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Volumn 336, Issue 2, 2004, Pages 527-537

Thermodynamic Dissection of the Binding Energetics of Proline-rich Peptides to the Abl-SH3 Domain: Implications for Rational Ligand Design

Author keywords

Binding energetics; Calorimetry; Ligand design; SH3 domains; Water mediated interactions

Indexed keywords

ABELSON KINASE; ALANYLPROLYLSERYLTYROSYLSERYLPROLYLPROLYLPROLYLPROLYLPROLINE; LIGAND; PEPTIDE; PROTEIN; PROTEIN SH3; UNCLASSIFIED DRUG; WATER;

EID: 0742306902     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.030     Document Type: Article
Times cited : (58)

References (46)
  • 1
    • 0033950079 scopus 로고    scopus 로고
    • The importance of being proline: The interaction of proline-rich motifs in signaling proteins with their cognate domains
    • Kay B.K., Williamson M.P., Sudol M. The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J. 232:2000;231-241.
    • (2000) FASEB J. , vol.232 , pp. 231-241
    • Kay, B.K.1    Williamson, M.P.2    Sudol, M.3
  • 2
    • 0033550310 scopus 로고    scopus 로고
    • SH3 domains with high affinity and engineered ligand specificities targeted to HIV-1 Nef
    • Hiipakka M., Poikonen K., Saksela K. SH3 domains with high affinity and engineered ligand specificities targeted to HIV-1 Nef. J. Mol. Biol. 293:1999;1097-1106.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1097-1106
    • Hiipakka, M.1    Poikonen, K.2    Saksela, K.3
  • 3
    • 0033544383 scopus 로고    scopus 로고
    • The conserved core of human immunodeficiency virus type 1 Nef Is essential for association with Lck and for enhanced viral replication in T-lymphocytes
    • Cheng H., Hoxie J., Parks W.P. The conserved core of human immunodeficiency virus type 1 Nef Is essential for association with Lck and for enhanced viral replication in T-lymphocytes. Virology. 264:1999;5-15.
    • (1999) Virology , vol.264 , pp. 5-15
    • Cheng, H.1    Hoxie, J.2    Parks, W.P.3
  • 4
    • 0034773599 scopus 로고    scopus 로고
    • SH2 and SH3 domains as targets for anti-proliferative agents
    • Vidal M., Gigoux V., Garbay C. SH2 and SH3 domains as targets for anti-proliferative agents. Crit. Rev. Oncol. Hematol. 40:2001;175-186.
    • (2001) Crit. Rev. Oncol. Hematol. , vol.40 , pp. 175-186
    • Vidal, M.1    Gigoux, V.2    Garbay, C.3
  • 5
    • 0037154214 scopus 로고    scopus 로고
    • Overexpression of the N-terminal domain of TSG-101 inhibits HIV-1 budding by blocking late domain function
    • Demirov D.G., Ono A., Orenstein J.M., Freed E.O. Overexpression of the N-terminal domain of TSG-101 inhibits HIV-1 budding by blocking late domain function. Proc. Natl Acad. Sci USA. 99:2002;955-960.
    • (2002) Proc. Natl Acad. Sci USA , vol.99 , pp. 955-960
    • Demirov, D.G.1    Ono, A.2    Orenstein, J.M.3    Freed, E.O.4
  • 6
    • 0035658023 scopus 로고    scopus 로고
    • HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 sites of particle assembly to facilitate egress
    • Martin-Serrano J., Zang T., Bieniasz P.D. HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 sites of particle assembly to facilitate egress. Nature Med. 7:2001;1313-1319.
    • (2001) Nature Med. , vol.7 , pp. 1313-1319
    • Martin-Serrano, J.1    Zang, T.2    Bieniasz, P.D.3
  • 7
    • 0036386853 scopus 로고    scopus 로고
    • A dipalmitoyl peptide that binds SH3 domain, disturbs intracellular signal transduction, and inhibits tumor growth in vivo
    • Lee K.-Y., Yoon J.H., Kim M., Roh S., Lee Y.-S., Seong B.-L., Kim K. A dipalmitoyl peptide that binds SH3 domain, disturbs intracellular signal transduction, and inhibits tumor growth in vivo. Biochem. Biophys. Res. Commun. 296:2002;434-442.
    • (2002) Biochem. Biophys. Res. Commun. , vol.296 , pp. 434-442
    • Lee, K.-Y.1    Yoon, J.H.2    Kim, M.3    Roh, S.4    Lee, Y.-S.5    Seong, B.-L.6    Kim, K.7
  • 8
    • 0035997943 scopus 로고    scopus 로고
    • A mammalian two-hybrid screening system for inhibitors of interaction between HIV Nef and the cellular tyrosine kinase Hck
    • Murakami Y., Fukazawa H., Kobatake T., Yamagoe S., Takebe Y., Tobiume M., et al. A mammalian two-hybrid screening system for inhibitors of interaction between HIV Nef and the cellular tyrosine kinase Hck. Antiviral Res. 55:2002;161-168.
    • (2002) Antiviral Res. , vol.55 , pp. 161-168
    • Murakami, Y.1    Fukazawa, H.2    Kobatake, T.3    Yamagoe, S.4    Takebe, Y.5    Tobiume, M.6
  • 9
    • 0035919704 scopus 로고    scopus 로고
    • Inhibition of cellular functions of HIV-1 Nef by artificial SH3 domains
    • Hiipakka M., Huotari P., Manninen A., Renkema G.H., Saksela K. Inhibition of cellular functions of HIV-1 Nef by artificial SH3 domains. Virology. 286:2001;152-159.
    • (2001) Virology , vol.286 , pp. 152-159
    • Hiipakka, M.1    Huotari, P.2    Manninen, A.3    Renkema, G.H.4    Saksela, K.5
  • 10
    • 0032509175 scopus 로고    scopus 로고
    • Exploiting the basis of proline recognition by SH3 and WW domains: Design of N-substituted inhibitors
    • Nguyen J.T., Turck C.W., Cohen F.E., Zuckermann R.N., Lim W.A. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science. 282:1998;2088-2092.
    • (1998) Science , vol.282 , pp. 2088-2092
    • Nguyen, J.T.1    Turck, C.W.2    Cohen, F.E.3    Zuckermann, R.N.4    Lim, W.A.5
  • 11
    • 0029782121 scopus 로고    scopus 로고
    • Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain
    • Pisabarro M.T., Serrano L. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain. Biochemistry. 35:1996;10634-10640.
    • (1996) Biochemistry , vol.35 , pp. 10634-10640
    • Pisabarro, M.T.1    Serrano, L.2
  • 12
    • 0032574705 scopus 로고    scopus 로고
    • The molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis
    • Luque I., Todd M.J., Gomez J., Semo N., Freire E. The molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis. Biochemistry. 37:1998;5791-5797.
    • (1998) Biochemistry , vol.37 , pp. 5791-5797
    • Luque, I.1    Todd, M.J.2    Gomez, J.3    Semo, N.4    Freire, E.5
  • 13
    • 0035861396 scopus 로고    scopus 로고
    • The application of thermodynamic methods in drug design
    • Velazquez-Campoy A., Luque I., Freire E. The application of thermodynamic methods in drug design. Thermochim. Acta. 380:2001;217-227.
    • (2001) Thermochim. Acta , vol.380 , pp. 217-227
    • Velazquez-Campoy, A.1    Luque, I.2    Freire, E.3
  • 14
    • 0036463987 scopus 로고    scopus 로고
    • Disabling Abl-perspectives on Abl kinase regulation and cancer therapeutics
    • Sawyers C.L. Disabling Abl-perspectives on Abl kinase regulation and cancer therapeutics. Cancer Cell. 1:2002;13-15.
    • (2002) Cancer Cell , vol.1 , pp. 13-15
    • Sawyers, C.L.1
  • 15
    • 0034634597 scopus 로고    scopus 로고
    • C-Abl has high intrinsic tyrosine kinase activity that is stimulated by mutation of the Src homology 3 domain and by autophosphorylation at two distinct regulatory sites
    • Brasher B.B., Van Etten R.A. c-Abl has high intrinsic tyrosine kinase activity that is stimulated by mutation of the Src homology 3 domain and by autophosphorylation at two distinct regulatory sites. J. Biol. Chem. 275:2000;35631-35637.
    • (2000) J. Biol. Chem. , vol.275 , pp. 35631-35637
    • Brasher, B.B.1    Van Etten, R.A.2
  • 16
    • 0035935998 scopus 로고    scopus 로고
    • Mutational analysis of the regulatory function of the c-Abl Src homology 3 domain
    • Brasher B.B., Roumiantsev S., Van Etten R.A. Mutational analysis of the regulatory function of the c-Abl Src homology 3 domain. Oncogene. 20:2001;7744-7752.
    • (2001) Oncogene , vol.20 , pp. 7744-7752
    • Brasher, B.B.1    Roumiantsev, S.2    Van Etten, R.A.3
  • 17
    • 0031882251 scopus 로고    scopus 로고
    • An intramolecular SH3-domain interaction regulates c-Abl activity
    • Barila D., Superti-Furga G. An intramolecular SH3-domain interaction regulates c-Abl activity. Nature Genet. 18:1998;280-282.
    • (1998) Nature Genet. , vol.18 , pp. 280-282
    • Barila, D.1    Superti-Furga, G.2
  • 18
    • 0037459344 scopus 로고    scopus 로고
    • Mechanisms of STI-571/imatinib resistance revealed by mutagenesis of BCR-ABL
    • Azam M., Latek R.R., Daley G.Q. Mechanisms of STI-571/imatinib resistance revealed by mutagenesis of BCR-ABL. Cell. 112:2003;831-843.
    • (2003) Cell , vol.112 , pp. 831-843
    • Azam, M.1    Latek, R.R.2    Daley, G.Q.3
  • 19
    • 0033815251 scopus 로고    scopus 로고
    • Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor
    • Velazquez-Campoy A., Luque I., Todd M.J., Milutinovich M., Kiso Y., Freire E. Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor. Protein Sci. 9:2000;1801-1809.
    • (2000) Protein Sci. , vol.9 , pp. 1801-1809
    • Velazquez-Campoy, A.1    Luque, I.2    Todd, M.J.3    Milutinovich, M.4    Kiso, Y.5    Freire, E.6
  • 20
    • 0028077037 scopus 로고
    • Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy
    • Wittekind M., Mapelli C., Farmer B.T. II, Suen K., Goldfarb V., Tsao J., et al. Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy. Biochemistry. 33:1994;13531-13539.
    • (1994) Biochemistry , vol.33 , pp. 13531-13539
    • Wittekind, M.1    Mapelli, C.2    Farmer II, B.T.3    Suen, K.4    Goldfarb, V.5    Tsao, J.6
  • 21
    • 0037372297 scopus 로고    scopus 로고
    • The effect of the polyproline II (PPII) conformation on the denatured state entropy
    • Ferreon J.C., Hilser V.J. The effect of the polyproline II (PPII) conformation on the denatured state entropy. Protein Sci. 12:2003;447-457.
    • (2003) Protein Sci. , vol.12 , pp. 447-457
    • Ferreon, J.C.1    Hilser, V.J.2
  • 22
    • 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., Morton C.J., Rossi C., et al. 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. 35:1996;15646-15653.
    • (1996) Biochemistry , vol.35 , pp. 15646-15653
    • Renzoni, D.A.1    Pugh, D.J.R.2    Siligardi, G.3    Das, P.4    Morton, C.J.5    Rossi, C.6
  • 23
    • 0035798419 scopus 로고    scopus 로고
    • The role of backbone motions in ligand binding to c-Src SH3 domain
    • Wang C., Pawley N.H., Nicholson L.K. The role of backbone motions in ligand binding to c-Src SH3 domain. J. Mol. Biol. 313:2001;873-887.
    • (2001) J. Mol. Biol. , vol.313 , pp. 873-887
    • Wang, C.1    Pawley, N.H.2    Nicholson, L.K.3
  • 24
    • 0029832524 scopus 로고    scopus 로고
    • Evaluation of linked protonation effects in protein binding using isothermal titration calorimetry
    • Baker B.M., Murphy K.P. Evaluation of linked protonation effects in protein binding using isothermal titration calorimetry. Biophys. J. 71:1996;2049-2055.
    • (1996) Biophys. J. , vol.71 , pp. 2049-2055
    • Baker, B.M.1    Murphy, K.P.2
  • 25
    • 0029080864 scopus 로고
    • Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin
    • Gomez J., Freire E. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252:1995;337-350.
    • (1995) J. Mol. Biol. , vol.252 , pp. 337-350
    • Gomez, J.1    Freire, E.2
  • 26
    • 0033642945 scopus 로고    scopus 로고
    • Structural stability of binding sites: Consequences for binding affinity and allosteric effects
    • Luque I., Freire E. Structural stability of binding sites: consequences for binding affinity and allosteric effects. Proteins: Struct. Funct. Genet. Suppl. 4:2000;63-71.
    • (2000) Proteins: Struct. Funct. Genet. , vol.4 , pp. 63-71
    • Luque, I.1    Freire, E.2
  • 27
    • 0036836538 scopus 로고    scopus 로고
    • Structural parameterization of the binding enthalpy of small ligands
    • Luque I., Freire E. Structural parameterization of the binding enthalpy of small ligands. Proteins: Struct. Funct. Genet. 49:2002;181-190.
    • (2002) Proteins: Struct. Funct. Genet. , vol.49 , pp. 181-190
    • Luque, I.1    Freire, E.2
  • 29
    • 0027936659 scopus 로고
    • Characterization of the interaction of natural proline-rich peptides with five different SH3 domains
    • Viguera A.R., Arrondo J.L.R., Musacchio A., Saraste M., Serrano L. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry. 33:1994;10925-10933.
    • (1994) Biochemistry , vol.33 , pp. 10925-10933
    • Viguera, A.R.1    Arrondo, J.L.R.2    Musacchio, A.3    Saraste, M.4    Serrano, L.5
  • 30
    • 0031556018 scopus 로고    scopus 로고
    • Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope
    • Covell D.G., Wallquist A. Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope. J. Mol. Biol. 269:1997;281-297.
    • (1997) J. Mol. Biol. , vol.269 , pp. 281-297
    • Covell, D.G.1    Wallquist, A.2
  • 31
    • 0028014642 scopus 로고
    • Bound water molecules and conformational stabilization help mediate an antigen-antibody associated
    • Bhat T.N., Bentley G.A., Boulot G., Greene M.I., Tello D., Dall'Acqua W., et al. Bound water molecules and conformational stabilization help mediate an antigen-antibody associated. Proc. Natl Acad. Sci. USA. 91:1994;1089-1093.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 1089-1093
    • Bhat, T.N.1    Bentley, G.A.2    Boulot, G.3    Greene, M.I.4    Tello, D.5    Dall'Acqua, W.6
  • 32
    • 0030474628 scopus 로고    scopus 로고
    • Bound water molecules at the interface between the HIV-1 protease and a potent inhibitor, KNI-272, determined by NMR
    • Wang Y.X., Freedberg D.I., Wingfield P.T., Stahl S.J., Kaufman J.D., Kiso Y., et al. Bound water molecules at the interface between the HIV-1 protease and a potent inhibitor, KNI-272, determined by NMR. J. Am. Chem. Soc. 118:1996;12287-12290.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 12287-12290
    • Wang, Y.X.1    Freedberg, D.I.2    Wingfield, P.T.3    Stahl, S.J.4    Kaufman, J.D.5    Kiso, Y.6
  • 33
    • 0029989480 scopus 로고    scopus 로고
    • A possible involvement of solvent-induced interactions in drug design
    • Wang H., Ben-Naim A. A possible involvement of solvent-induced interactions in drug design. J. Med. Chem. 39:1996;1531-1539.
    • (1996) J. Med. Chem. , vol.39 , pp. 1531-1539
    • Wang, H.1    Ben-Naim, A.2
  • 34
    • 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., Wilmanns M. Crystal structure of the Abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions. J. Mol. Biol. 281:1998;513-521.
    • (1998) J. Mol. Biol. , vol.281 , pp. 513-521
    • Pisabarro, M.T.1    Serrano, L.2    Wilmanns, M.3
  • 35
    • 0028148629 scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • Lim W.A., Richards F.M., Fox R.O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature. 372:1994;375-379.
    • (1994) Nature , vol.372 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 36
    • 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., Schreiber S.L. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science. 266:1994;1241-1247.
    • (1994) Science , vol.266 , pp. 1241-1247
    • Feng, S.1    Chen, J.K.2    Yu, H.3    Simon, J.A.4    Schreiber, S.L.5
  • 37
    • 0030950608 scopus 로고    scopus 로고
    • Modular peptide recognition domains in eukariotic signaling
    • Kuriyan J., Cowburn D. Modular peptide recognition domains in eukariotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26:1997;259-288.
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 259-288
    • Kuriyan, J.1    Cowburn, D.2
  • 38
    • 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., Nicholson L.K. Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR. J. Mol. Biol. 304:2000;497-505.
    • (2000) J. Mol. Biol. , vol.304 , pp. 497-505
    • Cordier, F.1    Wang, C.2    Grzesiek, S.3    Nicholson, L.K.4
  • 39
    • 0033104768 scopus 로고    scopus 로고
    • Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities
    • Vijayakumar M., Qian H., Zhou H.X. Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities. Proteins: Struct. Funct. Genet. 34:1999;497-507.
    • (1999) Proteins: Struct. Funct. Genet. , vol.34 , pp. 497-507
    • Vijayakumar, M.1    Qian, H.2    Zhou, H.X.3
  • 41
    • 0029983371 scopus 로고    scopus 로고
    • T7 vectors with modified T7lac promoter for expression of proteins in Escherichia coli
    • Peranen J., Rikkonen M., Hyvonen M., Kaairainen L. T7 vectors with modified T7lac promoter for expression of proteins in Escherichia coli. Anal. Biochem. 236:1996;371-373.
    • (1996) Anal. Biochem. , vol.236 , pp. 371-373
    • Peranen, J.1    Rikkonen, M.2    Hyvonen, M.3    Kaairainen, L.4
  • 42
    • 0028485085 scopus 로고
    • High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides
    • Musacchio A., Saraste M., Wilmanns M. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nature Struct. Biol. 1:1994;546-551.
    • (1994) Nature Struct. Biol. , vol.1 , pp. 546-551
    • Musacchio, A.1    Saraste, M.2    Wilmanns, M.3
  • 43
    • 0024448151 scopus 로고
    • Calculation of protein extinction coefficients from amino acid sequence data
    • Gill S.C., Von Hippel P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:1989;319-326.
    • (1989) Anal. Biochem. , vol.182 , pp. 319-326
    • Gill, S.C.1    Von Hippel, P.H.2
  • 44
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 45
    • 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., Takahashi K. Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride. Proteins: Struct. Funct. Genet. 33:1998;159-166.
    • (1998) Proteins: Struct. Funct. Genet. , vol.33 , pp. 159-166
    • Fukada, H.1    Takahashi, K.2


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