Literature DB >> 20150513

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization.

Shina C L Kamerlin1, Pankaz K Sharma, Zhen T Chu, Arieh Warshel.   

Abstract

One of the best systems for exploring the origin of enzyme catalysis has been the reaction of ketosteroid isomerase (KSI). Studies of the binding of phenolates to KSI have been taken as proof that the electrostatic preorganization effect only makes a minor contribution to the binding of the real, multiring, transition state (TS). However, our simulation study has determined that the difference between the phenolates and the TS arises from the fact that the nonpolar state of the phenolate can rotate freely relative to the oxyanion hole and thus loses the preorganization contribution. A recent study explored the reactivity of both small and multiring systems and concluded that their similar reactivity contradicts our preorganization idea. Herein, we establish that the available experiments in fact provide what is perhaps the best proof and clarification of the preorganization idea and its crucial role in enzyme catalysis. First, we analyze the binding energy and the pK(a) of equilenin and identify direct experimental evidence for our prediction about the differential electrostatic stabilization of the large TS and the small phenolates. Subsequently, we show that the similar reactivity of the small and large systems is also due to an electrostatic preorganization effect but that this effect only appears in the intermediate state because the TS is not free to rotate. This establishes the electrostatic origin of enzyme catalysis. We also clarify the crucial importance of having a well-defined physical concept when examining catalytic effects and the need for quantitative tools for analyzing such effects.

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Year:  2010        PMID: 20150513      PMCID: PMC2840163          DOI: 10.1073/pnas.0914579107

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  15 in total

1.  Nature of the intermediate in the 3-oxo-delta 5-steroid isomerase reaction.

Authors:  B F Zeng; P L Bounds; R F Steiner; R M Pollack
Journal:  Biochemistry       Date:  1992-02-11       Impact factor: 3.162

Review 2.  Electrostatic basis for enzyme catalysis.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; Yun Xiang; Hanbin Liu; Mats H M Olsson
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

Review 3.  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

4.  Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?

Authors:  Paul A Sigala; Aaron T Fafarman; Patrick E Bogard; Steven G Boxer; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2007-09-14       Impact factor: 15.419

5.  Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase.

Authors:  Arieh Warshel; Pankaz K Sharma; Zhen T Chu; Johan Aqvist
Journal:  Biochemistry       Date:  2007-02-13       Impact factor: 3.162

6.  Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase.

Authors:  Jason P Schwans; Daniel A Kraut; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-12       Impact factor: 11.205

7.  Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.

Authors:  Paul A Sigala; Daniel A Kraut; Jose M M Caaveiro; Brandon Pybus; Eliza A Ruben; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2008-09-23       Impact factor: 15.419

8.  Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.

Authors:  Daniel A Kraut; Paul A Sigala; Timothy D Fenn; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-11       Impact factor: 11.205

Review 9.  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

10.  Evaluation of the internal equilibrium constant for 3-oxo-delta 5-steroid isomerase using the D38E and D38N mutants: the energetic basis for catalysis.

Authors:  D C Hawkinson; R M Pollack; N P Ambulos
Journal:  Biochemistry       Date:  1994-10-11       Impact factor: 3.162

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  36 in total

1.  Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

Authors:  Dhruva K Chakravorty; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2010-06-02       Impact factor: 15.419

2.  Frustration in protein-DNA binding influences conformational switching and target search kinetics.

Authors:  Amir Marcovitz; Yaakov Levy
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-14       Impact factor: 11.205

3.  Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles.

Authors:  Stephen D Fried; Steven G Boxer
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-09       Impact factor: 11.205

4.  Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases.

Authors:  Garima Jindal; Balajee Ramachandran; Ram Prasad Bora; Arieh Warshel
Journal:  ACS Catal       Date:  2017-03-30       Impact factor: 13.084

5.  Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling.

Authors:  Philip Hanoian; Paul A Sigala; Daniel Herschlag; Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2010-11-12       Impact factor: 3.162

6.  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

Review 7.  Specificity in transition state binding: the Pauling model revisited.

Authors:  Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2013-02-04       Impact factor: 3.162

Review 8.  Computer aided enzyme design and catalytic concepts.

Authors:  Maria P Frushicheva; Matthew J L Mills; Patrick Schopf; Manoj K Singh; Ram B Prasad; Arieh Warshel
Journal:  Curr Opin Chem Biol       Date:  2014-05-08       Impact factor: 8.822

Review 9.  Catalytic efficiency of enzymes: a theoretical analysis.

Authors:  Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2012-12-20       Impact factor: 3.162

Review 10.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

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