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Open Access Software

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

Mickaël Krzeminski1, Karine Loth12, Rolf Boelens1 and Alexandre MJJ Bonvin1*

Author Affiliations

1 Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584 CH, Utrecht, The Netherlands

2 Centre de biophysique moléculaire, UPR n°4301 CNRS, affiliated to the University of Orléans and to Inserm, rue Charles Sadron, 45071 Orléans Cedex 2, France

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BMC Bioinformatics 2010, 11:51  doi:10.1186/1471-2105-11-51

Published: 26 January 2010

Abstract

Background

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 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties.

Results

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.

Conclusions

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.