Literature DB >> 18067303

Fast enzyme dynamics at the active site of formate dehydrogenase.

Jigar N Bandaria1, Samrat Dutta, Sarah E Hill, Amnon Kohen, Christopher M Cheatum.   

Abstract

The role of femtosecond-picosecond structural dynamics of proteins in enzyme-catalyzed reactions is a hotly debated topic. We report infrared photon echo measurement of the formate dehydrogenase-NAD+-azide ternary complex. In contrast to earlier studies of protein dynamics, the data show complete spectral diffusion on the femtosecond-picosecond time scale with no static heterogeneity. This result indicates that this transition-state analogue complex completely samples the distribution of structures that determine the distribution of azide vibrational frequencies within a few picoseconds and that there are no slower motions that perturb the H-bond network at the active site.

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Year:  2007        PMID: 18067303      PMCID: PMC2533850          DOI: 10.1021/ja077599o

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  15 in total

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Journal:  J Am Chem Soc       Date:  2003-11-12       Impact factor: 15.419

2.  Approaches for the calculation of vibrational frequencies in liquids: comparison to benchmarks for azide/water clusters.

Authors:  Shuzhou Li; J R Schmidt; S A Corcelli; C P Lawrence; J L Skinner
Journal:  J Chem Phys       Date:  2006-05-28       Impact factor: 3.488

3.  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

Review 4.  Tunneling and dynamics in enzymatic hydride transfer.

Authors:  Zachary D Nagel; Judith P Klinman
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

5.  Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations.

Authors:  Ilya J Finkelstein; Anne Goj; Brian L McClain; Aaron M Massari; Kusai A Merchant; Roger F Loring; M D Fayer
Journal:  J Phys Chem B       Date:  2005-09-08       Impact factor: 2.991

6.  Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes.

Authors:  M Lim; P Hamm; R M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-22       Impact factor: 11.205

Review 7.  NAD(+)-dependent formate dehydrogenase.

Authors:  V O Popov; V S Lamzin
Journal:  Biochem J       Date:  1994-08-01       Impact factor: 3.857

8.  Kinetic and chemical mechanisms of yeast formate dehydrogenase.

Authors:  J S Blanchard; W W Cleland
Journal:  Biochemistry       Date:  1980-07-22       Impact factor: 3.162

Review 9.  Hydrogen tunneling and protein motion in enzyme reactions.

Authors:  Sharon Hammes-Schiffer
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

10.  Variation of transition-state structure as a function of the nucleotide in reactions catalyzed by dehydrogenases. 2. Formate dehydrogenase.

Authors:  J D Hermes; S W Morrical; M H O'Leary; W W Cleland
Journal:  Biochemistry       Date:  1984-11-06       Impact factor: 3.162

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  27 in total

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2.  A Biophysical Perspective on Enzyme Catalysis.

Authors:  Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

3.  Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase.

Authors:  Jigar N Bandaria; Samrat Dutta; Michael W Nydegger; William Rock; Amnon Kohen; Christopher M Cheatum
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

4.  Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

Authors:  Qi Guo; Lokesh Gakhar; Kyle Wickersham; Kevin Francis; Alexandra Vardi-Kilshtain; Dan T Major; Christopher M Cheatum; Amnon Kohen
Journal:  Biochemistry       Date:  2016-05-03       Impact factor: 3.162

5.  Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase.

Authors:  Santosh Kumar Jha; Minbiao Ji; Kelly J Gaffney; Steven G Boxer
Journal:  Proc Natl Acad Sci U S A       Date:  2011-09-26       Impact factor: 11.205

Review 6.  Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.

Authors:  Ayanjeet Ghosh; Joshua S Ostrander; Martin T Zanni
Journal:  Chem Rev       Date:  2017-01-06       Impact factor: 60.622

7.  Using empirical phase diagrams to understand the role of intramolecular dynamics in immunoglobulin G stability.

Authors:  Joshua D Ramsey; Michelle L Gill; Tim J Kamerzell; E Shane Price; Sangeeta B Joshi; Steven M Bishop; Cynthia N Oliver; C Russell Middaugh
Journal:  J Pharm Sci       Date:  2009-07       Impact factor: 3.534

Review 8.  Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer.

Authors:  Christopher M Cheatum; Amnon Kohen
Journal:  Top Curr Chem       Date:  2013

9.  Enzymatic transition states and dynamic motion in barrier crossing.

Authors:  Steven D Schwartz; Vern L Schramm
Journal:  Nat Chem Biol       Date:  2009-08       Impact factor: 15.040

10.  Examination of enzymatic H-tunneling through kinetics and dynamics.

Authors:  Jigar N Bandaria; Christopher M Cheatum; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2009-07-29       Impact factor: 15.419

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