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Simple approach for ranking structure determining residues
Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regard...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924125/ https://www.ncbi.nlm.nih.gov/pubmed/27366642 http://dx.doi.org/10.7717/peerj.2136 |
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author | Luna-Martínez, Oscar D. Vidal-Limón, Abraham Villalba-Velázquez, Miryam I. Sánchez-Alcalá, Rosalba Garduño-Juárez, Ramón Uversky, Vladimir N. Becerril, Baltazar |
author_facet | Luna-Martínez, Oscar D. Vidal-Limón, Abraham Villalba-Velázquez, Miryam I. Sánchez-Alcalá, Rosalba Garduño-Juárez, Ramón Uversky, Vladimir N. Becerril, Baltazar |
author_sort | Luna-Martínez, Oscar D. |
collection | PubMed |
description | Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. |
format | Online Article Text |
id | pubmed-4924125 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-49241252016-06-30 Simple approach for ranking structure determining residues Luna-Martínez, Oscar D. Vidal-Limón, Abraham Villalba-Velázquez, Miryam I. Sánchez-Alcalá, Rosalba Garduño-Juárez, Ramón Uversky, Vladimir N. Becerril, Baltazar PeerJ Biochemistry Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PeerJ Inc. 2016-06-22 /pmc/articles/PMC4924125/ /pubmed/27366642 http://dx.doi.org/10.7717/peerj.2136 Text en ©2016 Luna-Martínez et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biochemistry Luna-Martínez, Oscar D. Vidal-Limón, Abraham Villalba-Velázquez, Miryam I. Sánchez-Alcalá, Rosalba Garduño-Juárez, Ramón Uversky, Vladimir N. Becerril, Baltazar Simple approach for ranking structure determining residues |
title | Simple approach for ranking structure determining residues |
title_full | Simple approach for ranking structure determining residues |
title_fullStr | Simple approach for ranking structure determining residues |
title_full_unstemmed | Simple approach for ranking structure determining residues |
title_short | Simple approach for ranking structure determining residues |
title_sort | simple approach for ranking structure determining residues |
topic | Biochemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4924125/ https://www.ncbi.nlm.nih.gov/pubmed/27366642 http://dx.doi.org/10.7717/peerj.2136 |
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