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Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics
Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterizati...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000Research
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755392/ https://www.ncbi.nlm.nih.gov/pubmed/26918164 http://dx.doi.org/10.12688/f1000research.7186.1 |
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author | Noel, Jeffrey K Morcos, Faruck Onuchic, Jose N |
author_facet | Noel, Jeffrey K Morcos, Faruck Onuchic, Jose N |
author_sort | Noel, Jeffrey K |
collection | PubMed |
description | Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape. |
format | Online Article Text |
id | pubmed-4755392 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
spelling | pubmed-47553922016-02-24 Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics Noel, Jeffrey K Morcos, Faruck Onuchic, Jose N F1000Res Review Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape. F1000Research 2016-01-26 /pmc/articles/PMC4755392/ /pubmed/26918164 http://dx.doi.org/10.12688/f1000research.7186.1 Text en Copyright: © 2016 Noel JK et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Noel, Jeffrey K Morcos, Faruck Onuchic, Jose N Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title | Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title_full | Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title_fullStr | Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title_full_unstemmed | Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title_short | Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
title_sort | sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755392/ https://www.ncbi.nlm.nih.gov/pubmed/26918164 http://dx.doi.org/10.12688/f1000research.7186.1 |
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