. Along this chapter, we will review these coarse-grained methods, and explain their physical foundations and their range of applicability.

DOI10.1016/B978-0-12-386485-7.00005-3