Literature DB >> 23246280

The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation.

A Joshua Wand1.   

Abstract

Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational entropy in molecular recognition by proteins. The method rests on using fast internal protein dynamics as a proxy. Initial results reveal a large and variable role for conformational entropy in the binding of ligands by proteins. Such a role for conformational entropy in molecular recognition has significant implications for enzymology, signal transduction, allosteric regulation and the development of protein-directed pharmaceuticals.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 23246280      PMCID: PMC3572299          DOI: 10.1016/j.sbi.2012.11.005

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  52 in total

1.  Microscopic origins of entropy, heat capacity and the glass transition in proteins.

Authors:  A L Lee; A J Wand
Journal:  Nature       Date:  2001-05-24       Impact factor: 49.962

2.  Temperature dependence of the internal dynamics of a calmodulin-peptide complex.

Authors:  Andrew L Lee; Kim A Sharp; James K Kranz; Xiang-Jin Song; A Joshua Wand
Journal:  Biochemistry       Date:  2002-11-19       Impact factor: 3.162

3.  Thermodynamic fluctuations in protein molecules.

Authors:  A Cooper
Journal:  Proc Natl Acad Sci U S A       Date:  1976-08       Impact factor: 11.205

4.  Insights into the local residual entropy of proteins provided by NMR relaxation.

Authors:  Z Li; S Raychaudhuri; A J Wand
Journal:  Protein Sci       Date:  1996-12       Impact factor: 6.725

5.  Evaluation of energetic and dynamic coupling networks in a PDZ domain protein.

Authors:  Ernesto J Fuentes; Steven A Gilmore; Randall V Mauldin; Andrew L Lee
Journal:  J Mol Biol       Date:  2006-09-01       Impact factor: 5.469

6.  Hot spots for allosteric regulation on protein surfaces.

Authors:  Kimberly A Reynolds; Richard N McLaughlin; Rama Ranganathan
Journal:  Cell       Date:  2011-12-23       Impact factor: 41.582

7.  Exposing the Moving Parts of Proteins with NMR Spectroscopy.

Authors:  J W Peng
Journal:  J Phys Chem Lett       Date:  2012-04-02       Impact factor: 6.475

8.  Hidden dynamic allostery in a PDZ domain.

Authors:  Chad M Petit; Jun Zhang; Paul J Sapienza; Ernesto J Fuentes; Andrew L Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2009-10-14       Impact factor: 11.205

9.  Nuclear magnetic resonance study of the role of M42 in the solution dynamics of Escherichia coli dihydrofolate reductase.

Authors:  Randall V Mauldin; Andrew L Lee
Journal:  Biochemistry       Date:  2010-03-02       Impact factor: 3.162

Review 10.  Theory of free energy and entropy in noncovalent binding.

Authors:  Huan-Xiang Zhou; Michael K Gilson
Journal:  Chem Rev       Date:  2009-09       Impact factor: 60.622

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  68 in total

1.  The unusual internal motion of the villin headpiece subdomain.

Authors:  Kyle W Harpole; Evan S O'Brien; Matthew A Clark; C James McKnight; Liliya Vugmeyster; A Joshua Wand
Journal:  Protein Sci       Date:  2015-10-29       Impact factor: 6.725

Review 2.  Protein Allostery and Conformational Dynamics.

Authors:  Jingjing Guo; Huan-Xiang Zhou
Journal:  Chem Rev       Date:  2016-02-15       Impact factor: 60.622

3.  Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase.

Authors:  Miao Wang; Kurt Warncke
Journal:  J Am Chem Soc       Date:  2013-10-01       Impact factor: 15.419

4.  Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins.

Authors:  Mee-Kyung Chung; Peter S White; Stephen J Lee; Michel R Gagné; Marcey L Waters
Journal:  J Am Chem Soc       Date:  2016-09-29       Impact factor: 15.419

5.  SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy.

Authors:  Bradley J Harden; Dominique P Frueh
Journal:  J Biomol NMR       Date:  2014-01-10       Impact factor: 2.835

6.  Disordered allostery: lessons from glucocorticoid receptor.

Authors:  Hesam N Motlagh; Jeremy A Anderson; Jing Li; Vincent J Hilser
Journal:  Biophys Rev       Date:  2015-04-23

7.  (19)F NMR reveals multiple conformations at the dimer interface of the nonstructural protein 1 effector domain from influenza A virus.

Authors:  James M Aramini; Keith Hamilton; Li-Chung Ma; G V T Swapna; Paul G Leonard; John E Ladbury; Robert M Krug; Gaetano T Montelione
Journal:  Structure       Date:  2014-02-27       Impact factor: 5.006

8.  Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of Escherichia coli ribonuclease H.

Authors:  Kate A Stafford; Fabien Ferrage; Jae-Hyun Cho; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2013-11-20       Impact factor: 15.419

9.  Thermodynamic and structural basis for relaxation of specificity in protein-DNA recognition.

Authors:  Paul J Sapienza; Tianyi Niu; Michael R Kurpiewski; Arabela Grigorescu; Linda Jen-Jacobson
Journal:  J Mol Biol       Date:  2013-09-14       Impact factor: 5.469

10.  Dual allosteric activation mechanisms in monomeric human glucokinase.

Authors:  A Carl Whittington; Mioara Larion; Joseph M Bowler; Kristen M Ramsey; Rafael Brüschweiler; Brian G Miller
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-17       Impact factor: 11.205

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