Literature DB >> 19355980

Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks.

Wenjun Zheng1, Bernard R Brooks, D Thirumalai.   

Abstract

Allostery forms the basis of intra-molecular communications in various enzymes, however the underlying conformational changes are largely elusive. Recently, we have proposed to employ an elastic model based normal mode analysis to investigate the allosteric transitions in several molecular nanomachines (including myosin II, DNA polymerase and chaperonin GroEL). After combining with bioinformatics analysis of the evolutionary sequence variations, we have been able to identify the highly conserved and robust modes of collective motions that are capable of transmitting molecular signals over long distances.

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Year:  2009        PMID: 19355980      PMCID: PMC3610319          DOI: 10.2174/138920309787847608

Source DB:  PubMed          Journal:  Curr Protein Pept Sci        ISSN: 1389-2037            Impact factor:   3.272


  44 in total

1.  Evolutionarily conserved pathways of energetic connectivity in protein families.

Authors:  S W Lockless; R Ranganathan
Journal:  Science       Date:  1999-10-08       Impact factor: 47.728

2.  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

3.  Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.

Authors:  W G Krebs; Vadim Alexandrov; Cyrus A Wilson; Nathaniel Echols; Haiyuan Yu; Mark Gerstein
Journal:  Proteins       Date:  2002-09-01

4.  A structural model for actin-induced nucleotide release in myosin.

Authors:  Thomas F Reubold; Susanne Eschenburg; Andreas Becker; F Jon Kull; Dietmar J Manstein
Journal:  Nat Struct Biol       Date:  2003-09-21

5.  Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

Authors:  Wenjun Zheng; Bernard R Brooks; D Thirumalai
Journal:  Biophys J       Date:  2007-06-08       Impact factor: 4.033

6.  Analysis of domain motions by approximate normal mode calculations.

Authors:  K Hinsen
Journal:  Proteins       Date:  1998-11-15

7.  Cold-sensitive mutations of Dictyostelium myosin heavy chain highlight functional domains of the myosin motor.

Authors:  B Patterson; J A Spudich
Journal:  Genetics       Date:  1996-06       Impact factor: 4.562

Review 8.  Structure-function analysis of the motor domain of myosin.

Authors:  K M Ruppel; J A Spudich
Journal:  Annu Rev Cell Dev Biol       Date:  1996       Impact factor: 13.827

9.  Principles that govern the folding of protein chains.

Authors:  C B Anfinsen
Journal:  Science       Date:  1973-07-20       Impact factor: 47.728

10.  Low fidelity mutants in the O-helix of Thermus aquaticus DNA polymerase I.

Authors:  M Suzuki; A K Avicola; L Hood; L A Loeb
Journal:  J Biol Chem       Date:  1997-04-25       Impact factor: 5.157

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  19 in total

1.  Identification of Allosteric Effects in Proteins by Elastic Network Models.

Authors:  Guang Hu
Journal:  Methods Mol Biol       Date:  2021

Review 2.  Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.

Authors:  D Thirumalai; Changbong Hyeon
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2018-06-19       Impact factor: 6.237

3.  Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.

Authors:  Wenjun Zheng; Mustafa Tekpinar
Journal:  Biophys J       Date:  2012-09-19       Impact factor: 4.033

4.  "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution.

Authors:  Jordi Silvestre-Ryan; Yuchun Lin; Jhih-Wei Chu
Journal:  PLoS Comput Biol       Date:  2011-03-24       Impact factor: 4.475

5.  Correlated rigid modes in protein families.

Authors:  D A Striegel; D Wojtowicz; T M Przytycka; V Periwal
Journal:  Phys Biol       Date:  2016-04-11       Impact factor: 2.583

6.  Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

Authors:  Anshuman Dixit; Gennady M Verkhivker
Journal:  PLoS One       Date:  2012-05-18       Impact factor: 3.240

7.  Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.

Authors:  Anshuman Dixit; Gennady M Verkhivker
Journal:  PLoS Comput Biol       Date:  2011-10-06       Impact factor: 4.475

8.  The energy landscape analysis of cancer mutations in protein kinases.

Authors:  Anshuman Dixit; Gennady M Verkhivker
Journal:  PLoS One       Date:  2011-10-06       Impact factor: 3.240

9.  Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members.

Authors:  Enrique Marcos; Ramon Crehuet; Ivet Bahar
Journal:  PLoS Comput Biol       Date:  2011-09-29       Impact factor: 4.475

Review 10.  Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning.

Authors:  Z Nevin Gerek; S Banu Ozkan
Journal:  PLoS Comput Biol       Date:  2011-10-06       Impact factor: 4.475

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