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SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.

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.
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Submitted on : Friday, January 27, 2012 - 1:04:04 PM
Last modification on : Thursday, December 9, 2021 - 3:42:08 PM




Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre Bonvin. SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.. BMC Bioinformatics, BioMed Central, 2010, 11 (1), pp.51. ⟨10.1186/1471-2105-11-51⟩. ⟨inserm-00663535⟩



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