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Volumn 135, Issue 17, 2011, Pages

Identification of key residues for protein conformational transition using elastic network model

Author keywords

[No Author keywords available]

Indexed keywords

BINDING CLEFTS; CONFORMATIONAL TRANSITIONS; COOPERATIVE MOTION; DNA POLYMERASE; ELASTIC NETWORK MODELS; FREE-ENERGY DIFFERENCE; FUNCTIONAL SITES; HEAT SHOCK PROTEIN 70; NUCLEOTIDE-BINDING DOMAIN; SUB-DOMAINS; SUBSTRATE-BINDING SITES; THERMODYNAMIC METHODS;

EID: 80855134367     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3651480     Document Type: Article
Times cited : (27)

References (67)
  • 3
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • DOI 10.1038/nature06522, PII NATURE06522
    • K. Henzler-Wildman and D. Kern, Nature (London) 450, 964 (2007). 10.1038/nature06522 (Pubitemid 350273626)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 12
    • 1242339659 scopus 로고    scopus 로고
    • A Family of Evolution-Entropy Hybrid Methods for Ranking Protein Residues by Importance
    • DOI 10.1016/j.jmb.2003.12.078
    • I. Mihalek, I. Res, and O. Lichtarge, J. Mol. Biol. 336, 1265 (2004). 10.1016/j.jmb.2003.12.078 (Pubitemid 38229712)
    • (2004) Journal of Molecular Biology , vol.336 , Issue.5 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 13
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • DOI 10.1093/bioinformatics/btm270
    • J. A. Capra and M. Singh, Bioinformatics 23, 1875 (2007). 10.1093/bioinformatics/btm270 (Pubitemid 47299827)
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 15
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • DOI 10.1126/science.286.5438.295
    • S. W. Lockless and R. Ranganathan, Science 286, 295 (1999). 10.1126/science.286.5438.295 (Pubitemid 29484693)
    • (1999) Science , vol.286 , Issue.5438 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 17
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in RXR heterodimers
    • DOI 10.1016/S0092-8674(04)00119-9, PII S0092867404001199
    • A. I. Shulman, C. Larson, D. J. Mangelsdorf, and R. Ranganathan, Cell 116, 417 (2004). 10.1016/S0092-8674(04)00119-9 (Pubitemid 38366318)
    • (2004) Cell , vol.116 , Issue.3 , pp. 417-429
    • Shulman, A.I.1    Larson, C.2    Mangelsdorf, D.J.3    Ranganathan, R.4
  • 19
    • 33749055796 scopus 로고    scopus 로고
    • Markov propagation of allosteric effects in biomolecular systems: Application to GroEL-GroES
    • DOI 10.1038/msb4100075, PII MSB4100075
    • C. Chennubhotla and I. Bahar, Mol. Syst. Biol. 2, 36 (2006). 10.1038/msb4100075 (Pubitemid 46061051)
    • (2006) Molecular Systems Biology , vol.2 , pp. 36
    • Chennubhotla, C.1    Bahar, I.2
  • 20
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • DOI 10.1038/msb4100063, PII M4100063, msb4100063
    • A. Del Sol, H. Fujihashi, D. Amoros, and R. Nussinov, Mol. Syst. Biol. 2, 2006.0019 (2006). 10.1038/msb4100063 (Pubitemid 43948162)
    • (2006) Molecular Systems Biology , vol.2 , pp. 20060019
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 22
    • 33749029273 scopus 로고    scopus 로고
    • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    • DOI 10.1002/prot.21146
    • K. Sharp and J. J. Skinner, Proteins 65, 347 (2006). 10.1002/prot.21146 (Pubitemid 44454109)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.2 , pp. 347-361
    • Sharp, K.1    Skinner, J.J.2
  • 23
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • DOI 10.1016/j.jmb.2005.05.043, PII S002228360500598X
    • N. Ota and D. A. Agard, J. Mol. Biol. 351, 345 (2005). 10.1016/j.jmb.2005.05.043 (Pubitemid 41007753)
    • (2005) Journal of Molecular Biology , vol.351 , Issue.2 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 27
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes of elastic network models?
    • DOI 10.1529/biophysj.106.095927
    • L. Yang, G. Song, and R. L. Jernigan, Biophys. J. 93, 920 (2007). 10.1529/biophysj.106.095927 (Pubitemid 47219784)
    • (2007) Biophysical Journal , vol.93 , Issue.3 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 29
    • 33846829648 scopus 로고    scopus 로고
    • Analysis of domain movements in glutamine-binding protein with simple models
    • DOI 10.1529/biophysj.106.086512
    • J. G. Su, X. Jiao, T. G. Sun, C. H. Li, W. Z. Chen, and C. X. Wang, Biophys. J. 92, 1326 (2007). 10.1529/biophysj.106.086512 (Pubitemid 46203193)
    • (2007) Biophysical Journal , vol.92 , Issue.4 , pp. 1326-1335
    • Ji, G.S.1    Jiao, X.2    Ting, G.S.3    Chun, H.L.4    Wei, Z.C.5    Cun, X.W.6
  • 34
    • 20444409186 scopus 로고    scopus 로고
    • Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes
    • DOI 10.1016/j.str.2005.03.015, PII S096921260500167X
    • L. Yang, and I. Bahar, Structure 13, 893 (2005). 10.1016/j.str.2005.03. 015 (Pubitemid 40804392)
    • (2005) Structure , vol.13 , Issue.6 , pp. 893-904
    • Yang, L.-W.1    Bahar, I.2
  • 35
    • 77956309711 scopus 로고    scopus 로고
    • 10.1016/j.str.2010.06.013
    • A. Dutta and I. Bahar, Structure 18, 1140 (2010). 10.1016/j.str.2010.06. 013
    • (2010) Structure , vol.18 , pp. 1140
    • Dutta, A.1    Bahar, I.2
  • 37
  • 38
    • 61849151934 scopus 로고    scopus 로고
    • 10.1103/PhysRevLett.102.088103
    • T. Haliloglu and B. Erman, Phys. Rev. Lett. 102, 088103 (2009). 10.1103/PhysRevLett.102.088103
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 088103
    • Haliloglu, T.1    Erman, B.2
  • 41
    • 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, Biophys. J. 93, 2289 (2007). 10.1529/biophysj.107.105270 (Pubitemid 47511128)
    • (2007) Biophysical Journal , vol.93 , Issue.7 , pp. 2289-2299
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 45
    • 28844456158 scopus 로고    scopus 로고
    • Allostery in a coarse-grained model of protein dynamics
    • DOI 10.1103/PhysRevLett.95.198103, 198103
    • D. Ming and M. E. Wall, Phys. Rev. Lett. 95, 198103 (2005). 10.1103/PhysRevLett.95.198103 (Pubitemid 41777245)
    • (2005) Physical Review Letters , vol.95 , Issue.19 , pp. 1-4
    • Ming, D.1    Wall, M.E.2
  • 46
    • 33846234709 scopus 로고    scopus 로고
    • 10.1063/1.2345620
    • M. E. Wall, AIP Conf. Proc. 851, 16 (2006). 10.1063/1.2345620
    • (2006) AIP Conf. Proc. , vol.851 , pp. 16
    • Wall, M.E.1
  • 47
    • 41449115497 scopus 로고    scopus 로고
    • Fast dynamics perturbation analysis for prediction of protein functional sites
    • DOI 10.1186/1472-6807-8-5
    • D. Ming, J. D. Cohn, and M. E. Wall, BMC Struct. Biol. 8, 5 (2008). 10.1186/1472-6807-8-5 (Pubitemid 351457968)
    • (2008) BMC Structural Biology , vol.8 , pp. 5
    • Ming, D.1    Cohn, J.D.2    Wall, M.E.3
  • 48
    • 0032489016 scopus 로고    scopus 로고
    • The Hsp70 and Hsp60 chaperone machines
    • DOI 10.1016/S0092-8674(00)80928-9
    • B. Bukau and A. L. Horwich, Cell 92, 351 (1998). 10.1016/S0092-8674(00) 80928-9 (Pubitemid 28093013)
    • (1998) Cell , vol.92 , Issue.3 , pp. 351-366
    • Bukau, B.1    Horwich, A.L.2
  • 53
    • 0025100372 scopus 로고
    • Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein
    • DOI 10.1038/346623a0
    • K. M. Flaherty, C. Deluca-Flaherty, and D. B. McKay, Nature (London) 346, 623 (1990). 10.1038/346623a0 (Pubitemid 20266393)
    • (1990) Nature , vol.346 , Issue.6285 , pp. 623-628
    • Flaherty, K.M.1    DeLuca-Flaherty, C.2    McKay, D.B.3
  • 59
    • 0033578346 scopus 로고    scopus 로고
    • Mapping the role of active site residues for transducing an ATP-induced conformational change in the bovine 70-kDa heat shock cognate protein
    • DOI 10.1021/bi990816g
    • E. R. Johnson and D. B. McKay, Biochemistry 38, 10823 (1999). 10.1021/bi990816g (Pubitemid 29404415)
    • (1999) Biochemistry , vol.38 , Issue.33 , pp. 10823-10830
    • Johnson, E.R.1    McKay, D.B.2
  • 60
    • 31544442176 scopus 로고    scopus 로고
    • Allosteric regulation of Hsp70 chaperones by a proline switch
    • DOI 10.1016/j.molcel.2005.12.017, PII S1097276505019003
    • M. Vogel, B. Bukau, and M. P. Mayer, Mol. Cell. 21, 359 (2006). 10.1016/j.molcel.2005.12.017 (Pubitemid 43163531)
    • (2006) Molecular Cell , vol.21 , Issue.3 , pp. 359-367
    • Vogel, M.1    Bukau, B.2    Mayer, M.P.3
  • 61
    • 0029817866 scopus 로고    scopus 로고
    • Crystal structures of human DNA polymerase β complexed with DNA: Implications for catalytic mechanism, processivity, and fidelity
    • DOI 10.1021/bi952955d
    • H. Pelletier, M. R. Sawaya, W. Wolfle, S. H. Wilson, and J. Kraut, Biochemistry 35, 1 2742 (1996). 10.1021/bi952955d (Pubitemid 26337329)
    • (1996) Biochemistry , vol.35 , Issue.39 , pp. 12742-12761
    • Pelletier, H.1    Sawaya, M.R.2    Wolfle, W.3    Wilson, S.H.4    Kraut, J.5
  • 64
    • 21244506296 scopus 로고    scopus 로고
    • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues
    • DOI 10.1529/biophysj.104.051342
    • T. Haliloglu, O. Keskin, B. Ma, and R. Nussinov, Biophy. J. 88, 1552 (2005). 10.1529/biophysj.104.051342 (Pubitemid 40976173)
    • (2005) Biophysical Journal , vol.88 , Issue.3 , pp. 1552-1559
    • Haliloglu, T.1    Keskin, O.2    Ma, B.3    Nussinov, R.4
  • 66
    • 0346492917 scopus 로고    scopus 로고
    • Folding core predictions from network models of proteins
    • DOI 10.1016/j.polymer.2003.10.080
    • A. J. Rader, and I. Bahar, Polymer 45, 659 (2004). 10.1016/j.polymer. 2003.10.080 (Pubitemid 38082199)
    • (2004) Polymer , vol.45 , Issue.2 , pp. 659-668
    • Rader, A.J.1    Bahar, I.2


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