Literature DB >> 17914231

Protein mechanics: a route from structure to function.

Richard Lavery1, Sophie Sacquin-Mora.   

Abstract

In order to better understand the mechanical properties of proteins, we have developed simulation tools which enable these properties to be analysed on a residue-by-residue basis. Although these calculations are relatively expensive with all-atom protein models, good results can be obtained much faster using coarse-grained approaches. The results show that proteins are surprisingly heterogeneous from a mechanical point of view and that functionally important residues often exhibit unusual mechanical behaviour. This finding offers a novel means for detecting functional sites and also potentially provides a route for understanding the links between structure and function in more general terms.

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Year:  2007        PMID: 17914231     DOI: 10.1007/s12038-007-0089-x

Source DB:  PubMed          Journal:  J Biosci        ISSN: 0250-5991            Impact factor:   1.826


  32 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Detoxification of environmental mutagens and carcinogens: structure, mechanism, and evolution of liver epoxide hydrolase.

Authors:  M A Argiriadi; C Morisseau; B D Hammock; D W Christianson
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-14       Impact factor: 11.205

3.  Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-08-26       Impact factor: 9.161

4.  Analysis of catalytic residues in enzyme active sites.

Authors:  Gail J Bartlett; Craig T Porter; Neera Borkakoti; Janet M Thornton
Journal:  J Mol Biol       Date:  2002-11-15       Impact factor: 5.469

5.  Structure of hemoglobin.

Authors:  M F PERUTZ
Journal:  Brookhaven Symp Biol       Date:  1960-11

6.  Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.

Authors:  Chakra Chennubhotla; A J Rader; Lee-Wei Yang; Ivet Bahar
Journal:  Phys Biol       Date:  2005-11-09       Impact factor: 2.583

7.  Investigating the local flexibility of functional residues in hemoproteins.

Authors:  Sophie Sacquin-Mora; Richard Lavery
Journal:  Biophys J       Date:  2006-01-20       Impact factor: 4.033

8.  A consensus view of protein dynamics.

Authors:  Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-10       Impact factor: 11.205

9.  Locating the active sites of enzymes using mechanical properties.

Authors:  Sophie Sacquin-Mora; Emilie Laforet; Richard Lavery
Journal:  Proteins       Date:  2007-05-01

10.  Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?

Authors:  O B Ptitsyn
Journal:  J Mol Biol       Date:  1998-05-08       Impact factor: 5.469

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  10 in total

1.  Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

Authors:  Sophie Sacquin-Mora
Journal:  J R Soc Interface       Date:  2015-11-06       Impact factor: 4.118

2.  Enzyme closure and nucleotide binding structurally lock guanylate kinase.

Authors:  Olivier Delalande; Sophie Sacquin-Mora; Marc Baaden
Journal:  Biophys J       Date:  2011-09-20       Impact factor: 4.033

3.  Probing the toxic mechanism of bisphenol A with acid phosphatase at the molecular level.

Authors:  Mengchen Xu; Rui Zhang; Wei Song; Wansong Zong; Rutao Liu
Journal:  Environ Sci Pollut Res Int       Date:  2018-02-08       Impact factor: 4.223

4.  Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics.

Authors:  A M Stadler; C J Garvey; A Bocahut; S Sacquin-Mora; I Digel; G J Schneider; F Natali; G M Artmann; G Zaccai
Journal:  J R Soc Interface       Date:  2012-06-13       Impact factor: 4.118

5.  Accounting for large amplitude protein deformation during in silico macromolecular docking.

Authors:  Karine Bastard; Adrien Saladin; Chantal Prévost
Journal:  Int J Mol Sci       Date:  2011-02-22       Impact factor: 5.923

6.  Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

Authors:  Kevin A James; Gennady M Verkhivker
Journal:  PLoS One       Date:  2014-11-26       Impact factor: 3.240

7.  Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.

Authors:  Nathalie Colloc'h; Sophie Sacquin-Mora; Giovanna Avella; Anne-Claire Dhaussy; Thierry Prangé; Beatrice Vallone; Eric Girard
Journal:  Sci Rep       Date:  2017-05-12       Impact factor: 4.379

Review 8.  Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops.

Authors:  Nadia Raboanatahiry; Baoshan Wang; Longjiang Yu; Maoteng Li
Journal:  Front Genet       Date:  2018-05-22       Impact factor: 4.599

9.  Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release.

Authors:  Angelo Felline; Francesco Raimondi; Sara Gentile; Francesca Fanelli
Journal:  Comput Struct Biotechnol J       Date:  2022-09-13       Impact factor: 6.155

10.  Great interactions: How binding incorrect partners can teach us about protein recognition and function.

Authors:  Lydie Vamparys; Benoist Laurent; Alessandra Carbone; Sophie Sacquin-Mora
Journal:  Proteins       Date:  2016-06-24
  10 in total

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