Literature DB >> 34480927

Evolutionary coupling range varies widely among enzymes depending on selection pressure.

Julian Echave1.   

Abstract

Recent studies proposed that enzyme-active sites induce evolutionary constraints at long distances. The physical origin of such long-range evolutionary coupling is unknown. Here, I use a recent biophysical model of evolution to study the relationship between physical and evolutionary couplings on a diverse data set of monomeric enzymes. I show that evolutionary coupling is not universally long-range. Rather, range varies widely among enzymes, from 2 to 20 Å. Furthermore, the evolutionary coupling range of an enzyme does not inform on the underlying physical coupling, which is short range for all enzymes. Rather, evolutionary coupling range is determined by functional selection pressure.
Copyright © 2021 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2021        PMID: 34480927      PMCID: PMC8553639          DOI: 10.1016/j.bpj.2021.08.042

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   3.699


  34 in total

1.  Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models.

Authors:  Cristian Micheletti; Paolo Carloni; Amos Maritan
Journal:  Proteins       Date:  2004-05-15

2.  Allostery in a coarse-grained model of protein dynamics.

Authors:  Dengming Ming; Michael E Wall
Journal:  Phys Rev Lett       Date:  2005-11-02       Impact factor: 9.161

3.  A perturbative view of protein structural variation.

Authors:  Julián Echave; Francisco M Fernández
Journal:  Proteins       Date:  2010-01

4.  Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes.

Authors:  Avital Sharir-Ivry; Yu Xia
Journal:  J Mol Biol       Date:  2019-07-17       Impact factor: 5.469

Review 5.  On the perturbation nature of allostery: sites, mutations, and signal modulation.

Authors:  Enrico Guarnera; Igor N Berezovsky
Journal:  Curr Opin Struct Biol       Date:  2018-11-12       Impact factor: 6.809

Review 6.  Modeling evolution using the probability of fixation: history and implications.

Authors:  David M McCandlish; Arlin Stoltzfus
Journal:  Q Rev Biol       Date:  2014-09       Impact factor: 4.875

7.  A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations.

Authors:  Nandakumar Rajasekaran; Ashok Sekhar; Athi N Naganathan
Journal:  J Phys Chem Lett       Date:  2017-09-20       Impact factor: 6.475

8.  Sequence entropy of folding and the absolute rate of amino acid substitutions.

Authors:  Richard A Goldstein; David D Pollock
Journal:  Nat Ecol Evol       Date:  2017-10-23       Impact factor: 15.460

9.  Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins.

Authors:  Holger Flechsig
Journal:  Biophys J       Date:  2017-08-08       Impact factor: 4.033

10.  Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes.

Authors:  Avital Sharir-Ivry; Yu Xia
Journal:  Evol Bioinform Online       Date:  2019-06-13       Impact factor: 1.625

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  1 in total

1.  Odd one out? Functional tuning of Zymomonas mobilis pyruvate kinase is narrower than its allosteric, human counterpart.

Authors:  Braelyn M Page; Tyler A Martin; Collette L Wright; Lauren A Fenton; Maite T Villar; Qingling Tang; Antonio Artigues; Audrey Lamb; Aron W Fenton; Liskin Swint-Kruse
Journal:  Protein Sci       Date:  2022-07       Impact factor: 6.993

  1 in total

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