SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes

BMC Bioinformatics. 2010;11(1):51 DOI 10.1186/1471-2105-11-51

 

Journal Homepage

Journal Title: BMC Bioinformatics

ISSN: 1471-2105 (Online)

Publisher: BMC

LCC Subject Category: Medicine: Medicine (General): Computer applications to medicine. Medical informatics | Science: Biology (General)

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML

 

AUTHORS

Loth Karine
Krzeminski Mickaël
Boelens Rolf
Bonvin Alexandre MJJ

EDITORIAL INFORMATION

Blind peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 19 weeks

 

Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR <sup>1</sup>H-<sup>15</sup>N HSQC experiments gives an excellent opportunity to discriminate both moieties.</p> <p>Results</p> <p>We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in protein complexes.</p> <p>Conclusions</p> <p>The proposed approach is suitable for partially unfolded states of proteins, local perturbations due to small ligands and protein-protein interfaces. The method is not restricted to NMR data, but is generic and can be applied to a wide variety of information.</p>