Literature DB >> 18310248

Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering.

Lars Meinhold1, David Clement, Moeava Tehei, Roy Daniel, John L Finney, Jeremy C Smith.   

Abstract

The temperature dependence of the dynamics of mesophilic and thermophilic dihydrofolate reductase is examined using elastic incoherent neutron scattering. It is demonstrated that the distribution of atomic displacement amplitudes can be derived from the elastic scattering data by assuming a (Weibull) functional form that resembles distributions seen in molecular dynamics simulations. The thermophilic enzyme has a significantly broader distribution than its mesophilic counterpart. Furthermore, although the rate of increase with temperature of the atomic mean-square displacements extracted from the dynamic structure factor is found to be comparable for both enzymes, the amplitudes are found to be slightly larger for the thermophilic enzyme. Therefore, these results imply that the thermophilic enzyme is the more flexible of the two.

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Year:  2008        PMID: 18310248      PMCID: PMC2397366          DOI: 10.1529/biophysj.107.121418

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  36 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Review: Protein function at thermal extremes: balancing stability and flexibility.

Authors:  P A Fields
Journal:  Comp Biochem Physiol A Mol Integr Physiol       Date:  2001-06       Impact factor: 2.320

3.  Structural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.

Authors:  J Fitter; J Heberle
Journal:  Biophys J       Date:  2000-09       Impact factor: 4.033

4.  Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution.

Authors:  Jennifer A Hayward; John L Finney; Roy M Daniel; Jeremy C Smith
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

5.  Protein dynamics in solution and powder measured by incoherent elastic neutron scattering: the influence of Q-range and energy resolution.

Authors:  Frank Gabel
Journal:  Eur Biophys J       Date:  2004-09-16       Impact factor: 1.733

Review 6.  How enzymes adapt: lessons from directed evolution.

Authors:  F H Arnold; P L Wintrode; K Miyazaki; A Gershenson
Journal:  Trends Biochem Sci       Date:  2001-02       Impact factor: 13.807

7.  Relation between stability, dynamics and enzyme activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus.

Authors:  P G Varley; R H Pain
Journal:  J Mol Biol       Date:  1991-07-20       Impact factor: 5.469

8.  Thermal motions in bacteriorhodopsin at different hydration levels studied by neutron scattering: correlation with kinetics and light-induced conformational changes.

Authors:  U Lehnert; V Réat; M Weik; G Zaccaï; C Pfister
Journal:  Biophys J       Date:  1998-10       Impact factor: 4.033

9.  Activity and stability of a thermostable alpha-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation.

Authors:  J Fitter; R Herrmann; N A Dencher; A Blume; T Hauss
Journal:  Biochemistry       Date:  2001-09-04       Impact factor: 3.162

10.  Escherichia coli dihydrofolate reductase: isolation and characterization of two isozymes.

Authors:  D P Baccanari; D Averett; C Briggs; J Burchall
Journal:  Biochemistry       Date:  1977-08-09       Impact factor: 3.162

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  21 in total

1.  Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.

Authors:  Enrique Marcos; Pau Mestres; Ramon Crehuet
Journal:  Biophys J       Date:  2011-12-07       Impact factor: 4.033

2.  Dynamics of thermodynamically stable, kinetically trapped, and inhibitor-bound states of pepsin.

Authors:  Derek R Dee; Brenna Myers; Rickey Y Yada
Journal:  Biophys J       Date:  2011-10-05       Impact factor: 4.033

3.  Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.

Authors:  Eric D Merkley; William W Parson; Valerie Daggett
Journal:  Protein Eng Des Sel       Date:  2010-01-18       Impact factor: 1.650

4.  Using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes P450.

Authors:  Yergalem T Meharenna; Thomas L Poulos
Journal:  Biochemistry       Date:  2010-08-10       Impact factor: 3.162

5.  Bio-protective effects of homologous disaccharides on biological macromolecules.

Authors:  S Magazù; F Migliardo; A Benedetto; R La Torre; L Hennet
Journal:  Eur Biophys J       Date:  2011-10-30       Impact factor: 1.733

6.  Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins.

Authors:  Derya Vural; Jeremy C Smith; Henry R Glyde
Journal:  Biophys J       Date:  2018-03-24       Impact factor: 4.033

7.  Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study.

Authors:  Rupesh Agarwal; Utsab R Shrestha; Xiang-Qiang Chu; Loukas Petridis; Jeremy C Smith
Journal:  Biophys J       Date:  2020-05-29       Impact factor: 4.033

8.  A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8.

Authors:  Eric D Merkley; Valerie Daggett; William W Parson
Journal:  Proteins       Date:  2011-11-12

9.  Conformational preferences underlying reduced activity of a thermophilic ribonuclease H.

Authors:  Kate A Stafford; Nikola Trbovic; Joel A Butterwick; Robert Abel; Richard A Friesner; Arthur G Palmer
Journal:  J Mol Biol       Date:  2014-12-27       Impact factor: 5.469

Review 10.  Thermophilic proteins: insight and perspective from in silico experiments.

Authors:  Fabio Sterpone; Simone Melchionna
Journal:  Chem Soc Rev       Date:  2011-10-05       Impact factor: 54.564

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