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Thermal Adaptation of Conformational Dynamics in Ribonuclease H

The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functio...

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Detalles Bibliográficos
Autores principales: Stafford, Kate A., Robustelli, Paul, Palmer, Arthur G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789780/
https://www.ncbi.nlm.nih.gov/pubmed/24098095
http://dx.doi.org/10.1371/journal.pcbi.1003218
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author Stafford, Kate A.
Robustelli, Paul
Palmer, Arthur G.
author_facet Stafford, Kate A.
Robustelli, Paul
Palmer, Arthur G.
author_sort Stafford, Kate A.
collection PubMed
description The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. In particular, ribonuclease HI (RNase H), an 18 kD globular protein that hydrolyzes the RNA strand of RNA:DNA hybrid substrates, has been extensively studied by NMR spectroscopy to characterize the differences in dynamics between homologs from the mesophilic organism E. coli and the thermophilic organism T. thermophilus. Herein, molecular dynamics simulations are reported for five homologous RNase H proteins of varying thermostabilities and enzymatic activities from organisms of markedly different preferred growth temperatures. For the E. coli and T. thermophilus proteins, strong agreement is obtained between simulated and experimental values for NMR order parameters and for dynamically averaged chemical shifts, suggesting that these simulations can be a productive platform for predicting the effects of individual amino acid residues on dynamic behavior. Analyses of the simulations reveal that a single residue differentiates between two different and otherwise conserved dynamic processes in a region of the protein known to form part of the substrate-binding interface. Additional key residues within these two categories are identified through the temperature-dependence of these conformational processes.
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spelling pubmed-37897802013-10-04 Thermal Adaptation of Conformational Dynamics in Ribonuclease H Stafford, Kate A. Robustelli, Paul Palmer, Arthur G. PLoS Comput Biol Research Article The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. In particular, ribonuclease HI (RNase H), an 18 kD globular protein that hydrolyzes the RNA strand of RNA:DNA hybrid substrates, has been extensively studied by NMR spectroscopy to characterize the differences in dynamics between homologs from the mesophilic organism E. coli and the thermophilic organism T. thermophilus. Herein, molecular dynamics simulations are reported for five homologous RNase H proteins of varying thermostabilities and enzymatic activities from organisms of markedly different preferred growth temperatures. For the E. coli and T. thermophilus proteins, strong agreement is obtained between simulated and experimental values for NMR order parameters and for dynamically averaged chemical shifts, suggesting that these simulations can be a productive platform for predicting the effects of individual amino acid residues on dynamic behavior. Analyses of the simulations reveal that a single residue differentiates between two different and otherwise conserved dynamic processes in a region of the protein known to form part of the substrate-binding interface. Additional key residues within these two categories are identified through the temperature-dependence of these conformational processes. Public Library of Science 2013-10-03 /pmc/articles/PMC3789780/ /pubmed/24098095 http://dx.doi.org/10.1371/journal.pcbi.1003218 Text en © 2013 Stafford 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
Stafford, Kate A.
Robustelli, Paul
Palmer, Arthur G.
Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title_full Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title_fullStr Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title_full_unstemmed Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title_short Thermal Adaptation of Conformational Dynamics in Ribonuclease H
title_sort thermal adaptation of conformational dynamics in ribonuclease h
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789780/
https://www.ncbi.nlm.nih.gov/pubmed/24098095
http://dx.doi.org/10.1371/journal.pcbi.1003218
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