Validating and improving elastic network models with molecular dynamics simulations

✍ Scribed by Tod D. Romo; Alan Grossfield

• Book ID: 105358147
• Publisher: John Wiley and Sons
• Year: 2010
• Tongue: English
• Weight: 536 KB
• Volume: 79
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/prot.22855

✦ Synopsis

Abstract

Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all‐atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis‐testing situations. Historically, ENMs have been validated via comparison to crystallographic B‐factors, but this comparison is relatively low‐resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM‐type models by quantitatively comparing their predictions to microsecond‐scale all‐atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well‐optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all‐atom simulations run for several hundred nanoseconds. Proteins 2010. © 2010 Wiley‐Liss, Inc.