Literature DB >> 18052079

On the relationship between thermal stability and catalytic power of enzymes.

Maite Roca1, Hanbin Liu, Benjamin Messer, Arieh Warshel.   

Abstract

The possible relationship between the thermal stability and the catalytic power of enzymes is of great current interest. In particular, it has been suggested that thermophilic or hyperthermophilic (Tm) enzymes have lower catalytic power at a given temperature than the corresponding mesophilic (Ms) enzymes, because the thermophilic enzymes are less flexible (assuming that flexibility and catalysis are directly correlated). These suggestions presume that the reduced dynamics of the thermophilic enzymes is the reason for their reduced catalytic power. The present paper takes the specific case of dihydrofolate reductase (DHFR) and explores the validity of the above argument by simulation approaches. It is found that the Tm enzymes have restricted motions in the direction of the folding coordinate, but this is not relevant to the chemical process, since the motions along the reaction coordinate are perpendicular to the folding motions. Moreover, it is shown that the rate of the chemical reaction is determined by the activation barrier and the corresponding reorganization energy, rather than by dynamics or flexibility in the ground state. In fact, as far as flexibility is concerned, we conclude that the displacement along the reaction coordinate is larger in the Tm enzyme than in the Ms enzyme and that the general trend in enzyme catalysis is that the best catalyst involves less motion during the reaction than the less optimal catalyst. The relationship between thermal stability and catalysis appears to reflect the fact that to obtain small electrostatic reorganization energy it is necessary to invest some folding energy in the overall preorganization process. Thus, the optimized catalysts are less stable. This trend is clearly observed in the DHFR case.

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Year:  2007        PMID: 18052079      PMCID: PMC3174049          DOI: 10.1021/bi701732a

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  42 in total

1.  Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism.

Authors:  A R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-15       Impact factor: 11.205

2.  How important are entropic contributions to enzyme catalysis?

Authors:  J Villa; M Strajbl; T M Glennon; Y Y Sham; Z T Chu; A Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-24       Impact factor: 11.205

3.  Multistate equilibrium unfolding of Escherichia coli dihydrofolate reductase: thermodynamic and spectroscopic description of the native, intermediate, and unfolded ensembles.

Authors:  R M Ionescu; V F Smith; J C O'Neill; C R Matthews
Journal:  Biochemistry       Date:  2000-08-08       Impact factor: 3.162

Review 4.  Dynamics of biochemical and biophysical reactions: insight from computer simulations.

Authors:  A Warshel; W W Parson
Journal:  Q Rev Biophys       Date:  2001-11       Impact factor: 5.318

5.  Probing the folding free energy landscape of the Src-SH3 protein domain.

Authors:  Joan-Emma Shea; Jose N Onuchic; Charles L Brooks
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-22       Impact factor: 11.205

Review 6.  Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis.

Authors:  Mats H M Olsson; William W Parson; Arieh Warshel
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

7.  The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability.

Authors:  T Dams; G Auerbach; G Bader; U Jacob; T Ploom; R Huber; R Jaenicke
Journal:  J Mol Biol       Date:  2000-03-31       Impact factor: 5.469

8.  Hydride transfer during catalysis by dihydrofolate reductase from Thermotoga maritima.

Authors:  Giovanni Maglia; Masood H Javed; Rudolf K Allemann
Journal:  Biochem J       Date:  2003-09-01       Impact factor: 3.857

9.  The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies.

Authors:  Hanbin Liu; Arieh Warshel
Journal:  Biochemistry       Date:  2007-05-01       Impact factor: 3.162

10.  Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase.

Authors:  Mireia Garcia-Viloca; Donald G Truhlar; Jiali Gao
Journal:  Biochemistry       Date:  2003-11-25       Impact factor: 3.162

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  27 in total

1.  Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution.

Authors:  Olga Khersonsky; Daniela Röthlisberger; Andrew M Wollacott; Paul Murphy; Orly Dym; Shira Albeck; Gert Kiss; K N Houk; David Baker; Dan S Tawfik
Journal:  J Mol Biol       Date:  2011-01-28       Impact factor: 5.469

2.  Rational stabilization of enzymes by computational redesign of surface charge-charge interactions.

Authors:  Alexey V Gribenko; Mayank M Patel; Jiajing Liu; Scott A McCallum; Chunyu Wang; George I Makhatadze
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-05       Impact factor: 11.205

3.  On the relationship between folding and chemical landscapes in enzyme catalysis.

Authors:  Maite Roca; Benjamin Messer; Donald Hilvert; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-08       Impact factor: 11.205

4.  Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions.

Authors:  Andrew J Adamczyk; Jie Cao; Shina C L Kamerlin; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-10       Impact factor: 11.205

5.  Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Authors:  Nikolay V Plotnikov; Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

Review 6.  Perspective: Defining and quantifying the role of dynamics in enzyme catalysis.

Authors:  Arieh Warshel; Ram Prasad Bora
Journal:  J Chem Phys       Date:  2016-05-14       Impact factor: 3.488

7.  Protein folding, protein collapse, and tanford's transfer model: lessons from single-molecule FRET.

Authors:  Guy Ziv; Gilad Haran
Journal:  J Am Chem Soc       Date:  2009-03-04       Impact factor: 15.419

8.  Interactions of oximino-substituted boronic acids and β-lactams with the CMY-2-derived extended-spectrum cephalosporinases CMY-30 and CMY-42.

Authors:  Stathis D Kotsakis; Emilia Caselli; Leonidas S Tzouvelekis; Efi Petinaki; Fabio Prati; Vivi Miriagou
Journal:  Antimicrob Agents Chemother       Date:  2012-12-10       Impact factor: 5.191

9.  On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.

Authors:  Enrique Marcos; Ramon Crehuet; Ivet Bahar
Journal:  PLoS Comput Biol       Date:  2010-04-08       Impact factor: 4.475

Review 10.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01
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