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Volumn 6, Issue 5, 2010, Pages 352-358

The role of conformational entropy in molecular recognition by calmodulin

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN;

EID: 77951281285     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.347     Document Type: Article
Times cited : (227)

References (50)
  • 1
    • 0036424666 scopus 로고    scopus 로고
    • Structural basis of macromolecular recognition
    • DOI 10.1016/S0065-3233(02)61001-0
    • Wodak, S.J. & Janin, J. Structural basis of macromolecular recognition. Adv. Protein Chem. 61, 9-73 (2002). (Pubitemid 35303453)
    • (2002) Advances in Protein Chemistry , vol.61 , pp. 9-73
    • Wodak, S.J.1    Janin, J.2
  • 2
    • 0031058541 scopus 로고    scopus 로고
    • The statisticalthermodynamic basis for computation of binding affinities: A critical review
    • Gilson, M.K., Given, J.A., Bush, B.L. & McCammon, J.A. The statisticalthermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72, 1047-1069 (1997).
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 3
    • 34447108978 scopus 로고    scopus 로고
    • Water, water everywhere-except where it matters?
    • Homans, S.W. Water, water everywhere-except where it matters? Drug Discov. Today 12, 534-539 (2007).
    • (2007) Drug Discov. Today , vol.12 , pp. 534-539
    • Homans, S.W.1
  • 4
    • 0017884417 scopus 로고
    • The hydrophobic effect and the organization of living matter
    • Tanford, C. The hydrophobic effect and the organization of living matter. Science 200, 1012-1018 (1978). (Pubitemid 8346922)
    • (1978) Science , vol.200 , Issue.4345 , pp. 1012-1018
    • Tanford, C.1
  • 5
    • 0026416668 scopus 로고
    • Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
    • Sharp, K.A., Nicholls, A., Fine, R.F. & Honig, B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252, 106-109 (1991). (Pubitemid 21916946)
    • (1991) Science , vol.252 , Issue.5002 , pp. 106-109
    • Sharp, K.A.1    Nicholls, A.2    Fine, R.F.3    Honig, B.4
  • 6
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • DOI 10.1038/nature04162, PII N04162
    • Chandler, D. Interfaces and the driving force of hydrophobic assembly. Nature 437, 640-647 (2005). (Pubitemid 41486526)
    • (2005) Nature , vol.437 , Issue.7059 , pp. 640-647
    • Chandler, D.1
  • 7
    • 0001666112 scopus 로고
    • Entropy changes accompanying association reactions of proteins
    • Steinberg, I.Z. & Scheraga, H.A. Entropy changes accompanying association reactions of proteins. J. Biol. Chem. 238, 172-181 (1963).
    • (1963) J. Biol. Chem. , vol.238 , pp. 172-181
    • Steinberg, I.Z.1    Scheraga, H.A.2
  • 8
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus, M., Ichiye, T. & Pettitt, B.M. Configurational entropy of native proteins. Biophys. J. 52, 1083-1085 (1987).
    • (1987) Biophys. J. , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 9
    • 0023643422 scopus 로고
    • Genetic and structural analysis of the proteins stability problem
    • Matthews, B.W. Genetic and structural analysis of the proteins stability problem. Biochemistry 26, 6885-6888 (1987).
    • (1987) Biochemistry , vol.26 , pp. 6885-6888
    • Matthews, B.W.1
  • 10
    • 0033988897 scopus 로고    scopus 로고
    • Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex
    • Lee, A.L., Kinnear, S.A. & Wand, A.J. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat. Struct. Biol. 7, 72-77 (2000).
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 72-77
    • Lee, A.L.1    Kinnear, S.A.2    Wand, A.J.3
  • 11
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • Frederick, K.K., Marlow, M.S., Valentine, K.G. & Wand, A.J. Conformational entropy in molecular recognition by proteins. Nature 448, 325-329 (2007).
    • (2007) Nature , vol.448 , pp. 325-329
    • Frederick, K.K.1    Marlow, M.S.2    Valentine, K.G.3    Wand, A.J.4
  • 12
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
    • Igumenova, T.I., Frederick, K.K. & Wand, A.J. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem. Rev. 106, 1672-1699 (2006).
    • (2006) Chem. Rev. , vol.106 , pp. 1672-1699
    • Igumenova, T.I.1    Frederick, K.K.2    Wand, A.J.3
  • 13
    • 0030473440 scopus 로고    scopus 로고
    • Insights into the local residual entropy of proteins provided by NMR relaxation
    • Li, Z., Raychaudhuri, S. & Wand, A.J. Insights into the local residual entropy of proteins provided by NMR relaxation. Protein Sci. 5, 2647-2650 (1996). (Pubitemid 26424878)
    • (1996) Protein Science , vol.5 , Issue.12 , pp. 2647-2650
    • Li, Z.1    Raychaudhuri, S.2    Wand, A.J.3
  • 14
    • 0347949547 scopus 로고    scopus 로고
    • Regulation of cell cycle progression by calcium/calmodulin-dependent pathways
    • DOI 10.1210/er.2003-0008
    • Kahl, C.R. & Means, A.R. Regulation of cell cycle progression by calcium/ calmodulin-dependent pathways. Endocr. Rev. 24, 719-736 (2003). (Pubitemid 38067696)
    • (2003) Endocrine Reviews , vol.24 , Issue.6 , pp. 719-736
    • Kahl, C.R.1    Means, A.R.2
  • 15
    • 0003161862 scopus 로고    scopus 로고
    • Calmodulin target database
    • Yap, K.L. et al. Calmodulin target database. J. Struct. Funct. Genomics 1, 8-14 (2000).
    • (2000) J. Struct. Funct. Genomics , vol.1 , pp. 8-14
    • Yap, K.L.1
  • 16
    • 0029176895 scopus 로고
    • Measurement of 2H T1 and T1gamma,pi relaxation times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution
    • Muhandiram, D.R., Yamazaki, T., Sykes, B.D. & Kay, L.E. Measurement of 2H T1 and T1-relaxation-times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution. J. Am. Chem. Soc. 117, 11536-11544 (1995). (Pubitemid 3006291)
    • (1995) Journal of the American Chemical Society , vol.117 , Issue.46 , pp. 11536-11544
    • Muhandiram, D.R.1    Yamazaki, T.2    Sykes, B.D.3    Kay, L.E.4
  • 17
    • 33746224059 scopus 로고    scopus 로고
    • Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulinbinding domain
    • Marlow, M.S. & Wand, A.J. Conformational dynamics of calmodulin in complex with the calmodulin-dependent kinase kinase alpha calmodulinbinding domain. Biochemistry 45, 8732-8741 (2006).
    • (2006) Biochemistry , vol.45 , pp. 8732-8741
    • Marlow, M.S.1    Wand, A.J.2
  • 18
    • 33747508183 scopus 로고    scopus 로고
    • Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy
    • Frederick, K.K., Kranz, J.K. & Wand, A.J. Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy. Biochemistry 45, 9841-9848 (2006).
    • (2006) Biochemistry , vol.45 , pp. 9841-9848
    • Frederick, K.K.1    Kranz, J.K.2    Wand, A.J.3
  • 19
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559 (1982).
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 20
    • 53849092076 scopus 로고    scopus 로고
    • Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation
    • Frederick, K.K., Sharp, K.A., Warischalk, N. & Wand, A.J. Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation. J. Phys. Chem. B 112, 12095-12103 (2008).
    • (2008) J. Phys. Chem. B , vol.112 , pp. 12095-12103
    • Frederick, K.K.1    Sharp, K.A.2    Warischalk, N.3    Wand, A.J.4
  • 21
    • 0029149085 scopus 로고
    • Molecular and structural basis of target recognition by calmodulin
    • Crivici, A. & Ikura, M. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24, 85-116 (1995).
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 85-116
    • Crivici, A.1    Ikura, M.2
  • 22
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormonereceptor interface
    • Clackson, T. & Wells, J.A. A hot spot of binding energy in a hormonereceptor interface. Science 267, 383-386 (1995).
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.A.2
  • 23
    • 0037137214 scopus 로고    scopus 로고
    • Temperature dependence of the internal dynamics of a calmodulin-peptide complex
    • DOI 10.1021/bi026380d
    • Lee, A.L., Sharp, K.A., Kranz, J.K., Song, X.J. & Wand, A.J. Temperature dependence of the internal dynamics of a calmodulin-peptide complex. Biochemistry 41, 13814-13825 (2002). (Pubitemid 35332720)
    • (2002) Biochemistry , vol.41 , Issue.46 , pp. 13814-13825
    • Lee, A.L.1    Sharp, K.A.2    Kranz, J.K.3    Song, X.-J.4    Wand, A.J.5
  • 24
    • 33744908076 scopus 로고    scopus 로고
    • Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy
    • DOI 10.1021/cr0404287
    • Palmer, A.G.I. & Massi, F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700-1719 (2006). (Pubitemid 43840531)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1700-1719
    • Palmer III, A.G.1    Massi, F.2
  • 26
    • 0037450635 scopus 로고    scopus 로고
    • Structural basis for endothelial nitric oxide synthase binding to calmodulin
    • DOI 10.1093/emboj/cdg078
    • Aoyagi, M., Arvai, A.S., Tainer, J.A. & Getzoff, E.D. Structural basis for endothelial nitric oxide synthase binding to calmodulin. EMBO J. 22, 766-775 (2003). (Pubitemid 36227779)
    • (2003) EMBO Journal , vol.22 , Issue.4 , pp. 766-775
    • Aoyagi, M.1    Arvai, A.S.2    Tainer, J.A.3    Getzoff, E.D.4
  • 27
    • 0026794065 scopus 로고
    • Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex
    • Meador, W.E., Means, A.R. & Quiocho, F.A. Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science 257, 1251-1255 (1992).
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 28
    • 2242474818 scopus 로고    scopus 로고
    • Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: Studies of the kinase activation mechanism
    • Clapperton, J.A., Martin, S.R., Smerdon, S.J., Gamblin, S.J. & Bayley, P.M. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism. Biochemistry 41, 14669-14679 (2002).
    • (2002) Biochemistry , vol.41 , pp. 14669-14679
    • Clapperton, J.A.1    Martin, S.R.2    Smerdon, S.J.3    Gamblin, S.J.4    Bayley, P.M.5
  • 30
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding
    • D'Aquino, J.A. et al. The magnitude of the backbone conformational entropy change in protein folding. Proteins 25, 143-156 (1996).
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1
  • 31
    • 25444519195 scopus 로고    scopus 로고
    • Backbone and side chain dynamics of mutant calmodulin-peptide complexes
    • Igumenova, T.I., Lee, A.L. & Wand, A.J. Backbone and side chain dynamics of mutant calmodulin-peptide complexes. Biochemistry 44, 12627-12639 (2005).
    • (2005) Biochemistry , vol.44 , pp. 12627-12639
    • Igumenova, T.I.1    Lee, A.L.2    Wand, A.J.3
  • 32
    • 0023657949 scopus 로고
    • Hydrophobic cluster analysis: An efficient new way to compare and analyse amino acid sequences
    • Gaboriaud, C., Bissery, V., Benchetrit, T. & Mornon, J.P. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 224, 149-155 (1987).
    • (1987) FEBS Lett. , vol.224 , pp. 149-155
    • Gaboriaud, C.1    Bissery, V.2    Benchetrit, T.3    Mornon, J.P.4
  • 33
    • 33750624445 scopus 로고    scopus 로고
    • Ionic volumes in solution
    • DOI 10.1016/j.bpc.2006.04.013, PII S030146220600127X
    • Marcus, Y. Ionic volumes in solution. Biophys. Chem. 124, 200-207 (2006). (Pubitemid 44692361)
    • (2006) Biophysical Chemistry , vol.124 , Issue.3 , pp. 200-207
    • Marcus, Y.1
  • 34
    • 0037176906 scopus 로고    scopus 로고
    • Dissection of the pathway of molecular recognition by calmodulin
    • Kranz, J.K., Flynn, P.F., Fuentes, E.J. & Wand, A.J. Dissection of the pathway of molecular recognition by calmodulin. Biochemistry 41, 2599-2608 (2002).
    • (2002) Biochemistry , vol.41 , pp. 2599-2608
    • Kranz, J.K.1    Flynn, P.F.2    Fuentes, E.J.3    Wand, A.J.4
  • 35
    • 4043156208 scopus 로고    scopus 로고
    • Direct determination of vibrational density of states change on ligand binding to a protein
    • Balog, E. et al. Direct determination of vibrational density of states change on ligand binding to a protein. Phys. Rev. Lett. 93, 028103 (2004).
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 028103
    • Balog, E.1
  • 36
    • 0028247281 scopus 로고
    • Side-chain entropy and packing in proteins
    • Bromberg, S. & Dill, K.A. Side-chain entropy and packing in proteins. Protein Sci. 3, 997-1009 (1994). (Pubitemid 24209892)
    • (1994) Protein Science , vol.3 , Issue.7 , pp. 997-1009
    • Bromberg, S.1    Dill, K.A.2
  • 37
    • 0028956081 scopus 로고
    • The energetics and dynamics of molecular recognition by calmodulin
    • Ehrhardt, M.R., Urbauer, J.L. & Wand, A.J. The energetics and dynamics of molecular recognition by calmodulin. Biochemistry 34, 2731-2738 (1995).
    • (1995) Biochemistry , vol.34 , pp. 2731-2738
    • Ehrhardt, M.R.1    Urbauer, J.L.2    Wand, A.J.3
  • 38
    • 0036468397 scopus 로고    scopus 로고
    • Coupling of folding and binding for unstructured proteins
    • Dyson, H.J. & Wright, P.E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12, 54-60 (2002).
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 54-60
    • Dyson, H.J.1    Wright, P.E.2
  • 39
    • 0032479048 scopus 로고    scopus 로고
    • 13C NMR relaxation data
    • DOI 10.1021/ja972215n
    • Chatfield, D.C., Szabo, A. & Brooks, B.R. Molecular dynamics of staphylococcal nuclease: comparison of simulation with 15N and 13C NMR relaxation data. J. Am. Chem. Soc. 120, 5301-5311 (1998). (Pubitemid 28328893)
    • (1998) Journal of the American Chemical Society , vol.120 , Issue.21 , pp. 5301-5311
    • Chatfield, D.C.1    Szabo, A.2    Brooks, B.R.3
  • 40
    • 0037457815 scopus 로고    scopus 로고
    • Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics
    • Prabhu, N.V., Lee, A.L., Wand, A.J. & Sharp, K.A. Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry 42, 562-570 (2003).
    • (2003) Biochemistry , vol.42 , pp. 562-570
    • Prabhu, N.V.1    Lee, A.L.2    Wand, A.J.3    Sharp, K.A.4
  • 41
    • 35948943745 scopus 로고    scopus 로고
    • Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: Application to the AMBER99SB force field
    • Showalter, S.A. & Brüschweiler, R. Validation of molecular dynamics simulations of biomolecules using NMR spin relaxation as benchmarks: application to the AMBER99SB force field. J. Chem. Theory Comput. 3, 961-975 (2007).
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 961-975
    • Showalter, S.A.1    Brüschweiler, R.2
  • 42
    • 67650529401 scopus 로고    scopus 로고
    • A dictionary for protein side-chain entropies from NMR order parameters
    • Li, D.W. & Brüschweiler, R. A dictionary for protein side-chain entropies from NMR order parameters. J. Am. Chem. Soc. 131, 7226-7227 (2009).
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7226-7227
    • Li, D.W.1    Brüschweiler, R.2
  • 43
    • 0037202183 scopus 로고    scopus 로고
    • Contact model for the prediction of NMR N-H order parameters in globular proteins
    • DOI 10.1021/ja027847a
    • Zhang, F. & Brüschweiler, R. Contact model for the prediction of NMR N-H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654-12655 (2002). (Pubitemid 35215977)
    • (2002) Journal of the American Chemical Society , vol.124 , Issue.43 , pp. 12654-12655
    • Zhang, F.1    Bruschweiler, R.2
  • 44
    • 63749108613 scopus 로고    scopus 로고
    • In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides
    • Li, D.W. & Brüschweiler, R. In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides. Phys. Rev. Lett. 102, 118108 (2009).
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 118108
    • Li, D.W.1    Brüschweiler, R.2
  • 45
    • 64049102289 scopus 로고    scopus 로고
    • Binding of small-molecular ligands to proteins: "What you see" is not always "what you get"
    • Mobley, D.L. & Dill, K.A. Binding of small-molecular ligands to proteins: "What you see" is not always "What you get". Structure 17, 489-498 (2009).
    • (2009) Structure , vol.17 , pp. 489-498
    • Mobley, D.L.1    Dill, K.A.2
  • 46
    • 0037053380 scopus 로고    scopus 로고
    • A direct test of the reductionist approach to structural studies of calmodulin activity: Relevance of peptide models of target proteins
    • Kranz, J.K., Lee, E.K., Nairn, A.C. & Wand, A.J. A direct test of the reductionist approach to structural studies of calmodulin activity: relevance of peptide models of target proteins. J. Biol. Chem. 277, 16351-16354 (2002).
    • (2002) J. Biol. Chem. , vol.277 , pp. 16351-16354
    • Kranz, J.K.1    Lee, E.K.2    Nairn, A.C.3    Wand, A.J.4
  • 47
    • 0024402002 scopus 로고
    • Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporine A
    • Dellwo, M.J. & Wand, A.J. Model-independent and model-dependent analysis of the global and internal dynamics of cyclosporine A. J. Am. Chem. Soc. 111, 4571-4578 (1989).
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 4571-4578
    • Dellwo, M.J.1    Wand, A.J.2
  • 48
    • 0034809982 scopus 로고    scopus 로고
    • Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: Application to methionine residues in a cavity mutant of T4 lysozyme
    • DOI 10.1021/ja004179p
    • Skrynnikov, N.R., Mulder, F.A.A., Hon, B., Dahlquist, F.W. & Kay, L.E. Probing slow time scale dynamics at methyl-containing side chains in proteins by relaxation dispersion NMR measurements: application to methionine residues in a cavity mutant of T4 lysozyme. J. Am. Chem. Soc. 123, 4556-4566 (2001). (Pubitemid 32923384)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.19 , pp. 4556-4566
    • Skrynnikov, N.R.1    Mulder, F.A.A.2    Hon, B.3    Dahlquist, F.W.4    Kay, L.E.5
  • 49
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
    • (1994) Acta Crystallogr. D Biol. Crystallogr. , vol.50 , pp. 760-763


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