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.

doi:10.1371/journal.pone.0145848

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

Journal Article · Thu Jan 07 00:00:00 EST 2016 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0145848· OSTI ID:1236763

Sammond, Deanne W. ^[1]; Kastelowitz, Noah ^[2]; Himmel, Michael E. ^[1]; Yin, Hang ^[2]; Crowley, Michael F. ^[1]; Bomble, Yannick J. ^[1]

National Renewable Energy Lab. (NREL), Golden, CO (United States)
Univ. of Colorado, Boulder, CO (United States)

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.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1236763

Report Number(s):: NREL/JA-2700-65616

Journal Information:: PLoS ONE, Vol. 11, Issue 1; Related Information: PLoS One; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 19 works

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09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
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enzyme structure
sequence alignment
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protein structure databases
protein domains

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

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