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Title: Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms

Abstract

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. As a result, 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.

Authors:
 [1];  [2];  [1];  [2];  [1];  [1]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  2. Univ. of Colorado, Boulder, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)
OSTI Identifier:
1236763
Report Number(s):
NREL/JA-2700-65616
Journal ID: ISSN 1932-6203
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Related Information: PLoS One; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; thermophilic; mesophilic; enzymes; atomic packing; clusters; sequence motif analysis; enzyme structure; sequence alignment; protein structure comparison; bacillus; dehydrogenases; protein structure databases; protein domains

Citation Formats

Sammond, Deanne W., Kastelowitz, Noah, Himmel, Michael E., Yin, Hang, Crowley, Michael F., and Bomble, Yannick J. Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0145848.
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. United States. doi:10.1371/journal.pone.0145848.
Sammond, Deanne W., Kastelowitz, Noah, Himmel, Michael E., Yin, Hang, Crowley, Michael F., and Bomble, Yannick J. Thu . "Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms". United States. doi:10.1371/journal.pone.0145848. https://www.osti.gov/servlets/purl/1236763.
@article{osti_1236763,
title = {Comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms},
author = {Sammond, Deanne W. and Kastelowitz, Noah and Himmel, Michael E. and Yin, Hang and Crowley, Michael F. and Bomble, Yannick J.},
abstractNote = {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. As a result, 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.},
doi = {10.1371/journal.pone.0145848},
journal = {PLoS ONE},
number = 1,
volume = 11,
place = {United States},
year = {Thu Jan 07 00:00:00 EST 2016},
month = {Thu Jan 07 00:00:00 EST 2016}
}

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Cited by: 5 works
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Works referenced in this record:

Additivity of mutational effects in proteins
journal, September 1990


Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production
journal, February 2007

  • Himmel, M. E.; Ding, S.-Y.; Johnson, D. K.
  • Science, Vol. 315, Issue 5813, p. 804-807
  • DOI: 10.1126/science.1137016