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Volumn 43, Issue 24, 2004, Pages 7787-7797

Thermodynamics of binding to SH3 domains: The energetic impact of polyproline II (PII) helix formation

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; ENTHALPY; HYDROPHOBICITY; ISOTHERMS; MOLECULAR STRUCTURE; POLYPROPYLENES;

EID: 2942733479     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049752m     Document Type: Article
Times cited : (52)

References (48)
  • 2
    • 0032553012 scopus 로고    scopus 로고
    • RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef
    • Arold, S., O'Brien, R., Franken, P., Strub, M., Hoh, F., Dumas, C., and Ladbury, J. E. (1998) RT Loop Flexibility Enhances the Specificity of Src Family SH3 Domains for HIV-1 Nef, Biochemistry 37, 14683-14691.
    • (1998) Biochemistry , vol.37 , pp. 14683-14691
    • Arold, S.1    O'Brien, R.2    Franken, P.3    Strub, M.4    Hoh, F.5    Dumas, C.6    Ladbury, J.E.7
  • 3
    • 0034008847 scopus 로고    scopus 로고
    • Searching for specificity in SH domains
    • Ladbury, J. E., and Arold, S. (2000) Searching for specificity in SH domains, Chem. Biol. 7, R3-R8.
    • (2000) Chem. Biol. , vol.7
    • Ladbury, J.E.1    Arold, S.2
  • 4
    • 0028805516 scopus 로고
    • A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein
    • Lee, C., Leung, B., Lemmon, M. A., Zheng, J., Cowburn, D., Kuriyan, J., and Saksela, K. (1995) A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein, EMBO J. 14, 5006-5015.
    • (1995) EMBO J. , vol.14 , pp. 5006-5015
    • Lee, C.1    Leung, B.2    Lemmon, M.A.3    Zheng, J.4    Cowburn, D.5    Kuriyan, J.6    Saksela, K.7
  • 5
    • 0035798419 scopus 로고    scopus 로고
    • The role of backbone motions in ligand binding to the c-Src SH3 domain
    • Wang, C., Pawley, N. H., and Nicholson, L. K. (2001) The Role of Backbone Motions in Ligand Binding to the c-Src SH3 Domain, J. Mol. Biol. 313, 873-887.
    • (2001) J. Mol. Biol. , vol.313 , pp. 873-887
    • Wang, C.1    Pawley, N.H.2    Nicholson, L.K.3
  • 6
    • 0029753011 scopus 로고    scopus 로고
    • Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase
    • Renzoni, D. A., Pugh, D. J. R., Siligardi, G., Das, P., Rossi, C., Waterfield, M. D., Campbell, I. D., and Ladbury, J. E. (1996) Structural and Thermodynamic Characterization of the Interaction of the SH3 Domain from Fyn with the Proline-Rich Binding Site on the p85 Subunit of PI3-Kinase, Biochemistry 35, 15646-15653.
    • (1996) Biochemistry , vol.35 , pp. 15646-15653
    • Renzoni, D.A.1    Pugh, D.J.R.2    Siligardi, G.3    Das, P.4    Rossi, C.5    Waterfield, M.D.6    Campbell, I.D.7    Ladbury, J.E.8
  • 7
    • 0032555743 scopus 로고    scopus 로고
    • Crystal structure of the Abl-SH3 domain complexed with a designed high-affinity peptide ligand: Implications for SH3-ligand interactions
    • Pisabarro, M. T., Serrano, L., and Wilmanns, M. (1998) Crystal Structure of the Abl-SH3 Domain Complexed with a Designed High-Affinity Peptide Ligand: Implications for SH3-Ligand Interactions, J. Mol. Biol. 281, 513-521.
    • (1998) J. Mol. Biol. , vol.281 , pp. 513-521
    • Pisabarro, M.T.1    Serrano, L.2    Wilmanns, M.3
  • 8
    • 0037372297 scopus 로고    scopus 로고
    • The effect of the polyproline II (PPII) conformation on the denatured state entropy
    • Ferreon, J. C., and Hilser, V. J. (2003) The effect of the polyproline II (PPII) conformation on the denatured state entropy, Protein Sci. 12, 447-457.
    • (2003) Protein Sci. , vol.12 , pp. 447-457
    • Ferreon, J.C.1    Hilser, V.J.2
  • 9
    • 0037407208 scopus 로고    scopus 로고
    • Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of SEM-5 indicate cooperative conformational coupling
    • Ferreon, J. C., and Hilser, V. J. (2003) Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of SEM-5 indicate cooperative conformational coupling, Protein Sci. 12, 982-996.
    • (2003) Protein Sci. , vol.12 , pp. 982-996
    • Ferreon, J.C.1    Hilser, V.J.2
  • 11
    • 0027910431 scopus 로고
    • Association of Sos Ras exchange protein with Grb2 is implicated in tyrosine kinase signal transduction and transformation
    • Egan, S. E., Giddings, B. W., Brooks, M. W., Buday, L., Sizeland, A. M., and Weinberg, R. A. (1993) Association of Sos Ras exchange protein with Grb2 is implicated in tyrosine kinase signal transduction and transformation, Nature 363, 45-51.
    • (1993) Nature , vol.363 , pp. 45-51
    • Egan, S.E.1    Giddings, B.W.2    Brooks, M.W.3    Buday, L.4    Sizeland, A.M.5    Weinberg, R.A.6
  • 12
    • 0013298211 scopus 로고    scopus 로고
    • Solution structure, dynamics, and thermodynamics of the native state ensemble of the Sem-5 C-terminal SH3 domain
    • Ferreon, J. C., Volk, D. E., Luxon, B. A., Gorenstein, D. G., and Hilser, V. J. (2003) Solution Structure, Dynamics, and Thermodynamics of the Native State Ensemble of the Sem-5 C-terminal SH3 Domain, Biochemistry 42, 5582-5591.
    • (2003) Biochemistry , vol.42 , pp. 5582-5591
    • Ferreon, J.C.1    Volk, D.E.2    Luxon, B.A.3    Gorenstein, D.G.4    Hilser, V.J.5
  • 14
    • 0031670461 scopus 로고    scopus 로고
    • Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride
    • Fukada, H., and Takahashi, K. (1998) Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride, Proteins: Struct., Funct., Genet. 33, 159-166.
    • (1998) Proteins: Struct., Funct., Genet. , vol.33 , pp. 159-166
    • Fukada, H.1    Takahashi, K.2
  • 16
    • 0028148629 scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • Lim, W. A., Richards, F. M., and Fox, R. O. (1994) Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains, Nature 372, 375-379.
    • (1994) Nature , vol.372 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 17
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and Richards, F. M. (1971) The interpretation of protein structures: Estimation of static accessibility, J. Mol. Biol. 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 18
    • 0030905238 scopus 로고    scopus 로고
    • Structure-based thermodynamic analysis of HIV-1 protease inhibitors
    • Bardi, J. S., Luque, I., and Freire, E. (1997) Structure-based thermodynamic analysis of HIV-1 protease inhibitors, Biochemistry 36, 6588-6596.
    • (1997) Biochemistry , vol.36 , pp. 6588-6596
    • Bardi, J.S.1    Luque, I.2    Freire, E.3
  • 19
    • 0029958659 scopus 로고    scopus 로고
    • Structure-based thermodynamic scale of α-helix propensities in amino acids
    • Luque, I., Mayorga, O. L., and Freire, E. (1996) Structure-based thermodynamic scale of α-helix propensities in amino acids, Biochemistry 35, 13681-13688.
    • (1996) Biochemistry , vol.35 , pp. 13681-13688
    • Luque, I.1    Mayorga, O.L.2    Freire, E.3
  • 20
    • 0029957505 scopus 로고    scopus 로고
    • The enthalpy change in protein folding and binding: Refinement of parameters for structure-based calculations
    • Hilser, V. J., Gomez, J., and Freire, E. (1996) The enthalpy change in protein folding and binding: Refinement of parameters for structure-based calculations, Proteins: Struct., Funct., Genet. 26, 123-133.
    • (1996) Proteins: Struct., Funct., Genet. , vol.26 , pp. 123-133
    • Hilser, V.J.1    Gomez, J.2    Freire, E.3
  • 21
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding
    • D'Aquino, J. A., Gomez, J., Hilser, V. J., Lee, K. H., Amzel, L. M., and Freire, E. (1996) The magnitude of the backbone conformational entropy change in protein folding, Proteins 25, 143-156.
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1    Gomez, J.2    Hilser, V.J.3    Lee, K.H.4    Amzel, L.M.5    Freire, E.6
  • 23
    • 0028146012 scopus 로고
    • Structure based prediction of protein folding intermediates
    • Xie, D., and Freire, E. (1994) Structure based prediction of protein folding intermediates, J. Mol. Biol. 242, 62-80.
    • (1994) J. Mol. Biol. , vol.242 , pp. 62-80
    • Xie, D.1    Freire, E.2
  • 24
    • 0027991081 scopus 로고
    • Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
    • Lee, K. H., Xie, D., Freire, E., and Amzel, L. M. (1994) Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation, Proteins 20, 68-84.
    • (1994) Proteins , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 25
    • 0027980359 scopus 로고
    • Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states
    • Xie, D., and Freire, E. (1994) Molecular basis of cooperativity in protein folding. V. Thermodynamic and structural conditions for the stabilization of compact denatured states, Proteins 19, 291-301.
    • (1994) Proteins , vol.19 , pp. 291-301
    • Xie, D.1    Freire, E.2
  • 26
    • 0028127923 scopus 로고
    • Entropy in biological binding processes: Estimation of translational entropy loss
    • Murphy, K. P., Xie, D., Thompson, K. S., Amzel, L. M., and Freire, E. (1994) Entropy in biological binding processes: Estimation of translational entropy loss, Proteins 18, 63-67.
    • (1994) Proteins , vol.18 , pp. 63-67
    • Murphy, K.P.1    Xie, D.2    Thompson, K.S.3    Amzel, L.M.4    Freire, E.5
  • 27
    • 0027270199 scopus 로고
    • Structural thermodynamics: Prediction of protein stability and protein binding affinities
    • Freire, E. (1993) Structural thermodynamics: Prediction of protein stability and protein binding affinities, Arch. Biochem. Biophys. 303, 181-184.
    • (1993) Arch. Biochem. Biophys. , vol.303 , pp. 181-184
    • Freire, E.1
  • 28
    • 0027537127 scopus 로고
    • Structural energetics of peptide recognition: Angiotensin II/antibody binding
    • Murphy, K. P., Xie, D., Garcia, K. C., Amzel, L. M., and Freire, E. (1993) Structural energetics of peptide recognition: Angiotensin II/antibody binding, Proteins 15, 113-120.
    • (1993) Proteins , vol.15 , pp. 113-120
    • Murphy, K.P.1    Xie, D.2    Garcia, K.C.3    Amzel, L.M.4    Freire, E.5
  • 29
    • 0026649261 scopus 로고
    • Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates
    • Murphy, K. P., Bhakuni, V., Xie, D., and Freire, E. (1992) Molecular basis of cooperativity in protein folding. III. Structural identification of cooperative folding units and folding intermediates, J. Mol. Biol. 227, 293-306.
    • (1992) J. Mol. Biol. , vol.227 , pp. 293-306
    • Murphy, K.P.1    Bhakuni, V.2    Xie, D.3    Freire, E.4
  • 30
    • 0026756702 scopus 로고
    • Thermodynamics of structural stability and cooperative folding behavior in proteins
    • Murphy, K. P., and Freire, E. (1992) Thermodynamics of structural stability and cooperative folding behavior in proteins, Adv. Protein Chem. 43, 313-361.
    • (1992) Adv. Protein Chem. , vol.43 , pp. 313-361
    • Murphy, K.P.1    Freire, E.2
  • 31
    • 0026327183 scopus 로고
    • Molecular basis of cooperativity in protein folding
    • Freire, E., and Murphy, K. P. (1991) Molecular basis of cooperativity in protein folding, J. Mol. Biol. 222, 687-698.
    • (1991) J. Mol. Biol. , vol.222 , pp. 687-698
    • Freire, E.1    Murphy, K.P.2
  • 32
    • 0029080864 scopus 로고
    • Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin
    • Gómez, J., and Freire, E. (1995) Thermodynamic Mapping of the Inhibitor Site of the Aspartic Protease Endothiapepsin, J. Mol. Biol. 252, 337-350.
    • (1995) J. Mol. Biol. , vol.252 , pp. 337-350
    • Gómez, J.1    Freire, E.2
  • 33
    • 0027537127 scopus 로고
    • Structural energetics of peptide recognition: Angiotensin II/antibody binding
    • Murphy, K. P., Xie, D., Garcia, K. C., and Amzel, L. M. (1993) Structural energetics of peptide recognition: Angiotensin II/antibody binding, Proteins: Struct., Funct., Genet. 15, 113-120.
    • (1993) Proteins: Struct., Funct., Genet. , vol.15 , pp. 113-120
    • Murphy, K.P.1    Xie, D.2    Garcia, K.C.3    Amzel, L.M.4
  • 34
    • 0019889063 scopus 로고
    • Thermodynamics of protein association reactions: Forces contributing to stability
    • Ross, P., and Subramanian, S. (1982) Thermodynamics of protein association reactions: Forces contributing to stability, Biochemistry 20, 3096-3102.
    • (1982) Biochemistry , vol.20 , pp. 3096-3102
    • Ross, P.1    Subramanian, S.2
  • 35
    • 0027962645 scopus 로고
    • Two binding orientations for peptides to the Src SH3 domain: Development of a general model for SH3-ligand interactions
    • Feng, S., Chen, J. K., Yu, H., Simon, J. A., and Schreiber, S. L. (1994) Two Binding Orientations for Peptides to the Src SH3 Domain: Development of a General Model for SH3-Ligand Interactions, Science 266, 1241-1246.
    • (1994) Science , vol.266 , pp. 1241-1246
    • Feng, S.1    Chen, J.K.2    Yu, H.3    Simon, J.A.4    Schreiber, S.L.5
  • 36
    • 0027191192 scopus 로고
    • Solution structure and ligand-binding site of the SH3 domain of the p85α subunit of phosphatidylinositol 3-kinase
    • Booker, G. W., Gout, I., Downing, A. K., Driscoll, P. C., Boyd, J., Waterfield, M. D., and Campbell, I. D. (1993) Solution Structure and Ligand-Binding Site of the SH3 Domain of the p85α Subunit of Phosphatidylinositol 3-Kinase, Cell 73, 813-822.
    • (1993) Cell , vol.73 , pp. 813-822
    • Booker, G.W.1    Gout, I.2    Downing, A.K.3    Driscoll, P.C.4    Boyd, J.5    Waterfield, M.D.6    Campbell, I.D.7
  • 37
    • 0027102571 scopus 로고
    • Solution structure of the SH3 domain of Src and identification of its ligand-binding site
    • Yu, H., Rosen, M. K., Shin, T. B., Seidel-Dugan, C., Brugge, J. S., and Schreiber, S. L. (1992) Solution Structure of the SH3 Domain of Src and Identification of Its Ligand-Binding Site, Science 258, 1665-1667.
    • (1992) Science , vol.258 , pp. 1665-1667
    • Yu, H.1    Rosen, M.K.2    Shin, T.B.3    Seidel-Dugan, C.4    Brugge, J.S.5    Schreiber, S.L.6
  • 40
    • 0030580089 scopus 로고    scopus 로고
    • Structure based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
    • Hilser, V. J., and Freire, E. (1996) Structure Based Calculation of the Equilibrium Folding Pathway of Proteins. Correlation with Hydrogen Exchange Protection Factors, J. Mol. Biol. 262, 756-772.
    • (1996) J. Mol. Biol. , vol.262 , pp. 756-772
    • Hilser, V.J.1    Freire, E.2
  • 41
    • 0031042186 scopus 로고    scopus 로고
    • Predicting the equilibrium protein folding pathway: Structure-based analysis of staphylococcal nuclease
    • Hilser, V. J., and Freire, E. (1997) Predicting the Equilibrium Protein Folding Pathway: Structure-Based Analysis of Staphylococcal Nuclease, Proteins: Struct., Funct., Genet. 27, 171-183.
    • (1997) Proteins: Struct., Funct., Genet. , vol.27 , pp. 171-183
    • Hilser, V.J.1    Freire, E.2
  • 42
    • 0030993784 scopus 로고    scopus 로고
    • Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: Structural mapping of cooperative interactions
    • Hilser, V. J., Townsend, B. D., and Freire, E. (1997) Structure-Based Statistical Thermodynamic Analysis of T4 Lysozyme Mutants: Structural Mapping of Cooperative Interactions, Biophys. Chem. 64, 69-79.
    • (1997) Biophys. Chem. , vol.64 , pp. 69-79
    • Hilser, V.J.1    Townsend, B.D.2    Freire, E.3
  • 43
    • 0032544060 scopus 로고    scopus 로고
    • The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble
    • Hilser, V. J., Dowdy, D., Oas, T. G., and Freire, E. (1998) The Structural Distribution of Cooperative Interactions in Proteins: Analysis of the Native State Ensemble, Proc. Natl. Acad. Sci. U.S.A. 95, 9903-9908.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 9903-9908
    • Hilser, V.J.1    Dowdy, D.2    Oas, T.G.3    Freire, E.4
  • 44
    • 0034623978 scopus 로고    scopus 로고
    • Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR
    • Cordier, F., Wang, C., Grzesiek, S., and Nicholson, L. K. (2000) Ligand-Induced Strain in Hydrogen Bonds of the c-Src SH3 Domain Detected by NMR, J. Mol. Biol. 304, 497-505.
    • (2000) J. Mol. Biol. , vol.304 , pp. 497-505
    • Cordier, F.1    Wang, C.2    Grzesiek, S.3    Nicholson, L.K.4
  • 46
    • 0031692650 scopus 로고    scopus 로고
    • Left-handed polyproline II helix formation is (Very) locally driven
    • Creamer, T. P. (1998) Left-Handed Polyproline II Helix Formation Is (Very) Locally Driven, Proteins: Struct., Funct., Genet. 33, 218-226.
    • (1998) Proteins: Struct., Funct., Genet. , vol.33 , pp. 218-226
    • Creamer, T.P.1
  • 48
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of molecular structures
    • Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: A program for display and analysis of molecular structures, J. Mol. Graphics 14, 51-55.
    • (1996) J. Mol. Graphics , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3


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