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Volumn 103, Issue 6, 2012, Pages 1285-1295

Weak intra-ring allosteric communications of the archaeal chaperonin thermosome revealed by normal mode analysis

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; ARCHAEAL PROTEIN; THERMOSOME;

EID: 84866487669     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.07.049     Document Type: Article
Times cited : (10)

References (55)
  • 2
    • 33646907087 scopus 로고    scopus 로고
    • GroEL-GroES-mediated protein folding
    • DOI 10.1021/cr040435v
    • A.L. Horwich, G.W. Farr, and W.A. Fenton GroEL-GroES-mediated protein folding Chem. Rev. 106 2006 1917 1930 (Pubitemid 43792786)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1917-1930
    • Horwich, A.L.1    Farr, G.W.2    Fenton, W.A.3
  • 3
    • 0030870719 scopus 로고    scopus 로고
    • The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex
    • DOI 10.1038/41944
    • 7 chaperonin complex Nature 388 1997 741 750 (Pubitemid 27375147)
    • (1997) Nature , vol.388 , Issue.6644 , pp. 741-750
    • Xu, Z.1    Horwich, A.L.2    Sigler, P.B.3
  • 4
    • 0027943510 scopus 로고
    • The crystal structure of the bacterial chaperonin GroEL at 2.8 Å
    • K. Braig, and Z. Otwinowski P.B. Sigler The crystal structure of the bacterial chaperonin GroEL at 2.8 Å Nature 371 1994 578 586
    • (1994) Nature , vol.371 , pp. 578-586
    • Braig, K.1    Otwinowski, Z.2    Sigler, P.B.3
  • 6
    • 0032464019 scopus 로고    scopus 로고
    • GroEL/GroES: Structure and function of a two-stroke folding machine
    • DOI 10.1006/jsbi.1998.4060
    • Z. Xu, and P.B. Sigler GroEL/GroES: structure and function of a two-stroke folding machine J. Struct. Biol. 124 1998 129 141 (Pubitemid 29143055)
    • (1998) Journal of Structural Biology , vol.124 , Issue.2-3 , pp. 129-141
    • Xu, Z.1    Sigler, P.B.2
  • 7
  • 8
    • 0027933369 scopus 로고
    • GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms
    • DOI 10.1016/0092-8674(94)90533-9
    • J.S. Weissman, and Y. Kashi A.L. Horwich GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms Cell 78 1994 693 702 (Pubitemid 24268591)
    • (1994) Cell , vol.78 , Issue.4 , pp. 693-702
    • Weissman, J.S.1    Kashi, Y.2    Fenton, W.A.3    Horwich, A.L.4
  • 9
    • 0030056969 scopus 로고    scopus 로고
    • Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction
    • DOI 10.1016/S0092-8674(00)81293-3
    • J.S. Weissman, and H.S. Rye A.L. Horwich Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction Cell 84 1996 481 490 (Pubitemid 26058572)
    • (1996) Cell , vol.84 , Issue.3 , pp. 481-490
    • Weissman, J.S.1    Rye, H.S.2    Fenton, W.A.3    Beechem, J.M.4    Horwich, A.L.5
  • 10
    • 0032478545 scopus 로고    scopus 로고
    • Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT
    • DOI 10.1016/S0092-8674(00)81152-6
    • L. Ditzel, and J. Löwe S. Steinbacher Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT Cell 93 1998 125 138 (Pubitemid 28173558)
    • (1998) Cell , vol.93 , Issue.1 , pp. 125-138
    • Ditzel, L.1    Lowe, J.2    Stock, D.3    Stetter, K.-O.4    Huber, H.5    Huber, R.6    Steinbacher, S.7
  • 12
    • 79961026866 scopus 로고    scopus 로고
    • The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins
    • C. Dekker, and S.M. Roe K.R. Willison The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins EMBO J. 30 2011 3078 3090
    • (2011) EMBO J. , vol.30 , pp. 3078-3090
    • Dekker, C.1    Roe, S.M.2    Willison, K.R.3
  • 13
    • 0030668929 scopus 로고    scopus 로고
    • Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin
    • DOI 10.1016/S0092-8674(00)80408-0
    • M. Klumpp, W. Baumeister, and L.O. Essen Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin Cell 91 1997 263 270 (Pubitemid 27456393)
    • (1997) Cell , vol.91 , Issue.2 , pp. 263-270
    • Klumpp, M.1    Baumeister, W.2    Essen, L.-O.3
  • 14
    • 0035983515 scopus 로고    scopus 로고
    • Crystal structure of the CCTγ apical domain: Implications for substrate binding to the eukaryotic cytosolic chaperonin
    • DOI 10.1016/S0022-2836(02)00190-0
    • G. Pappenberger, and J.A. Wilsher L.H. Pearl Crystal structure of the CCTγ apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin J. Mol. Biol. 318 2002 1367 1379 (Pubitemid 34754004)
    • (2002) Journal of Molecular Biology , vol.318 , Issue.5 , pp. 1367-1379
    • Pappenberger, G.1    Wilsher, J.A.2    Mark Roe, S.3    Counsell, D.J.4    Willison, K.R.5    Pearl, L.H.6
  • 15
    • 0025995773 scopus 로고
    • Cooperativity in ATP hydrolysis by GroEL is increased by GroES
    • T.E. Gray, and A.R. Fersht Cooperativity in ATP hydrolysis by GroEL is increased by GroES FEBS Lett. 292 1991 254 258
    • (1991) FEBS Lett. , vol.292 , pp. 254-258
    • Gray, T.E.1    Fersht, A.R.2
  • 16
    • 0026649378 scopus 로고
    • Positive cooperativity in the functioning of molecular chaperone GroEL
    • E.S. Bochkareva, and N.M. Lissin A.S. Girshovich Positive cooperativity in the functioning of molecular chaperone GroEL J. Biol. Chem. 267 1992 6796 6800
    • (1992) J. Biol. Chem. , vol.267 , pp. 6796-6800
    • Bochkareva, E.S.1    Lissin, N.M.2    Girshovich, A.S.3
  • 17
    • 16244380542 scopus 로고    scopus 로고
    • Cooperativity in the thermosome
    • DOI 10.1016/j.jmb.2005.01.066
    • M.G. Bigotti, and A.R. Clarke Cooperativity in the thermosome J. Mol. Biol. 348 2005 13 26 (Pubitemid 40461837)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.1 , pp. 13-26
    • Bigotti, M.G.1    Clarke, A.R.2
  • 18
    • 0035100716 scopus 로고    scopus 로고
    • Nested allosteric interactions in the cytoplasmic chaperonin containing TCP-1
    • DOI 10.1110/ps.44401
    • G. Kafri, K.R. Willison, and A. Horovitz Nested allosteric interactions in the cytoplasmic chaperonin containing TCP-1 Protein Sci. 10 2001 445 449 (Pubitemid 32225664)
    • (2001) Protein Science , vol.10 , Issue.2 , pp. 445-449
    • Kafri, G.1    Willison, K.R.2    Horovitz, A.3
  • 19
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • J. Monod, J. Wyman, and J.P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 20
    • 0029004759 scopus 로고
    • Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL
    • O. Yifrach, and A. Horovitz Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL Biochemistry 34 1995 5303 5308
    • (1995) Biochemistry , vol.34 , pp. 5303-5308
    • Yifrach, O.1    Horovitz, A.2
  • 22
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • D.E. Koshland Jr., G. Némethy, and D. Filmer Comparison of experimental binding data and theoretical models in proteins containing subunits Biochemistry 5 1966 365 385
    • (1966) Biochemistry , vol.5 , pp. 365-385
    • Koshland Jr., D.E.1    Némethy, G.2    Filmer, D.3
  • 23
    • 17844378217 scopus 로고    scopus 로고
    • Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis
    • DOI 10.1038/nsmb901
    • D. Rivenzon-Segal, and S.G. Wolf A. Horovitz Sequential ATP-induced allosteric transitions of the cytoplasmic chaperonin containing TCP-1 revealed by EM analysis Nat. Struct. Mol. Biol. 12 2005 233 237 (Pubitemid 43079364)
    • (2005) Nature Structural and Molecular Biology , vol.12 , Issue.3 , pp. 233-237
    • Rivenzon-Segal, D.1    Wolf, S.G.2    Shimon, L.3    Willison, K.R.4    Horovitz, A.5
  • 25
    • 0034665864 scopus 로고    scopus 로고
    • A dynamic model for the allosteric mechanism of GroEL
    • J. Ma, and P.B. Sigler M. Karplus A dynamic model for the allosteric mechanism of GroEL J. Mol. Biol. 302 2000 303 313
    • (2000) J. Mol. Biol. , vol.302 , pp. 303-313
    • Ma, J.1    Sigler, P.B.2    Karplus, M.3
  • 26
    • 41049092674 scopus 로고    scopus 로고
    • Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL
    • DOI 10.1039/b717819k
    • C. Chennubhotla, Z. Yang, and I. Bahar Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL Mol. Biosyst. 4 2008 287 292 (Pubitemid 351422583)
    • (2008) Molecular BioSystems , vol.4 , Issue.4 , pp. 287-292
    • Chennubhotla, C.1    Yang, Z.2    Bahar, I.3
  • 27
    • 0037080323 scopus 로고    scopus 로고
    • Molecular mechanisms of chaperonin GroEL-GroES function
    • DOI 10.1021/bi011393x
    • O. Keskin, and I. Bahar R.L. Jernigan Molecular mechanisms of chaperonin GroEL-GroES function Biochemistry 41 2002 491 501 (Pubitemid 34062018)
    • (2002) Biochemistry , vol.41 , Issue.2 , pp. 491-501
    • Keskin, O.1    Bahar, I.2    Flatow, D.3    Covell, D.G.4    Jernigan, R.L.5
  • 28
    • 34848852941 scopus 로고    scopus 로고
    • Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations
    • DOI 10.1529/biophysj.107.105270
    • W. Zheng, B.R. Brooks, and D. Thirumalai Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations Biophys. J. 93 2007 2289 2299 (Pubitemid 47511128)
    • (2007) Biophysical Journal , vol.93 , Issue.7 , pp. 2289-2299
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 29
    • 61649124866 scopus 로고    scopus 로고
    • Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle
    • R. Tehver, J. Chen, and D. Thirumalai Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle J. Mol. Biol. 387 2009 390 406
    • (2009) J. Mol. Biol. , vol.387 , pp. 390-406
    • Tehver, R.1    Chen, J.2    Thirumalai, D.3
  • 30
    • 41449090651 scopus 로고    scopus 로고
    • Multiple States of a Nucleotide-Bound Group 2 Chaperonin
    • DOI 10.1016/j.str.2008.01.016, PII S0969212608000701
    • D.K. Clare, and S. Stagg H.R. Saibil Multiple states of a nucleotide-bound group 2 chaperonin Structure 16 2008 528 534 (Pubitemid 351458705)
    • (2008) Structure , vol.16 , Issue.4 , pp. 528-534
    • Clare, D.K.1    Stagg, S.2    Quispe, J.3    Farr, G.W.4    Horwich, A.L.5    Saibil, H.R.6
  • 31
    • 0037285752 scopus 로고    scopus 로고
    • A core-weighted fitting method for docking atomic structures into low-resolution maps: Application to cryo-electron microscopy
    • DOI 10.1016/S1047-8477(02)00570-1, PII S1047847702005701
    • X. Wu, and J.L. Milne B.R. Brooks A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy J. Struct. Biol. 141 2003 63 76 (Pubitemid 36269107)
    • (2003) Journal of Structural Biology , vol.141 , Issue.1 , pp. 63-76
    • Wu, X.1    Milne, J.L.S.2    Borgnia, M.J.3    Rostapshov, A.V.4    Subramaniam, S.5    Brooks, B.R.6
  • 33
    • 0242509772 scopus 로고    scopus 로고
    • Self-guided Langevin dynamics simulation method
    • X. Wu, and B.R. Brooks Self-guided Langevin dynamics simulation method Chem. Phys. Lett. 381 2003 512 518
    • (2003) Chem. Phys. Lett. , vol.381 , pp. 512-518
    • Wu, X.1    Brooks, B.R.2
  • 34
    • 0037375367 scopus 로고    scopus 로고
    • Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials
    • DOI 10.1002/prot.10330
    • S.A. Hassan, and E.L. Mehler H. Weinstein Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials Proteins 51 2003 109 125 (Pubitemid 36293037)
    • (2003) Proteins: Structure, Function and Genetics , vol.51 , Issue.1 , pp. 109-125
    • Hassan, S.A.1    Mehler, E.L.2    Zhang, D.3    Weinstein, H.4
  • 35
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 77 1996 1905 1908 (Pubitemid 126625816)
    • (1996) Physical Review Letters , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.M.1
  • 36
    • 33646742004 scopus 로고    scopus 로고
    • Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
    • W. Zheng, B.R. Brooks, and D. Thirumalai Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations Proc. Natl. Acad. Sci. USA 103 2006 7664 7669
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 7664-7669
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 37
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • DOI 10.1002/prot.340230410
    • O. Marques, and Y.-H. Sanejouand Hinge-bending motion in citrate synthase arising from normal mode calculations Proteins 23 1995 557 560 (Pubitemid 26009518)
    • (1995) Proteins: Structure, Function and Genetics , vol.23 , Issue.4 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.-H.2
  • 38
    • 0000216012 scopus 로고
    • Collective protein dynamics and nuclear spin relaxation
    • R. Brüschweiler Collective protein dynamics and nuclear spin relaxation J. Chem. Phys. 102 1995 3396 3403
    • (1995) J. Chem. Phys. , vol.102 , pp. 3396-3403
    • Brüschweiler, R.1
  • 39
    • 17044427535 scopus 로고    scopus 로고
    • Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved
    • W. Zheng, and B.R. Brooks D. Thirumalai Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved Structure 13 2005 565 577
    • (2005) Structure , vol.13 , pp. 565-577
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 40
    • 0842332836 scopus 로고    scopus 로고
    • NMR Studies on the Substrate-binding Domains of the Thermosome: Structural Plasticity in the Protrusion Region
    • DOI 10.1016/j.jmb.2003.12.035
    • M. Heller, and M. John H. Kessler NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region J. Mol. Biol. 336 2004 717 729 (Pubitemid 38183024)
    • (2004) Journal of Molecular Biology , vol.336 , Issue.3 , pp. 717-729
    • Heller, M.1    John, M.2    Coles, M.3    Bosch, G.4    Baumeister, W.5    Kessler, H.6
  • 41
    • 0032701797 scopus 로고    scopus 로고
    • Group II chaperonins: New TRiC(k)s and turns of a protein folding machine
    • DOI 10.1006/jmbi.1999.3008
    • I. Gutsche, L.O. Essen, and W. Baumeister Group II chaperonins: new TRiC(k)s and turns of a protein folding machine J. Mol. Biol. 293 1999 295 312 (Pubitemid 29516171)
    • (1999) Journal of Molecular Biology , vol.293 , Issue.2 , pp. 295-312
    • Gutsche, I.1    Essen, L.-O.2    Baumeister, W.3
  • 42
    • 0038737003 scopus 로고    scopus 로고
    • Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis
    • DOI 10.1016/S0092-8674(03)00307-6
    • A.S. Meyer, and J.R. Gillespie J. Frydman Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis Cell 113 2003 369 381 (Pubitemid 36556118)
    • (2003) Cell , vol.113 , Issue.3 , pp. 369-381
    • Meyer, A.S.1    Gillespie, J.R.2    Walther, D.3    Millet, I.S.4    Doniach, S.5    Frydman, J.6
  • 43
    • 78650980445 scopus 로고    scopus 로고
    • Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin
    • I.G. Muñoz, and H. Yébenes G. Montoya Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin Nat. Struct. Mol. Biol. 18 2011 14 19
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 14-19
    • Muñoz, I.G.1    Yébenes, H.2    Montoya, G.3
  • 44
    • 77951232896 scopus 로고    scopus 로고
    • Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT
    • M. Jayasinghe, C. Tewmey, and G. Stan Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT Proteins 78 2010 1254 1265
    • (2010) Proteins , vol.78 , pp. 1254-1265
    • Jayasinghe, M.1    Tewmey, C.2    Stan, G.3
  • 46
    • 0034669110 scopus 로고    scopus 로고
    • Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations
    • O. Llorca, and J. Martín-Benito J.M. Valpuesta Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations EMBO J. 19 2000 5971 5979
    • (2000) EMBO J. , vol.19 , pp. 5971-5979
    • Llorca, O.1    Martín-Benito, J.2    Valpuesta, J.M.3
  • 47
    • 45649083920 scopus 로고    scopus 로고
    • Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET
    • N. Papo, and Y. Kipnis A. Horovitz Concerted release of substrate domains from GroEL by ATP is demonstrated with FRET J. Mol. Biol. 380 2008 717 725
    • (2008) J. Mol. Biol. , vol.380 , pp. 717-725
    • Papo, N.1    Kipnis, Y.2    Horovitz, A.3
  • 49
    • 34547830871 scopus 로고    scopus 로고
    • Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: A lattice study
    • E. Jacob, A. Horovitz, and R. Unger Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study Bioinformatics 23 2007 i240 i248
    • (2007) Bioinformatics , vol.23
    • Jacob, E.1    Horovitz, A.2    Unger, R.3
  • 50
    • 77955282609 scopus 로고    scopus 로고
    • Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes
    • M. Amit, and S.J. Weisberg A. Horovitz Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes J. Mol. Biol. 401 2010 532 543
    • (2010) J. Mol. Biol. , vol.401 , pp. 532-543
    • Amit, M.1    Weisberg, S.J.2    Horovitz, A.3
  • 51
    • 66149129564 scopus 로고    scopus 로고
    • Coupling between normal modes drives protein conformational dynamics: Illustrations using allosteric transitions in myosin II
    • W. Zheng, and D. Thirumalai Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II Biophys. J. 96 2009 2128 2137
    • (2009) Biophys. J. , vol.96 , pp. 2128-2137
    • Zheng, W.1    Thirumalai, D.2
  • 52
    • 70349661903 scopus 로고    scopus 로고
    • Global motions of the nuclear pore complex: Insights from elastic network models
    • T.R. Lezon, A. Sali, and I. Bahar Global motions of the nuclear pore complex: insights from elastic network models PLoS Comput. Biol. 5 2009 e1000496
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000496
    • Lezon, T.R.1    Sali, A.2    Bahar, I.3
  • 53
    • 79952293131 scopus 로고    scopus 로고
    • Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase
    • A. Kravats, M. Jayasinghe, and G. Stan Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase Proc. Natl. Acad. Sci. USA 108 2011 2234 2239
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 2234-2239
    • Kravats, A.1    Jayasinghe, M.2    Stan, G.3
  • 55
    • 84874194443 scopus 로고    scopus 로고
    • POV-Ray Team Persistence of Vision Raytracer Williamstown, Victoria, Australia
    • POV-Ray Team POV-Ray 1991, 1997 Persistence of Vision Raytracer Williamstown, Victoria, Australia
    • POV-Ray 1991, 1997


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