Literature DB >> 16798805

Coupling of global and local vibrational modes in dynamic allostery of proteins.

Rhoda J Hawkins1, Tom C B McLeish.   

Abstract

It is now recognized that internal global protein dynamics play an important role in the allosteric function of many proteins. Alterations of protein flexibility on effector binding affect the entropic cost of binding at a distant site. We present a coarse-grained model for a potential amplification of such entropic allostery due to coupling of fast, localized modes to the slow, global modes. We show how such coupling can give rise to large compensating entropic and enthalpic terms. The model corresponds to the pattern of calorimetry and NMR data from experiments on the Met repressor.

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Year:  2006        PMID: 16798805      PMCID: PMC1557547          DOI: 10.1529/biophysj.106.082180

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  31 in total

1.  Site-site communication in the EF-hand Ca2+-binding protein calbindin D9k.

Authors:  L Mäler; J Blankenship; M Rance; W J Chazin
Journal:  Nat Struct Biol       Date:  2000-03

2.  ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.

Authors:  Karsten Suhre; Yves-Henri Sanejouand
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  Coarse-grained model of entropic allostery.

Authors:  Rhoda J Hawkins; Tom C B McLeish
Journal:  Phys Rev Lett       Date:  2004-08-25       Impact factor: 9.161

4.  Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy.

Authors:  Zimei Bu; Ralf Biehl; Michael Monkenbusch; Dieter Richter; David J E Callaway
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-23       Impact factor: 11.205

5.  Dynamic allostery of protein alpha helical coiled-coils.

Authors:  Rhoda J Hawkins; Tom C B McLeish
Journal:  J R Soc Interface       Date:  2006-02-22       Impact factor: 4.118

6.  Tryptophan fluorescence reveals the conformational state of a dynamic loop in recombinant porcine fructose-1,6-bisphosphatase.

Authors:  S W Nelson; C V Iancu; J Y Choe; R B Honzatko; H J Fromm
Journal:  Biochemistry       Date:  2000-09-12       Impact factor: 3.162

7.  Calorimetric studies of the energetics of protein-DNA interactions in the E. coli methionine repressor (MetJ) system.

Authors:  A Cooper; A McAlpine; P G Stockley
Journal:  FEBS Lett       Date:  1994-07-04       Impact factor: 4.124

8.  Allostery without conformational change. A plausible model.

Authors:  A Cooper; D T Dryden
Journal:  Eur Biophys J       Date:  1984       Impact factor: 1.733

9.  Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics.

Authors:  Sutjano Jusuf; Patrick J Loll; Paul H Axelsen
Journal:  J Am Chem Soc       Date:  2003-04-02       Impact factor: 15.419

Review 10.  Structure and function of Escherichia coli met repressor: similarities and contrasts with trp repressor.

Authors:  S E Phillips; P G Stockley
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  1996-04-29       Impact factor: 6.237

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  27 in total

1.  Substrate-modulated thermal fluctuations affect long-range allosteric signaling in protein homodimers: exemplified in CAP.

Authors:  Hedvika Toncrova; Tom C B McLeish
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

2.  Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?

Authors:  Tom C B McLeish; Martin J Cann; Thomas L Rodgers
Journal:  Biophys J       Date:  2015-08-31       Impact factor: 4.033

3.  A Biophysical Perspective on Enzyme Catalysis.

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

Review 4.  Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation.

Authors:  Ivet Bahar; Chakra Chennubhotla; Dror Tobi
Journal:  Curr Opin Struct Biol       Date:  2007-11-19       Impact factor: 6.809

Review 5.  Allostery: absence of a change in shape does not imply that allostery is not at play.

Authors:  Chung-Jung Tsai; Antonio del Sol; Ruth Nussinov
Journal:  J Mol Biol       Date:  2008-02-29       Impact factor: 5.469

Review 6.  Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.

Authors:  Ivet Bahar; Timothy R Lezon; Ahmet Bakan; Indira H Shrivastava
Journal:  Chem Rev       Date:  2010-03-10       Impact factor: 60.622

7.  Dynamically Driven Protein Allostery Exhibits Disparate Responses for Fast and Slow Motions.

Authors:  Jingjing Guo; Huan-Xiang Zhou
Journal:  Biophys J       Date:  2015-06-16       Impact factor: 4.033

8.  Evolutionary basis for the coupled-domain motions in Thermus thermophilus leucyl-tRNA synthetase.

Authors:  Kristina Mary Ellen Weimer; Brianne Leigh Shane; Michael Brunetto; Sudeep Bhattacharyya; Sanchita Hati
Journal:  J Biol Chem       Date:  2009-02-02       Impact factor: 5.157

9.  Dynamic allostery in the methionine repressor revealed by force distribution analysis.

Authors:  Wolfram Stacklies; Fei Xia; Frauke Gräter
Journal:  PLoS Comput Biol       Date:  2009-11-20       Impact factor: 4.475

10.  Circadian KaiC phosphorylation: a multi-layer network.

Authors:  Congxin Li; Xiaofang Chen; Pengye Wang; Weichi Wang
Journal:  PLoS Comput Biol       Date:  2009-11-20       Impact factor: 4.475

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