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

BMC Bioinformatics

Software

Mickaël Krzeminski¹  Rolf Boelens¹  Alexandre MJJ Bonvin¹  Karine Loth² 

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

关键词: Nuclear Magnetic Resonance;    HSQC Spectrum;    Nuclear Magnetic Resonance Structure;    Ambiguous State;    Chemical Shift Perturbation;   

DOI  :  10.1186/1471-2105-11-51

 received in 2009-08-19, accepted in 2010-01-26,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Krzeminski et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.