Literature DB >> 31157122

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

Manuel Delgado1, Stefan Görlich2, James E Longbotham2, Nigel S Scrutton2, Sam Hay2, Vicent Moliner1,3, Iñaki Tuñón4.   

Abstract

Hydride transfer is one of the most common reactions catalyzed by enzymatic systems and it has become an object of study due to possible significant quantum tunneling effects. In the present work, we provide a combination of theoretical QM/MM simulations and experimental measurements of the rate constants and kinetic isotopic effects (KIEs) for the hydride transfer reaction catalyzed by morphinone reductase, MR. Quantum mechanical tunneling coefficients, computed in the framework of variational transition-state theory, play a significant role in this reaction, reaching values of 23.8 ± 5.5 for the lightest isotopologue; one of the largest values reported for enzymatic systems. This prediction is supported by the agreement between the theoretically predicted rate constants and the corresponding experimental values. Simulations indicate that the role of protein motions can be satisfactorily described as equilibrium fluctuations along the reaction coordinate, in line with a high degree of preorganization displayed by this enzyme.

Entities:  

Keywords:  Hydride transfer; Kinetic Isotope Effects; Morphinone Reductase; QM/MM; molecular dynamics

Year:  2017        PMID: 31157122      PMCID: PMC6542656          DOI: 10.1021/acscatal.7b00201

Source DB:  PubMed          Journal:  ACS Catal            Impact factor:   13.084


  44 in total

1.  QM/MM studies show substantial tunneling for the hydrogen-transfer reaction in methylamine dehydrogenase.

Authors:  P F Faulder; G Tresadern; K K Chohan; N S Scrutton; M J Sutcliffe; I H Hillier; N A Burton
Journal:  J Am Chem Soc       Date:  2001-09-05       Impact factor: 15.419

2.  Crystal structure of bacterial morphinone reductase and properties of the C191A mutant enzyme.

Authors:  Terez Barna; Hanan Latif Messiha; Carlo Petosa; Neil C Bruce; Nigel S Scrutton; Peter C E Moody
Journal:  J Biol Chem       Date:  2002-06-04       Impact factor: 5.157

Review 3.  The incorporation of quantum effects in enzyme kinetics modeling.

Authors:  Donald G Truhlar; Jiali Gao; Cristobal Alhambra; Mireia Garcia-Viloca; José Corchado; Maria Luz Sánchez; Jordi Villà
Journal:  Acc Chem Res       Date:  2002-06       Impact factor: 22.384

Review 4.  How enzymes work: analysis by modern rate theory and computer simulations.

Authors:  Mireia Garcia-Viloca; Jiali Gao; Martin Karplus; Donald G Truhlar
Journal:  Science       Date:  2004-01-09       Impact factor: 47.728

5.  Hydride transfer reaction catalyzed by hyperthermophilic dihydrofolate reductase is dominated by quantum mechanical tunneling and is promoted by both inter- and intramonomeric correlated motions.

Authors:  Jiayun Pang; Jingzhi Pu; Jiali Gao; Donald G Truhlar; Rudolf K Allemann
Journal:  J Am Chem Soc       Date:  2006-06-21       Impact factor: 15.419

6.  Atomic description of an enzyme reaction dominated by proton tunneling.

Authors:  Laura Masgrau; Anna Roujeinikova; Linus O Johannissen; Parvinder Hothi; Jaswir Basran; Kara E Ranaghan; Adrian J Mulholland; Michael J Sutcliffe; Nigel S Scrutton; David Leys
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

7.  Very fast empirical prediction and rationalization of protein pKa values.

Authors:  Hui Li; Andrew D Robertson; Jan H Jensen
Journal:  Proteins       Date:  2005-12-01

8.  Coupling between protein and reaction dynamics in enzymatic processes: application of Grote-Hynes Theory to catechol O-methyltransferase.

Authors:  Maite Roca; Vicente Moliner; Iñaki Tuñón; James T Hynes
Journal:  J Am Chem Soc       Date:  2006-05-10       Impact factor: 15.419

9.  RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I.

Authors:  Gerd B Rocha; Ricardo O Freire; Alfredo M Simas; James J P Stewart
Journal:  J Comput Chem       Date:  2006-07-30       Impact factor: 3.376

10.  H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase.

Authors:  Jaswir Basran; Richard J Harris; Michael J Sutcliffe; Nigel S Scrutton
Journal:  J Biol Chem       Date:  2003-08-26       Impact factor: 5.157

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  5 in total

Review 1.  Moving beyond static snapshots: Protein dynamics and the Protein Data Bank.

Authors:  Mitchell D Miller; George N Phillips
Journal:  J Biol Chem       Date:  2021-05-04       Impact factor: 5.157

2.  Linking inhibitor motions to proteolytic stability of sunflower trypsin inhibitor-1.

Authors:  Wanqing Wei; Jing Ma; Daiqian Xie; Yanzi Zhou
Journal:  RSC Adv       Date:  2019-05-03       Impact factor: 4.036

3.  Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase.

Authors:  Archie C Reyes; Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2018-07-10       Impact factor: 3.162

4.  Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes.

Authors:  Andreea I Iorgu; Nicola J Baxter; Matthew J Cliff; Colin Levy; Jonathan P Waltho; Sam Hay; Nigel S Scrutton
Journal:  ACS Catal       Date:  2018-10-26       Impact factor: 13.084

5.  Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases.

Authors:  Andreea I Iorgu; Tobias M Hedison; Sam Hay; Nigel S Scrutton
Journal:  FEBS J       Date:  2019-05-13       Impact factor: 5.542

  5 in total

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