Issue 47, 2014

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings

Abstract

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

Graphical abstract: Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings

Supplementary files

Article information

Article type
Paper
Submitted
15 Jul 2014
Accepted
10 Oct 2014
First published
13 Oct 2014
This article is Open Access
Creative Commons BY license

Phys. Chem. Chem. Phys., 2014,16, 26030-26039

Author version available

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings

M. Sanchez-Martinez and R. Crehuet, Phys. Chem. Chem. Phys., 2014, 16, 26030 DOI: 10.1039/C4CP03114H

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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