Cargando…
Classification of Domain Movements in Proteins Using Dynamic Contact Graphs
A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832408/ https://www.ncbi.nlm.nih.gov/pubmed/24260562 http://dx.doi.org/10.1371/journal.pone.0081224 |
_version_ | 1782291673490915328 |
---|---|
author | Taylor, Daniel Cawley, Gavin Hayward, Steven |
author_facet | Taylor, Daniel Cawley, Gavin Hayward, Steven |
author_sort | Taylor, Daniel |
collection | PubMed |
description | A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from one conformation to the other. We argue that there are five types of elemental contact changes and that these relate to five model domain movements called: “free”, “open-closed”, “anchored”, “sliding-twist”, and “see-saw.” A directed graph is introduced called the “Dynamic Contact Graph” which represents the contact changes in a domain movement. In many cases a graph, or part of a graph, provides a clear visual metaphor for the movement it represents and is a motif that can be easily recognised. The Dynamic Contact Graphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic Contact Graphs, those that represent elemental contact changes, allowing us to count the number of instances of each type of elemental contact change in the domain movement. This naturally leads to sixteen classes into which the 1822 domain movements are classified. |
format | Online Article Text |
id | pubmed-3832408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-38324082013-11-20 Classification of Domain Movements in Proteins Using Dynamic Contact Graphs Taylor, Daniel Cawley, Gavin Hayward, Steven PLoS One Research Article A new method for the classification of domain movements in proteins is described and applied to 1822 pairs of structures from the Protein Data Bank that represent a domain movement in two-domain proteins. The method is based on changes in contacts between residues from the two domains in moving from one conformation to the other. We argue that there are five types of elemental contact changes and that these relate to five model domain movements called: “free”, “open-closed”, “anchored”, “sliding-twist”, and “see-saw.” A directed graph is introduced called the “Dynamic Contact Graph” which represents the contact changes in a domain movement. In many cases a graph, or part of a graph, provides a clear visual metaphor for the movement it represents and is a motif that can be easily recognised. The Dynamic Contact Graphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic Contact Graphs, those that represent elemental contact changes, allowing us to count the number of instances of each type of elemental contact change in the domain movement. This naturally leads to sixteen classes into which the 1822 domain movements are classified. Public Library of Science 2013-11-18 /pmc/articles/PMC3832408/ /pubmed/24260562 http://dx.doi.org/10.1371/journal.pone.0081224 Text en © 2013 Taylor 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Taylor, Daniel Cawley, Gavin Hayward, Steven Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title | Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title_full | Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title_fullStr | Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title_full_unstemmed | Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title_short | Classification of Domain Movements in Proteins Using Dynamic Contact Graphs |
title_sort | classification of domain movements in proteins using dynamic contact graphs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832408/ https://www.ncbi.nlm.nih.gov/pubmed/24260562 http://dx.doi.org/10.1371/journal.pone.0081224 |
work_keys_str_mv | AT taylordaniel classificationofdomainmovementsinproteinsusingdynamiccontactgraphs AT cawleygavin classificationofdomainmovementsinproteinsusingdynamiccontactgraphs AT haywardsteven classificationofdomainmovementsinproteinsusingdynamiccontactgraphs |