DOI: 10.1371/journal.pcbi.1002004. Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

10.1371/journal.pcbi.1002004

Crossref journal-article

Public Library of Science (PLoS)

PLoS Computational Biology (340)

Bibliography

Skjaerven, L., Grant, B., Muga, A., Teigen, K., McCammon, J. A., Reuter, N., & Martinez, A. (2011). Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. PLoS Computational Biology, 7(3), e1002004.

Authors 7

Lars Skjaerven (first)
Barry Grant (additional)
Arturo Muga (additional)
Knut Teigen (additional)
J. Andrew McCammon (additional)
Nathalie Reuter (additional)
Aurora Martinez (additional)

References 78 Referenced 28

10.1073/pnas.75.1.131 / Proc Natl Acad Sci USA / Identification of a host protein necessary for bacteriophage morphogenesis (the groe gene product). by CP Georgopoulos (1978)
10.1038/45977 / Nature / Identification of in vivo substrates of the chaperonin groel. by WA Houry (1999)
10.1016/j.cell.2005.05.028 / Cell / Proteome-wide analysis of chaperonin-dependent protein folding in escherichia coli. by MJ Kerner (2005)
10.1128/jb.171.3.1379-1385.1989 / J Bacteriol / The groes and groel heat shock gene products of escherichia coli are essential for bacterial growth at all temperatures. by O Fayet (1989)
10.1073/pnas.0600433103 / Proc Natl Acad Sci USA / Residues in substrate proteins that interact with groel in the capture process are buried in the native state. by G Stan (2006)
10.1126/science.284.5415.822 / Science / Chaperonin function: folding by forced unfolding. by M Shtilerman (1999)
10.1038/nsmb.1394 / Nat Struct Mol Biol / Groel stimulates protein folding through forced unfolding. by Z Lin (2008)
10.1038/371578a0 / Nature / The crystal structure of the bacterial chaperonin groel at 2.8 å. by K Braig (1994)
10.1038/nsb0296-170 / Nat Struct Biol / The 2.4 å crystal structure of the bacterial chaperonin groel complexed with atp gamma s. by DC Boisvert (1996)
10.1038/41944 / Nature / The crystal structure of the asymmetric groel-groes-(adp)7 chaperonin complex. by Z Xu (1997)
10.1016/j.sbi.2005.10.001 / Curr Opin Struct Biol / Allosteric regulation of chaperonins. by A Horovitz (2005)
10.1021/cr040435v / Chem Rev / Groel-groes-mediated protein folding. by AL Horwich (2006)
10.1016/S0092-8674(01)00617-1 / Cell / Atp-bound states of groel captured by cryo-electron microscopy. by NA Ranson (2001)
10.1038/nsmb1046 / Nat Struct Mol Biol / Allosteric signaling of atp hydrolysis in groel-groes complexes. by NA Ranson (2006)
10.1016/S0092-8674(00)80742-4 / Cell / Groel-groes cycling: Atp and nonnative polypeptide direct alternation of folding-active rings. by HS Rye (1999)
10.1038/42047 / Nature / Distinct actions of cis and trans atp within the double ring of the chaperonin groel. by HS Rye (1997)
10.1021/bi020117v / Biochemistry / Dissociation of the groel-groes asymmetric complex is accelerated by increased cooperativity in atp binding to the groel ring distal to groes. by Y Fridmann (2002)
10.1038/nsb0902-646 / Nat Struct Biol / Molecular dynamics simulations of biomolecules. by M Karplus (2002)
10.1016/j.theochem.2008.09.024 / J Mol Struct THEOCHEM / Normal mode analysis for proteins. by L Skjaerven (2009)
10.1016/j.sbi.2005.08.007 / Curr Opin Struct Biol / Coarse-grained normal mode analysis in structural biology. by I Bahar (2005)
10.1016/j.str.2005.02.002 / Structure / Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. by J Ma (2005)
{'key': 'ref22', 'first-page': '25', 'article-title': 'Coarse-grained models reveal functional dynamics–i. elastic network models–theories, comparisons and perspectives.', 'volume': '2', 'author': 'LW Yang', 'year': '2008', 'journal-title': 'Bioinform Biol Insights'} / Bioinform Biol Insights / Coarse-grained models reveal functional dynamics–i. elastic network models–theories, comparisons and perspectives. by LW Yang (2008)
10.1002/prot.22875 / Proteins / Principal component and normal mode analysis of proteins; a quantitative comparison using the groel subunit. by L Skjaerven (2011)
10.1002/prot.340230410 / Proteins / Hinge-bending motion in citrate synthase arising from normal mode calculations. by O Marques (1995)
10.1016/j.jmb.2004.04.044 / J Mol Biol / A normal mode analysis of structural plasticity in the biomolecular motor f(1)-atpase. by Q Cui (2004)
10.1006/jmbi.1996.0257 / J Mol Biol / Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary t-like, quaternary r-like intermediate structures. by L Mouawad (1996)
10.1073/pnas.95.15.8502 / Proc Natl Acad Sci USA / The allosteric mechanism of the chaperonin groel: a dynamic analysis. by J Ma (1998)
10.1529/biophysj.107.105270 / Biophys J / Allosteric transitions in the chaperonin groel are captured by a dominant normal mode that is most robust to sequence variations. by W Zheng (2007)
10.1021/bi011393x / Biochemistry / Molecular mechanisms of chaperonin groel-groes function. by O Keskin (2002)
10.1006/jmbi.2000.4014 / J Mol Biol / A dynamic model for the allosteric mechanism of groel. by J Ma (2000)
10.1073/pnas.0608759103 / Proc Natl Acad Sci USA / Dynamics of allosteric transitions in groel. by C Hyeon (2006)
10.1006/jmbi.1998.2568 / J Mol Biol / Conformational changes in the chaperonin groel: new insights into the allosteric mechanism. by BL de Groot (1999)
10.1529/biophysj.107.108043 / Biophys J / Spontaneous conformational changes in the e. coli groel subunit from all-atom molecular dynamics simulations. by Y Sliozberg (2007)
10.1073/pnas.0914540107 / Proc Natl Acad Sci USA / Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. by CF Abrams (2010)
10.1110/ps.9.3.476 / Protein Sci / Conservation among hsp60 sequences in relation to structure, function, and evolution. by L Brocchieri (2000)
10.1016/S0301-4622(02)00298-3 / Biophys Chem / Annealing function of groel: structural and bioinformatic analysis. by G Stan (2003)
10.1038/msb4100075 / Mol Syst Biol / Markov propagation of allosteric effects in biomolecular systems: application to groel-groes. by C Chennubhotla (2006)
10.1371/journal.pcbi.1000526 / PLoS Comput Biol / Perturbation-based markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of groel-groes. by HM Lu (2009)
10.1371/journal.pcbi.1000360 / PLoS Comput Biol / Allosteric transitions of supramolecular systems explored by network models: Application to chaperonin groel. by Z Yang (2009)
10.1016/j.jmb.2008.12.032 / J Mol Biol / Allostery wiring diagrams in the transitions that drive the groel reaction cycle. by R Tehver (2009)
10.1002/pro.5560070314 / Protein Sci / Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. by L Caves (1998)
10.1073/pnas.92.8.3288 / Proc Natl Acad Sci USA / A sampling problem in molecular dynamics simulations of macromolecules. by JB Clarage (1995)
10.1038/348339a0 / Nature / (mg-atp)-dependent self-assembly of molecular chaperone groel. by NM Lissin (1990)
10.1016/S0021-9258(18)82157-3 / J Biol Chem / The n terminus of the molecular chaperonin groel is a crucial structural element for its assembly. by A Horovitz (1993)
10.1016/0014-5793(93)80838-L / Febs Lett / Truncated groel monomer has the ability to promote folding of rhodanese without groes and atp. by Y Makino (1993)
10.1016/S0021-9258(17)37227-7 / J Biol Chem / Monomeric chaperonin-60 and its 50-kda fragment possess the ability to interact with non-native proteins, to suppress aggregation, and to promote protein folding. by H Taguchi (1994)
10.1074/jbc.270.4.1535 / J Biol Chem / Hydrophobic surfaces that are hidden in chaperonin cpn60 can be exposed by formation of assembly-competent monomers or by ionic perturbation of the oligomer. by PM Horowitz (1995)
10.1074/jbc.270.35.20404 / J Biol Chem / A monomeric variant of groel binds nucleotides but is inactive as a molecular chaperone. by Z White (1995)
10.1093/bioinformatics/btl461 / Bioinformatics / Bio3d: an r package for the comparative analysis of protein structures. by BJ Grant (2006)
10.1021/ja016233n / J Am Chem Soc / Cooperativity in drug-dna recognition: a molecular dynamics study. by SA Harris (2001)
10.1073/pnas.92.8.3288 / Proc Natl Acad Sci USA / A sampling problem in molecular-dynamics simulations of macromolecules. by J Clarage (1995)
10.1007/s00018-009-0014-6 / Cell Mol Life Sci / Functional aspects of protein flexibility. by K Teilum (2009)
10.1038/nchembio.232 / Nat Chem Biol / The role of dynamic conformational ensembles in biomolecular recognition. by DD Boehr (2009)
10.1016/j.str.2009.06.008 / Structure / The origin of allosteric functional modulation: multiple pre-existing pathways. by A del Sol (2009)
10.1016/j.sbi.2003.10.008 / Curr Opin Struct Biol / The role of dynamics in allosteric regulation. by D Kern (2003)
10.1110/ps.03259908 / Protein Sci / Allostery and cooperativity revisited. by Q Cui (2008)
10.1073/pnas.0910246107 / Proc Natl Acad Sci USA / Out-of-equilibrium conformational cycling of groel under saturating atp concentrations. by GA Frank (2010)
10.1016/j.jmb.2004.07.015 / J Mol Biol / Exploring the structural dynamics of the e.coli chaperonin groel using translation-libration-screw crystallographic refinement of intermediate states. by C Chaudhry (2004)
10.1093/protein/3.2.77 / Protein Eng / The structure of interfaces between subunits of dimeric and tetrameric proteins. by S Miller (1989)
10.1016/0022-2836(88)90606-7 / J Mol Biol / Surface, subunit interfaces and interior of oligomeric proteins. by J Janin (1988)
10.1021/bi00865a047 / Biochemistry / Comparison of experimental binding data and theoretical models in proteins containing subunits. by DE Koshland (1966)
10.1021/bi901847q / Biochemistry / Energetics of nucleotide-induced dnak conformational states. by SG Taneva (2010)
10.1016/S0167-4838(99)00049-7 / Biochim Biophys Acta / Thermodynamics of nucleotide binding to the chaperonin groel studied by isothermal titration calorimetry: evidence for noncooperative nucleotide binding. by TP Terada (1999)
10.1002/prot.10180 / Proteins / Mapping pathways of allosteric communication in groel by analysis of correlated mutations. by I Kass (2002)
10.1016/j.jmb.2009.11.074 / J Mol Biol / Characterisation of a groel single-ring mutant that supports growth of escherichia coli and has groes-dependent atpase activity. by E Kovacs (2010)
10.1107/S0907444902003451 / Acta Crystallogr D / The protein data bank. by H Berman (2002)
10.1002/prot.340110305 / Proteins / Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. by T Ichiye (1991)
10.1002/prot.340170408 / Proteins / Essential dynamics of proteins. by A Amadei (1993)
10.1016/j.jmb.2005.09.096 / J Mol Biol / Crystal structure of wild-type chaperonin groel. by C Bartolucci (2005)
10.1016/S0022-2836(03)00184-0 / J Mol Biol / Structural basis for groel-assisted protein folding from the crystal structure of (groel-kmgatp)14 at 2.0a resolution. by J Wang (2003)
{'key': 'ref71', 'article-title': 'Amber 10.', 'author': 'D Case', 'year': '2008'} / Amber 10. by D Case (2008)
10.1002/jcc.10349 / J Comput Chem / A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. by Y Duan (2003)
10.1002/prot.10470 / Proteins / Distinguish protein decoys by using a scoring function based on a new amber force field, short molecular dynamics simulations, and the generalized born solvent model. by M Lee (2004)
10.1002/jcc.10262 / J Comput Chem / Development of polyphosphate parameters for use with the amber force field. by K Meagher (2003)
10.1063/1.445869 / J Chem Phys / Comparison of simple potential functions for simulating liquid water. by W Jorgensen (1983)
10.1021/ct700119m / J Chem Theory Comput / Clustering molecular dynamics trajectories: 1. characterizing the performance of different clustering algorithms. by J Shao (2007)
{'key': 'ref77', 'article-title': 'The pymol molecular graphics system.', 'volume': 'LLC', 'author': 'W DeLano', 'year': '2010', 'journal-title': 'Schrödinger,'} / Schrödinger, / The pymol molecular graphics system. by W DeLano (2010)
10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U / Proteins / On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. by A Amadei (1999)

Dates

Type	When
Created	14 years, 5 months ago (March 10, 2011, 4:42 p.m.)
Deposited	3 years, 9 months ago (Nov. 20, 2021, 1:45 a.m.)
Indexed	5 months, 1 week ago (March 19, 2025, 12:24 p.m.)
Issued	14 years, 5 months ago (March 10, 2011)
Published	14 years, 5 months ago (March 10, 2011)
Published Online	14 years, 5 months ago (March 10, 2011)

Funders 0

None

BibTeX

@article{Skjaerven_2011, title={Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations}, volume={7}, ISSN={1553-7358}, url={http://dx.doi.org/10.1371/journal.pcbi.1002004}, DOI={10.1371/journal.pcbi.1002004}, number={3}, journal={PLoS Computational Biology}, publisher={Public Library of Science (PLoS)}, author={Skjaerven, Lars and Grant, Barry and Muga, Arturo and Teigen, Knut and McCammon, J. Andrew and Reuter, Nathalie and Martinez, Aurora}, editor={Ma, Jianpeng}, year={2011}, month=mar, pages={e1002004} }

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      "first-page": "131",
      "DOI": "10.1073/pnas.75.1.131",
      "article-title": "Identification of a host protein necessary for bacteriophage morphogenesis (the groe gene product).",
      "volume": "75",
      "author": "CP Georgopoulos",
      "year": "1978",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref2",
      "doi-asserted-by": "crossref",
      "first-page": "147",
      "DOI": "10.1038/45977",
      "article-title": "Identification of in vivo substrates of the chaperonin groel.",
      "volume": "402",
      "author": "WA Houry",
      "year": "1999",
      "journal-title": "Nature"
    },
    {
      "key": "ref3",
      "doi-asserted-by": "crossref",
      "first-page": "209",
      "DOI": "10.1016/j.cell.2005.05.028",
      "article-title": "Proteome-wide analysis of chaperonin-dependent protein folding in escherichia coli.",
      "volume": "122",
      "author": "MJ Kerner",
      "year": "2005",
      "journal-title": "Cell"
    },
    {
      "key": "ref4",
      "doi-asserted-by": "crossref",
      "first-page": "1379",
      "DOI": "10.1128/jb.171.3.1379-1385.1989",
      "article-title": "The groes and groel heat shock gene products of escherichia coli are essential for bacterial growth at all temperatures.",
      "volume": "171",
      "author": "O Fayet",
      "year": "1989",
      "journal-title": "J Bacteriol"
    },
    {
      "key": "ref5",
      "doi-asserted-by": "crossref",
      "first-page": "4433",
      "DOI": "10.1073/pnas.0600433103",
      "article-title": "Residues in substrate proteins that interact with groel in the capture process are buried in the native state.",
      "volume": "103",
      "author": "G Stan",
      "year": "2006",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref6",
      "doi-asserted-by": "crossref",
      "first-page": "822",
      "DOI": "10.1126/science.284.5415.822",
      "article-title": "Chaperonin function: folding by forced unfolding.",
      "volume": "284",
      "author": "M Shtilerman",
      "year": "1999",
      "journal-title": "Science"
    },
    {
      "key": "ref7",
      "doi-asserted-by": "crossref",
      "first-page": "303",
      "DOI": "10.1038/nsmb.1394",
      "article-title": "Groel stimulates protein folding through forced unfolding.",
      "volume": "15",
      "author": "Z Lin",
      "year": "2008",
      "journal-title": "Nat Struct Mol Biol"
    },
    {
      "key": "ref8",
      "doi-asserted-by": "crossref",
      "first-page": "578",
      "DOI": "10.1038/371578a0",
      "article-title": "The crystal structure of the bacterial chaperonin groel at 2.8 \u00e5.",
      "volume": "371",
      "author": "K Braig",
      "year": "1994",
      "journal-title": "Nature"
    },
    {
      "key": "ref9",
      "doi-asserted-by": "crossref",
      "first-page": "170",
      "DOI": "10.1038/nsb0296-170",
      "article-title": "The 2.4 \u00e5 crystal structure of the bacterial chaperonin groel complexed with atp gamma s.",
      "volume": "3",
      "author": "DC Boisvert",
      "year": "1996",
      "journal-title": "Nat Struct Biol"
    },
    {
      "key": "ref10",
      "doi-asserted-by": "crossref",
      "first-page": "741",
      "DOI": "10.1038/41944",
      "article-title": "The crystal structure of the asymmetric groel-groes-(adp)7 chaperonin complex.",
      "volume": "388",
      "author": "Z Xu",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "ref11",
      "doi-asserted-by": "crossref",
      "first-page": "646",
      "DOI": "10.1016/j.sbi.2005.10.001",
      "article-title": "Allosteric regulation of chaperonins.",
      "volume": "15",
      "author": "A Horovitz",
      "year": "2005",
      "journal-title": "Curr Opin Struct Biol"
    },
    {
      "key": "ref12",
      "doi-asserted-by": "crossref",
      "first-page": "1917",
      "DOI": "10.1021/cr040435v",
      "article-title": "Groel-groes-mediated protein folding.",
      "volume": "106",
      "author": "AL Horwich",
      "year": "2006",
      "journal-title": "Chem Rev"
    },
    {
      "key": "ref13",
      "doi-asserted-by": "crossref",
      "first-page": "869",
      "DOI": "10.1016/S0092-8674(01)00617-1",
      "article-title": "Atp-bound states of groel captured by cryo-electron microscopy.",
      "volume": "107",
      "author": "NA Ranson",
      "year": "2001",
      "journal-title": "Cell"
    },
    {
      "key": "ref14",
      "doi-asserted-by": "crossref",
      "first-page": "147",
      "DOI": "10.1038/nsmb1046",
      "article-title": "Allosteric signaling of atp hydrolysis in groel-groes complexes.",
      "volume": "13",
      "author": "NA Ranson",
      "year": "2006",
      "journal-title": "Nat Struct Mol Biol"
    },
    {
      "key": "ref15",
      "doi-asserted-by": "crossref",
      "first-page": "325",
      "DOI": "10.1016/S0092-8674(00)80742-4",
      "article-title": "Groel-groes cycling: Atp and nonnative polypeptide direct alternation of folding-active rings.",
      "volume": "97",
      "author": "HS Rye",
      "year": "1999",
      "journal-title": "Cell"
    },
    {
      "key": "ref16",
      "doi-asserted-by": "crossref",
      "first-page": "792",
      "DOI": "10.1038/42047",
      "article-title": "Distinct actions of cis and trans atp within the double ring of the chaperonin groel.",
      "volume": "388",
      "author": "HS Rye",
      "year": "1997",
      "journal-title": "Nature"
    },
    {
      "key": "ref17",
      "doi-asserted-by": "crossref",
      "first-page": "5938",
      "DOI": "10.1021/bi020117v",
      "article-title": "Dissociation of the groel-groes asymmetric complex is accelerated by increased cooperativity in atp binding to the groel ring distal to groes.",
      "volume": "41",
      "author": "Y Fridmann",
      "year": "2002",
      "journal-title": "Biochemistry"
    },
    {
      "key": "ref18",
      "doi-asserted-by": "crossref",
      "first-page": "646",
      "DOI": "10.1038/nsb0902-646",
      "article-title": "Molecular dynamics simulations of biomolecules.",
      "volume": "9",
      "author": "M Karplus",
      "year": "2002",
      "journal-title": "Nat Struct Biol"
    },
    {
      "key": "ref19",
      "doi-asserted-by": "crossref",
      "first-page": "42",
      "DOI": "10.1016/j.theochem.2008.09.024",
      "article-title": "Normal mode analysis for proteins.",
      "volume": "898",
      "author": "L Skjaerven",
      "year": "2009",
      "journal-title": "J Mol Struct THEOCHEM"
    },
    {
      "key": "ref20",
      "doi-asserted-by": "crossref",
      "first-page": "586",
      "DOI": "10.1016/j.sbi.2005.08.007",
      "article-title": "Coarse-grained normal mode analysis in structural biology.",
      "volume": "15",
      "author": "I Bahar",
      "year": "2005",
      "journal-title": "Curr Opin Struct Biol"
    },
    {
      "key": "ref21",
      "doi-asserted-by": "crossref",
      "first-page": "373",
      "DOI": "10.1016/j.str.2005.02.002",
      "article-title": "Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.",
      "volume": "13",
      "author": "J Ma",
      "year": "2005",
      "journal-title": "Structure"
    },
    {
      "key": "ref22",
      "first-page": "25",
      "article-title": "Coarse-grained models reveal functional dynamics\u2013i. elastic network models\u2013theories, comparisons and perspectives.",
      "volume": "2",
      "author": "LW Yang",
      "year": "2008",
      "journal-title": "Bioinform Biol Insights"
    },
    {
      "key": "ref23",
      "doi-asserted-by": "crossref",
      "first-page": "232",
      "DOI": "10.1002/prot.22875",
      "article-title": "Principal component and normal mode analysis of proteins; a quantitative comparison using the groel subunit.",
      "volume": "79",
      "author": "L Skjaerven",
      "year": "2011",
      "journal-title": "Proteins"
    },
    {
      "key": "ref24",
      "doi-asserted-by": "crossref",
      "first-page": "557",
      "DOI": "10.1002/prot.340230410",
      "article-title": "Hinge-bending motion in citrate synthase arising from normal mode calculations.",
      "volume": "23",
      "author": "O Marques",
      "year": "1995",
      "journal-title": "Proteins"
    },
    {
      "key": "ref25",
      "doi-asserted-by": "crossref",
      "first-page": "345",
      "DOI": "10.1016/j.jmb.2004.04.044",
      "article-title": "A normal mode analysis of structural plasticity in the biomolecular motor f(1)-atpase.",
      "volume": "340",
      "author": "Q Cui",
      "year": "2004",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref26",
      "doi-asserted-by": "crossref",
      "first-page": "393",
      "DOI": "10.1006/jmbi.1996.0257",
      "article-title": "Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary t-like, quaternary r-like intermediate structures.",
      "volume": "258",
      "author": "L Mouawad",
      "year": "1996",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref27",
      "doi-asserted-by": "crossref",
      "first-page": "8502",
      "DOI": "10.1073/pnas.95.15.8502",
      "article-title": "The allosteric mechanism of the chaperonin groel: a dynamic analysis.",
      "volume": "95",
      "author": "J Ma",
      "year": "1998",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref28",
      "doi-asserted-by": "crossref",
      "first-page": "2289",
      "DOI": "10.1529/biophysj.107.105270",
      "article-title": "Allosteric transitions in the chaperonin groel are captured by a dominant normal mode that is most robust to sequence variations.",
      "volume": "93",
      "author": "W Zheng",
      "year": "2007",
      "journal-title": "Biophys J"
    },
    {
      "key": "ref29",
      "doi-asserted-by": "crossref",
      "first-page": "491",
      "DOI": "10.1021/bi011393x",
      "article-title": "Molecular mechanisms of chaperonin groel-groes function.",
      "volume": "41",
      "author": "O Keskin",
      "year": "2002",
      "journal-title": "Biochemistry"
    },
    {
      "key": "ref30",
      "doi-asserted-by": "crossref",
      "first-page": "303",
      "DOI": "10.1006/jmbi.2000.4014",
      "article-title": "A dynamic model for the allosteric mechanism of groel.",
      "volume": "302",
      "author": "J Ma",
      "year": "2000",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref31",
      "doi-asserted-by": "crossref",
      "first-page": "18939",
      "DOI": "10.1073/pnas.0608759103",
      "article-title": "Dynamics of allosteric transitions in groel.",
      "volume": "103",
      "author": "C Hyeon",
      "year": "2006",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref32",
      "doi-asserted-by": "crossref",
      "first-page": "1241",
      "DOI": "10.1006/jmbi.1998.2568",
      "article-title": "Conformational changes in the chaperonin groel: new insights into the allosteric mechanism.",
      "volume": "286",
      "author": "BL de Groot",
      "year": "1999",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref33",
      "doi-asserted-by": "crossref",
      "first-page": "1906",
      "DOI": "10.1529/biophysj.107.108043",
      "article-title": "Spontaneous conformational changes in the e. coli groel subunit from all-atom molecular dynamics simulations.",
      "volume": "93",
      "author": "Y Sliozberg",
      "year": "2007",
      "journal-title": "Biophys J"
    },
    {
      "key": "ref34",
      "doi-asserted-by": "crossref",
      "first-page": "4961",
      "DOI": "10.1073/pnas.0914540107",
      "article-title": "Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.",
      "volume": "107",
      "author": "CF Abrams",
      "year": "2010",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref35",
      "doi-asserted-by": "crossref",
      "first-page": "476",
      "DOI": "10.1110/ps.9.3.476",
      "article-title": "Conservation among hsp60 sequences in relation to structure, function, and evolution.",
      "volume": "9",
      "author": "L Brocchieri",
      "year": "2000",
      "journal-title": "Protein Sci"
    },
    {
      "key": "ref36",
      "doi-asserted-by": "crossref",
      "first-page": "453",
      "DOI": "10.1016/S0301-4622(02)00298-3",
      "article-title": "Annealing function of groel: structural and bioinformatic analysis.",
      "volume": "100",
      "author": "G Stan",
      "year": "2003",
      "journal-title": "Biophys Chem"
    },
    {
      "key": "ref37",
      "doi-asserted-by": "crossref",
      "first-page": "36",
      "DOI": "10.1038/msb4100075",
      "article-title": "Markov propagation of allosteric effects in biomolecular systems: application to groel-groes.",
      "volume": "2",
      "author": "C Chennubhotla",
      "year": "2006",
      "journal-title": "Mol Syst Biol"
    },
    {
      "key": "ref38",
      "doi-asserted-by": "crossref",
      "first-page": "e1000526",
      "DOI": "10.1371/journal.pcbi.1000526",
      "article-title": "Perturbation-based markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of groel-groes.",
      "volume": "5",
      "author": "HM Lu",
      "year": "2009",
      "journal-title": "PLoS Comput Biol"
    },
    {
      "key": "ref39",
      "doi-asserted-by": "crossref",
      "first-page": "e1000360",
      "DOI": "10.1371/journal.pcbi.1000360",
      "article-title": "Allosteric transitions of supramolecular systems explored by network models: Application to chaperonin groel.",
      "volume": "5",
      "author": "Z Yang",
      "year": "2009",
      "journal-title": "PLoS Comput Biol"
    },
    {
      "key": "ref40",
      "doi-asserted-by": "crossref",
      "first-page": "390",
      "DOI": "10.1016/j.jmb.2008.12.032",
      "article-title": "Allostery wiring diagrams in the transitions that drive the groel reaction cycle.",
      "volume": "387",
      "author": "R Tehver",
      "year": "2009",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref41",
      "doi-asserted-by": "crossref",
      "first-page": "649",
      "DOI": "10.1002/pro.5560070314",
      "article-title": "Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin.",
      "volume": "7",
      "author": "L Caves",
      "year": "1998",
      "journal-title": "Protein Sci"
    },
    {
      "key": "ref42",
      "doi-asserted-by": "crossref",
      "first-page": "3288",
      "DOI": "10.1073/pnas.92.8.3288",
      "article-title": "A sampling problem in molecular dynamics simulations of macromolecules.",
      "volume": "92",
      "author": "JB Clarage",
      "year": "1995",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref43",
      "doi-asserted-by": "crossref",
      "first-page": "339",
      "DOI": "10.1038/348339a0",
      "article-title": "(mg-atp)-dependent self-assembly of molecular chaperone groel.",
      "volume": "348",
      "author": "NM Lissin",
      "year": "1990",
      "journal-title": "Nature"
    },
    {
      "key": "ref44",
      "doi-asserted-by": "crossref",
      "first-page": "9957",
      "DOI": "10.1016/S0021-9258(18)82157-3",
      "article-title": "The n terminus of the molecular chaperonin groel is a crucial structural element for its assembly.",
      "volume": "268",
      "author": "A Horovitz",
      "year": "1993",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref45",
      "doi-asserted-by": "crossref",
      "first-page": "363",
      "DOI": "10.1016/0014-5793(93)80838-L",
      "article-title": "Truncated groel monomer has the ability to promote folding of rhodanese without groes and atp.",
      "volume": "336",
      "author": "Y Makino",
      "year": "1993",
      "journal-title": "Febs Lett"
    },
    {
      "key": "ref46",
      "doi-asserted-by": "crossref",
      "first-page": "8529",
      "DOI": "10.1016/S0021-9258(17)37227-7",
      "article-title": "Monomeric chaperonin-60 and its 50-kda fragment possess the ability to interact with non-native proteins, to suppress aggregation, and to promote protein folding.",
      "volume": "269",
      "author": "H Taguchi",
      "year": "1994",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref47",
      "doi-asserted-by": "crossref",
      "first-page": "1535",
      "DOI": "10.1074/jbc.270.4.1535",
      "article-title": "Hydrophobic surfaces that are hidden in chaperonin cpn60 can be exposed by formation of assembly-competent monomers or by ionic perturbation of the oligomer.",
      "volume": "270",
      "author": "PM Horowitz",
      "year": "1995",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref48",
      "doi-asserted-by": "crossref",
      "first-page": "20404",
      "DOI": "10.1074/jbc.270.35.20404",
      "article-title": "A monomeric variant of groel binds nucleotides but is inactive as a molecular chaperone.",
      "volume": "270",
      "author": "Z White",
      "year": "1995",
      "journal-title": "J Biol Chem"
    },
    {
      "key": "ref49",
      "doi-asserted-by": "crossref",
      "first-page": "2695",
      "DOI": "10.1093/bioinformatics/btl461",
      "article-title": "Bio3d: an r package for the comparative analysis of protein structures.",
      "volume": "22",
      "author": "BJ Grant",
      "year": "2006",
      "journal-title": "Bioinformatics"
    },
    {
      "key": "ref50",
      "doi-asserted-by": "crossref",
      "first-page": "12658",
      "DOI": "10.1021/ja016233n",
      "article-title": "Cooperativity in drug-dna recognition: a molecular dynamics study.",
      "volume": "123",
      "author": "SA Harris",
      "year": "2001",
      "journal-title": "J Am Chem Soc"
    },
    {
      "key": "ref51",
      "doi-asserted-by": "crossref",
      "first-page": "3288",
      "DOI": "10.1073/pnas.92.8.3288",
      "article-title": "A sampling problem in molecular-dynamics simulations of macromolecules.",
      "volume": "92",
      "author": "J Clarage",
      "year": "1995",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref52",
      "doi-asserted-by": "crossref",
      "first-page": "2231",
      "DOI": "10.1007/s00018-009-0014-6",
      "article-title": "Functional aspects of protein flexibility.",
      "volume": "66",
      "author": "K Teilum",
      "year": "2009",
      "journal-title": "Cell Mol Life Sci"
    },
    {
      "key": "ref53",
      "doi-asserted-by": "crossref",
      "first-page": "789",
      "DOI": "10.1038/nchembio.232",
      "article-title": "The role of dynamic conformational ensembles in biomolecular recognition.",
      "volume": "5",
      "author": "DD Boehr",
      "year": "2009",
      "journal-title": "Nat Chem Biol"
    },
    {
      "key": "ref54",
      "doi-asserted-by": "crossref",
      "first-page": "1042",
      "DOI": "10.1016/j.str.2009.06.008",
      "article-title": "The origin of allosteric functional modulation: multiple pre-existing pathways.",
      "volume": "17",
      "author": "A del Sol",
      "year": "2009",
      "journal-title": "Structure"
    },
    {
      "key": "ref55",
      "doi-asserted-by": "crossref",
      "first-page": "748",
      "DOI": "10.1016/j.sbi.2003.10.008",
      "article-title": "The role of dynamics in allosteric regulation.",
      "volume": "13",
      "author": "D Kern",
      "year": "2003",
      "journal-title": "Curr Opin Struct Biol"
    },
    {
      "key": "ref56",
      "doi-asserted-by": "crossref",
      "first-page": "1295",
      "DOI": "10.1110/ps.03259908",
      "article-title": "Allostery and cooperativity revisited.",
      "volume": "17",
      "author": "Q Cui",
      "year": "2008",
      "journal-title": "Protein Sci"
    },
    {
      "key": "ref57",
      "doi-asserted-by": "crossref",
      "first-page": "6270",
      "DOI": "10.1073/pnas.0910246107",
      "article-title": "Out-of-equilibrium conformational cycling of groel under saturating atp concentrations.",
      "volume": "107",
      "author": "GA Frank",
      "year": "2010",
      "journal-title": "Proc Natl Acad Sci USA"
    },
    {
      "key": "ref58",
      "doi-asserted-by": "crossref",
      "first-page": "229",
      "DOI": "10.1016/j.jmb.2004.07.015",
      "article-title": "Exploring the structural dynamics of the e.coli chaperonin groel using translation-libration-screw crystallographic refinement of intermediate states.",
      "volume": "342",
      "author": "C Chaudhry",
      "year": "2004",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref59",
      "doi-asserted-by": "crossref",
      "first-page": "77",
      "DOI": "10.1093/protein/3.2.77",
      "article-title": "The structure of interfaces between subunits of dimeric and tetrameric proteins.",
      "volume": "3",
      "author": "S Miller",
      "year": "1989",
      "journal-title": "Protein Eng"
    },
    {
      "key": "ref60",
      "doi-asserted-by": "crossref",
      "first-page": "155",
      "DOI": "10.1016/0022-2836(88)90606-7",
      "article-title": "Surface, subunit interfaces and interior of oligomeric proteins.",
      "volume": "204",
      "author": "J Janin",
      "year": "1988",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref61",
      "doi-asserted-by": "crossref",
      "first-page": "365",
      "DOI": "10.1021/bi00865a047",
      "article-title": "Comparison of experimental binding data and theoretical models in proteins containing subunits.",
      "volume": "5",
      "author": "DE Koshland",
      "year": "1966",
      "journal-title": "Biochemistry"
    },
    {
      "key": "ref62",
      "doi-asserted-by": "crossref",
      "first-page": "1338",
      "DOI": "10.1021/bi901847q",
      "article-title": "Energetics of nucleotide-induced dnak conformational states.",
      "volume": "49",
      "author": "SG Taneva",
      "year": "2010",
      "journal-title": "Biochemistry"
    },
    {
      "key": "ref63",
      "doi-asserted-by": "crossref",
      "first-page": "269",
      "DOI": "10.1016/S0167-4838(99)00049-7",
      "article-title": "Thermodynamics of nucleotide binding to the chaperonin groel studied by isothermal titration calorimetry: evidence for noncooperative nucleotide binding.",
      "volume": "1431",
      "author": "TP Terada",
      "year": "1999",
      "journal-title": "Biochim Biophys Acta"
    },
    {
      "key": "ref64",
      "doi-asserted-by": "crossref",
      "first-page": "611",
      "DOI": "10.1002/prot.10180",
      "article-title": "Mapping pathways of allosteric communication in groel by analysis of correlated mutations.",
      "volume": "48",
      "author": "I Kass",
      "year": "2002",
      "journal-title": "Proteins"
    },
    {
      "key": "ref65",
      "doi-asserted-by": "crossref",
      "first-page": "1271",
      "DOI": "10.1016/j.jmb.2009.11.074",
      "article-title": "Characterisation of a groel single-ring mutant that supports growth of escherichia coli and has groes-dependent atpase activity.",
      "volume": "396",
      "author": "E Kovacs",
      "year": "2010",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref66",
      "doi-asserted-by": "crossref",
      "first-page": "899",
      "DOI": "10.1107/S0907444902003451",
      "article-title": "The protein data bank.",
      "volume": "58",
      "author": "H Berman",
      "year": "2002",
      "journal-title": "Acta Crystallogr D"
    },
    {
      "key": "ref67",
      "doi-asserted-by": "crossref",
      "first-page": "205",
      "DOI": "10.1002/prot.340110305",
      "article-title": "Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.",
      "volume": "11",
      "author": "T Ichiye",
      "year": "1991",
      "journal-title": "Proteins"
    },
    {
      "key": "ref68",
      "doi-asserted-by": "crossref",
      "first-page": "412",
      "DOI": "10.1002/prot.340170408",
      "article-title": "Essential dynamics of proteins.",
      "volume": "17",
      "author": "A Amadei",
      "year": "1993",
      "journal-title": "Proteins"
    },
    {
      "key": "ref69",
      "doi-asserted-by": "crossref",
      "first-page": "940",
      "DOI": "10.1016/j.jmb.2005.09.096",
      "article-title": "Crystal structure of wild-type chaperonin groel.",
      "volume": "354",
      "author": "C Bartolucci",
      "year": "2005",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref70",
      "doi-asserted-by": "crossref",
      "first-page": "843",
      "DOI": "10.1016/S0022-2836(03)00184-0",
      "article-title": "Structural basis for groel-assisted protein folding from the crystal structure of (groel-kmgatp)14 at 2.0a resolution.",
      "volume": "327",
      "author": "J Wang",
      "year": "2003",
      "journal-title": "J Mol Biol"
    },
    {
      "key": "ref71",
      "article-title": "Amber 10.",
      "author": "D Case",
      "year": "2008"
    },
    {
      "key": "ref72",
      "doi-asserted-by": "crossref",
      "first-page": "1999",
      "DOI": "10.1002/jcc.10349",
      "article-title": "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.",
      "volume": "24",
      "author": "Y Duan",
      "year": "2003",
      "journal-title": "J Comput Chem"
    },
    {
      "key": "ref73",
      "doi-asserted-by": "crossref",
      "first-page": "620",
      "DOI": "10.1002/prot.10470",
      "article-title": "Distinguish protein decoys by using a scoring function based on a new amber force field, short molecular dynamics simulations, and the generalized born solvent model.",
      "volume": "55",
      "author": "M Lee",
      "year": "2004",
      "journal-title": "Proteins"
    },
    {
      "key": "ref74",
      "doi-asserted-by": "crossref",
      "first-page": "1016",
      "DOI": "10.1002/jcc.10262",
      "article-title": "Development of polyphosphate parameters for use with the amber force field.",
      "volume": "24",
      "author": "K Meagher",
      "year": "2003",
      "journal-title": "J Comput Chem"
    },
    {
      "key": "ref75",
      "doi-asserted-by": "crossref",
      "first-page": "926",
      "DOI": "10.1063/1.445869",
      "article-title": "Comparison of simple potential functions for simulating liquid water.",
      "volume": "79",
      "author": "W Jorgensen",
      "year": "1983",
      "journal-title": "J Chem Phys"
    },
    {
      "key": "ref76",
      "doi-asserted-by": "crossref",
      "first-page": "2312",
      "DOI": "10.1021/ct700119m",
      "article-title": "Clustering molecular dynamics trajectories: 1. characterizing the performance of different clustering algorithms.",
      "volume": "3",
      "author": "J Shao",
      "year": "2007",
      "journal-title": "J Chem Theory Comput"
    },
    {
      "key": "ref77",
      "article-title": "The pymol molecular graphics system.",
      "volume": "LLC",
      "author": "W DeLano",
      "year": "2010",
      "journal-title": "Schr\u00f6dinger,"
    },
    {
      "key": "ref78",
      "doi-asserted-by": "crossref",
      "first-page": "419",
      "DOI": "10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U",
      "article-title": "On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins&apos; molecular dynamics simulations.",
      "volume": "36",
      "author": "A Amadei",
      "year": "1999",
      "journal-title": "Proteins"
    }
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