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

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 re...

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Autores principales: Krzeminski, Mickaël, Loth, Karine, Boelens, Rolf, Bonvin, Alexandre MJJ
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823710/
https://www.ncbi.nlm.nih.gov/pubmed/20102599
http://dx.doi.org/10.1186/1471-2105-11-51
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author Krzeminski, Mickaël
Loth, Karine
Boelens, Rolf
Bonvin, Alexandre MJJ
author_facet Krzeminski, Mickaël
Loth, Karine
Boelens, Rolf
Bonvin, Alexandre MJJ
author_sort Krzeminski, Mickaël
collection PubMed
description 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 (1)H-(15)N 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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spelling pubmed-28237102010-02-18 SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes Krzeminski, Mickaël Loth, Karine Boelens, Rolf Bonvin, Alexandre MJJ BMC Bioinformatics Software 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 (1)H-(15)N 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. BioMed Central 2010-01-26 /pmc/articles/PMC2823710/ /pubmed/20102599 http://dx.doi.org/10.1186/1471-2105-11-51 Text en Copyright ©2010 Krzeminski et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Software
Krzeminski, Mickaël
Loth, Karine
Boelens, Rolf
Bonvin, Alexandre MJJ
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title_full SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title_fullStr SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title_full_unstemmed SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title_short SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes
title_sort samplex: automatic mapping of perturbed and unperturbed regions of proteins and complexes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823710/
https://www.ncbi.nlm.nih.gov/pubmed/20102599
http://dx.doi.org/10.1186/1471-2105-11-51
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