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Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural a...

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Autores principales: Sammond, Deanne W., Kastelowitz, Noah, Himmel, Michael E., Yin, Hang, Crowley, Michael F., Bomble, Yannick J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704809/
https://www.ncbi.nlm.nih.gov/pubmed/26741367
http://dx.doi.org/10.1371/journal.pone.0145848
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author Sammond, Deanne W.
Kastelowitz, Noah
Himmel, Michael E.
Yin, Hang
Crowley, Michael F.
Bomble, Yannick J.
author_facet Sammond, Deanne W.
Kastelowitz, Noah
Himmel, Michael E.
Yin, Hang
Crowley, Michael F.
Bomble, Yannick J.
author_sort Sammond, Deanne W.
collection PubMed
description Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.
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spelling pubmed-47048092016-01-15 Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms Sammond, Deanne W. Kastelowitz, Noah Himmel, Michael E. Yin, Hang Crowley, Michael F. Bomble, Yannick J. PLoS One Research Article Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. Public Library of Science 2016-01-07 /pmc/articles/PMC4704809/ /pubmed/26741367 http://dx.doi.org/10.1371/journal.pone.0145848 Text en © 2016 Sammond 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, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sammond, Deanne W.
Kastelowitz, Noah
Himmel, Michael E.
Yin, Hang
Crowley, Michael F.
Bomble, Yannick J.
Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title_full Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title_fullStr Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title_full_unstemmed Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title_short Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms
title_sort comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704809/
https://www.ncbi.nlm.nih.gov/pubmed/26741367
http://dx.doi.org/10.1371/journal.pone.0145848
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