Literature DB >> 28101963

Extreme biophysics: Enzymes under pressure.

Qi Huang1, Jocelyn M Rodgers1,2, Russell J Hemley3, Toshiko Ichiye1.   

Abstract

A critical question about piezophilic (pressure-loving) microbes is how their constituent molecules maintain function under high pressure. Here, factors are examined that may lead to the increased activity under pressure in dihydrofolate reductase from the piezophilic Moritella profunda compared to the homologous enzyme from the mesophilic Escherichia coli. Molecular dynamics simulations are performed at various temperatures and pressures to examine how pressure affects the flexibility of the enzymes from these two microbes, since both stability and flexibility are necessary for enzyme activity. The results suggest that collective motions on the 10-ns timescale are responsible for the flexibility necessary for "corresponding states" activity at the growth conditions of the parent organism. In addition, the results suggest that while the lower stability of many enzymes from deep-sea microbes may be an adaptation for greater flexibility at low temperatures, high pressure may enhance their adaptation to low temperatures.
© 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Entities:  

Keywords:  atomic fluctuations; extremophiles; pressure and temperature dependence

Mesh:

Substances:

Year:  2017        PMID: 28101963      PMCID: PMC6334844          DOI: 10.1002/jcc.24737

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  35 in total

1.  Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

Authors:  Lars Meinhold; Jeremy C Smith; Akio Kitao; Ahmed H Zewail
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-23       Impact factor: 11.205

2.  Elastic incoherent neutron scattering as a probe of high pressure induced changes in protein flexibility.

Authors:  A Filabozzi; A Deriu; M T Di Bari; D Russo; S Croci; A Di Venere
Journal:  Biochim Biophys Acta       Date:  2009-09-06

3.  Canonical dynamics: Equilibrium phase-space distributions.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

4.  Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.

Authors:  M R Sawaya; J Kraut
Journal:  Biochemistry       Date:  1997-01-21       Impact factor: 3.162

5.  What makes proteins work: exploring life in P-T-X.

Authors:  Toshiko Ichiye
Journal:  Phys Biol       Date:  2016-11-15       Impact factor: 2.583

Review 6.  Pressure stability of proteins.

Authors:  J L Silva; G Weber
Journal:  Annu Rev Phys Chem       Date:  1993       Impact factor: 12.703

7.  Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation.

Authors:  Nozomi Ando; Buz Barstow; Walter A Baase; Andrew Fields; Brian W Matthews; Sol M Gruner
Journal:  Biochemistry       Date:  2008-09-25       Impact factor: 3.162

8.  Protective effect of sucrose and sodium chloride for Lactococcus lactis during sublethal and lethal high-pressure treatments.

Authors:  Adriana Molina-Höppner; Wolfgang Doster; Rudi F Vogel; Michael G Gänzle
Journal:  Appl Environ Microbiol       Date:  2004-04       Impact factor: 4.792

9.  Loop interactions during catalysis by dihydrofolate reductase from Moritella profunda.

Authors:  Enas M Behiry; Rhiannon M Evans; Jiannan Guo; E Joel Loveridge; Rudolf K Allemann
Journal:  Biochemistry       Date:  2014-07-18       Impact factor: 3.162

Review 10.  Psychrophilic enzymes: from folding to function and biotechnology.

Authors:  Georges Feller
Journal:  Scientifica (Cairo)       Date:  2013-01-17
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  14 in total

1.  Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations.

Authors:  Tetsuro Nagai; Florence Tama; Osamu Miyashita
Journal:  Biophys J       Date:  2018-12-13       Impact factor: 4.033

2.  Adaptations for Pressure and Temperature Effects on Loop Motion in Escherichia coli and Moritella profunda Dihydrofolate Reductase.

Authors:  Qi Huang; Jocelyn M Rodgers; Russell J Hemley; Toshiko Ichiye
Journal:  High Press Res       Date:  2019-03-05       Impact factor: 1.431

3.  Virial Based Berendsen Barostat on GPUs using AMOEBA in Tinker-OpenMM.

Authors:  Matthew Harger; Pengyu Ren
Journal:  Results Chem       Date:  2019-06-20

4.  Quasiharmonic Analysis of the Energy Landscapes of Dihydrofolate Reductase from Piezophiles and Mesophiles.

Authors:  Qi Huang; Jocelyn M Rodgers; Russell J Hemley; Toshiko Ichiye
Journal:  J Phys Chem B       Date:  2018-02-08       Impact factor: 2.991

Review 5.  Enzymes from piezophiles.

Authors:  Toshiko Ichiye
Journal:  Semin Cell Dev Biol       Date:  2018-02-01       Impact factor: 7.727

6.  Quasiharmonic analysis of protein energy landscapes from pressure-temperature molecular dynamics simulations.

Authors:  Jocelyn M Rodgers; Russell J Hemley; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2017-09-28       Impact factor: 3.488

7.  How adding a single methylene to dihydrofolate reductase can change its conformational dynamics.

Authors:  Ryan W Penhallurick; Alliyah Harold; Maya D Durnal; Toshiko Ichiye
Journal:  J Chem Phys       Date:  2021-04-28       Impact factor: 3.488

8.  Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation.

Authors:  Ole Christian Hagestad; Lingwei Hou; Jeanette H Andersen; Espen H Hansen; Bjørn Altermark; Chun Li; Eric Kuhnert; Russell J Cox; Pedro W Crous; Joseph W Spatafora; Kathleen Lail; Mojgan Amirebrahimi; Anna Lipzen; Jasmyn Pangilinan; William Andreopoulos; Richard D Hayes; Vivian Ng; Igor V Grigoriev; Stephen A Jackson; Thomas D S Sutton; Alan D W Dobson; Teppo Rämä
Journal:  IMA Fungus       Date:  2021-08-09       Impact factor: 3.515

9.  High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP.

Authors:  Takayuki Nagae; Hiroyuki Yamada; Nobuhisa Watanabe
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-09-03       Impact factor: 7.652

10.  Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile.

Authors:  Qi Huang; Jocelyn M Rodgers; Russell J Hemley; Toshiko Ichiye
Journal:  Int J Mol Sci       Date:  2019-03-22       Impact factor: 5.923

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