Literature DB >> 26952190

Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function.

George P Lisi1, J Patrick Loria2.   

Abstract

Conformational motions play an essential role in enzyme function, often facilitating the formation of enzyme-substrate complexes and/or product release. Although considerable debate remains regarding the role of molecular motions in the conversion of enzymatic substrates to products, numerous examples have found motions to be crucial for optimization of enzyme scaffolds, effective substrate binding, and product dissociation. Conformational fluctuations are often rate-limiting to enzyme catalysis, primarily through product release, with the chemical reaction occurring much more quickly. As a result, the direct involvement of motions at various stages along the enzyme reaction coordinate remains largely unknown and untested. In the following review, we describe the use of solution NMR techniques designed to probe various timescales of molecular motions and detail examples in which motions play a role in propagating catalytic effects from the active site and directly participate in essential aspects of enzyme function.
Copyright © 2015 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  CPMG; Enzymes; NMR; R1rho; Relaxation dispersion

Mesh:

Substances:

Year:  2015        PMID: 26952190      PMCID: PMC4785347          DOI: 10.1016/j.pnmrs.2015.11.001

Source DB:  PubMed          Journal:  Prog Nucl Magn Reson Spectrosc        ISSN: 0079-6565            Impact factor:   9.795


  112 in total

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2.  Ribonuclease A.

Authors:  Ronald T. Raines
Journal:  Chem Rev       Date:  1998-05-07       Impact factor: 60.622

3.  Probing the kinetic landscape of transient peptide-protein interactions by use of peptide (15)n NMR relaxation dispersion spectroscopy: binding of an antithrombin peptide to human prothrombin.

Authors:  Dmitri Tolkatchev; Ping Xu; Feng Ni
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4.  Direct observation of protein-ligand interaction kinetics.

Authors:  Tanja Mittag; Brian Schaffhausen; Ulrich L Günther
Journal:  Biochemistry       Date:  2003-09-30       Impact factor: 3.162

5.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

6.  Insights into the reaction of protein-tyrosine phosphatase 1B: crystal structures for transition state analogs of both catalytic steps.

Authors:  Tiago A S Brandão; Alvan C Hengge; Sean J Johnson
Journal:  J Biol Chem       Date:  2010-03-16       Impact factor: 5.157

7.  Ligand binding reduces conformational flexibility in the active site of tyrosine phosphatase related to biofilm formation A (TpbA) from Pseudomonasaeruginosa.

Authors:  Dorothy Koveal; Michael W Clarkson; Thomas K Wood; Rebecca Page; Wolfgang Peti
Journal:  J Mol Biol       Date:  2013-03-21       Impact factor: 5.469

8.  Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?

Authors:  D Flemming Hansen; Pramodh Vallurupalli; Patrik Lundström; Philipp Neudecker; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2008-02-01       Impact factor: 15.419

9.  Spectral density function mapping using 15N relaxation data exclusively.

Authors:  N A Farrow; O Zhang; A Szabo; D A Torchia; L E Kay
Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

10.  The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.

Authors:  Nicolas Doucet; Eric D Watt; J Patrick Loria
Journal:  Biochemistry       Date:  2009-08-04       Impact factor: 3.162

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  21 in total

1.  Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

Authors:  Meng S Choy; Yang Li; Luciana E S F Machado; Micha B A Kunze; Christopher R Connors; Xingyu Wei; Kresten Lindorff-Larsen; Rebecca Page; Wolfgang Peti
Journal:  Mol Cell       Date:  2017-02-16       Impact factor: 17.970

2.  Probing the excited-state chemical shifts and exchange parameters by nitrogen-decoupled amide proton chemical exchange saturation transfer (HNdec-CEST).

Authors:  Qinglin Wu; Benjamin A Fenton; Jessica L Wojtaszek; Pei Zhou
Journal:  Chem Commun (Camb)       Date:  2017-07-27       Impact factor: 6.222

3.  Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies.

Authors:  Rupal Gupta; Huilan Zhang; Manman Lu; Guangjin Hou; Marc Caporini; Melanie Rosay; Werner Maas; Jochem Struppe; Jinwoo Ahn; In-Ja L Byeon; Hartmut Oschkinat; Kristaps Jaudzems; Emeline Barbet-Massin; Lyndon Emsley; Guido Pintacuda; Anne Lesage; Angela M Gronenborn; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2019-06-11       Impact factor: 2.991

Review 4.  NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes.

Authors:  Kyle W East; Erin Skeens; Jennifer Y Cui; Helen B Belato; Brandon Mitchell; Rohaine Hsu; Victor S Batista; Giulia Palermo; George P Lisi
Journal:  Biophys Rev       Date:  2019-12-14

5.  Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.

Authors:  Zachary R Churcher; Devid Garaev; Howard N Hunter; Philip E Johnson
Journal:  Biophys J       Date:  2020-08-15       Impact factor: 4.033

6.  The Michaelis Complex of Arginine Kinase Samples the Transition State at a Frequency That Matches the Catalytic Rate.

Authors:  Yu Peng; Alexandar L Hansen; Lei Bruschweiler-Li; Omar Davulcu; Jack J Skalicky; Michael S Chapman; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2017-03-27       Impact factor: 15.419

7.  Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.

Authors:  Xu Liu; David C Speckhard; Tyson R Shepherd; Young Joo Sun; Sarah R Hengel; Liping Yu; C Andrew Fowler; Lokesh Gakhar; Ernesto J Fuentes
Journal:  Structure       Date:  2016-10-27       Impact factor: 5.006

8.  Cooperative dynamics across distinct structural elements regulate PTP1B activity.

Authors:  Kristiane R Torgeson; Michael W Clarkson; Ganesan Senthil Kumar; Rebecca Page; Wolfgang Peti
Journal:  J Biol Chem       Date:  2020-07-31       Impact factor: 5.157

9.  1H, 13C, 15N backbone and side chain resonance assignment of the HNH nuclease from Streptococcus pyogenes CRISPR-Cas9.

Authors:  Helen B Belato; Kyle W East; George P Lisi
Journal:  Biomol NMR Assign       Date:  2019-08-03       Impact factor: 0.746

10.  Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding.

Authors:  Chitra Narayanan; David N Bernard; Myriam Létourneau; Jacinthe Gagnon; Donald Gagné; Khushboo Bafna; Charles Calmettes; Jean-François Couture; Pratul K Agarwal; Nicolas Doucet
Journal:  Biochemistry       Date:  2020-01-24       Impact factor: 3.162

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