메뉴 건너뛰기




Volumn 14, Issue 12, 2006, Pages 1801-1809

Demonstration of Long-Range Interactions in a PDZ Domain by NMR, Kinetics, and Protein Engineering

Author keywords

PROTEINS

Indexed keywords

PDZ PROTEIN; PHOSPHATASE; TYROSINE PHOSPHATASE;

EID: 33845186553     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2006.10.010     Document Type: Article
Times cited : (97)

References (46)
  • 1
    • 0343459675 scopus 로고
    • The program XEASY for computer-supported NMR spectral analysis of biological macromolecules
    • Bartels C., Xia T.-H., Billeter M., Güntert P., and Wüthrich K. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR 6 (1995) 277-293
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Bartels, C.1    Xia, T.-H.2    Billeter, M.3    Güntert, P.4    Wüthrich, K.5
  • 4
    • 11144251770 scopus 로고    scopus 로고
    • Thrombin: a paradigm for enzymes allosterically activated by monovalent cations
    • Di Cera E. Thrombin: a paradigm for enzymes allosterically activated by monovalent cations. C. R. Biol. 327 (2004) 1065-1076
    • (2004) C. R. Biol. , vol.327 , pp. 1065-1076
    • Di Cera, E.1
  • 5
    • 31344432159 scopus 로고    scopus 로고
    • Determination of network of residues that regulate allostery in protein families using sequence analysis
    • Dima R.I., and Thirumalai D. Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15 (2006) 258-268
    • (2006) Protein Sci. , vol.15 , pp. 258-268
    • Dima, R.I.1    Thirumalai, D.2
  • 6
    • 0034048847 scopus 로고    scopus 로고
    • Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data
    • Dosset P., Hus J.C., Blackledge M., and Marion D. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16 (2000) 23-28
    • (2000) J. Biomol. NMR , vol.16 , pp. 23-28
    • Dosset, P.1    Hus, J.C.2    Blackledge, M.3    Marion, D.4
  • 7
    • 0030604722 scopus 로고    scopus 로고
    • Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ
    • Doyle D.A., Lee A., Lewis J., Kim E., Sheng M., and MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 85 (1996) 1067-1076
    • (1996) Cell , vol.85 , pp. 1067-1076
    • Doyle, D.A.1    Lee, A.2    Lewis, J.3    Kim, E.4    Sheng, M.5    MacKinnon, R.6
  • 8
    • 0034632672 scopus 로고    scopus 로고
    • The Adenomatous Polyposis Coli-protein (APC) interacts with the protein tyrosine phosphatase PTP-BL via an alternatively spliced PDZ domain
    • Erdmann K.S., Kuhlmann J., Lessmann V., Herrmann L., Eulenburg V., Muller O., and Heumann R. The Adenomatous Polyposis Coli-protein (APC) interacts with the protein tyrosine phosphatase PTP-BL via an alternatively spliced PDZ domain. Oncogene 19 (2000) 3894-3901
    • (2000) Oncogene , vol.19 , pp. 3894-3901
    • Erdmann, K.S.1    Kuhlmann, J.2    Lessmann, V.3    Herrmann, L.4    Eulenburg, V.5    Muller, O.6    Heumann, R.7
  • 10
    • 0026511656 scopus 로고
    • The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
    • Fersht A.R., Matouschek A., and Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992) 771-782
    • (1992) J. Mol. Biol. , vol.224 , pp. 771-782
    • Fersht, A.R.1    Matouschek, A.2    Serrano, L.3
  • 11
    • 0001289724 scopus 로고
    • Einfluss der Konfiguration auf die Wirkung der Enzyme
    • Fischer E. Einfluss der Konfiguration auf die Wirkung der Enzyme. Ber. Dtsch. Chem. Ges. 27 (1894) 2984-2993
    • (1894) Ber. Dtsch. Chem. Ges. , vol.27 , pp. 2984-2993
    • Fischer, E.1
  • 12
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes E.J., Der C.J., and Lee A.L. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol. 335 (2004) 1105-1115
    • (2004) J. Mol. Biol. , vol.335 , pp. 1105-1115
    • Fuentes, E.J.1    Der, C.J.2    Lee, A.L.3
  • 13
    • 0035834649 scopus 로고    scopus 로고
    • Identification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-Ras
    • Gao X., Satoh T., Liao Y., Song C., Hu C.D., Kariya Ki K., and Kataoka T. Identification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-Ras. J. Biol. Chem. 276 (2001) 42219-42225
    • (2001) J. Biol. Chem. , vol.276 , pp. 42219-42225
    • Gao, X.1    Satoh, T.2    Liao, Y.3    Song, C.4    Hu, C.D.5    Kariya Ki, K.6    Kataoka, T.7
  • 18
    • 6344219895 scopus 로고    scopus 로고
    • Is allostery an intrinsic property of all dynamic proteins?
    • Gunasekaran K., Ma B., and Nussinov R. Is allostery an intrinsic property of all dynamic proteins?. Proteins 57 (2004) 433-443
    • (2004) Proteins , vol.57 , pp. 433-443
    • Gunasekaran, K.1    Ma, B.2    Nussinov, R.3
  • 19
    • 0033617473 scopus 로고    scopus 로고
    • Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex
    • Hillier B.J., Christopherson K.S., Prehoda K.E., Bredt D.S., and Lim W.A. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 284 (1999) 812-815
    • (1999) Science , vol.284 , pp. 812-815
    • Hillier, B.J.1    Christopherson, K.S.2    Prehoda, K.E.3    Bredt, D.S.4    Lim, W.A.5
  • 20
    • 0037155199 scopus 로고    scopus 로고
    • PDZ domains: structural modules for protein complex assembly
    • Hung A.Y., and Sheng M. PDZ domains: structural modules for protein complex assembly. J. Biol. Chem. 277 (2002) 5699-5702
    • (2002) J. Biol. Chem. , vol.277 , pp. 5699-5702
    • Hung, A.Y.1    Sheng, M.2
  • 22
    • 5044224260 scopus 로고    scopus 로고
    • PDZ domain proteins of synapses
    • Kim E., and Sheng M. PDZ domain proteins of synapses. Nat. Rev. Neurosci. 5 (2004) 771-781
    • (2004) Nat. Rev. Neurosci. , vol.5 , pp. 771-781
    • Kim, E.1    Sheng, M.2
  • 23
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland Jr. D.E., Nemethy G., and Filmer D. 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    Nemethy, G.2    Filmer, D.3
  • 24
    • 0036301446 scopus 로고    scopus 로고
    • Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the β2-β3 loop to PDZ domain-ligand interactions
    • Kozlov G., Banville D., Gehring K., and Ekiel I. Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the β2-β3 loop to PDZ domain-ligand interactions. J. Mol. Biol. 320 (2002) 813-820
    • (2002) J. Mol. Biol. , vol.320 , pp. 813-820
    • Kozlov, G.1    Banville, D.2    Gehring, K.3    Ekiel, I.4
  • 25
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
    • Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 477-486
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 26
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionary conserved pathways of energetic connectivity in protein families
    • Lockless S.W., and Ranganathan R. Evolutionary conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 27
    • 0034061258 scopus 로고    scopus 로고
    • Structural analysis of WW domains and design of a WW prototype
    • Macias M.J., Gervais V., Civera C., and Oschkinat H. Structural analysis of WW domains and design of a WW prototype. Nat. Struct. Biol. 7 (2000) 376-379
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 376-379
    • Macias, M.J.1    Gervais, V.2    Civera, C.3    Oschkinat, H.4
  • 28
    • 0028941877 scopus 로고
    • Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme
    • Mandel A.M., Akke M., and Palmer III A.G. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246 (1995) 144-163
    • (1995) J. Mol. Biol. , vol.246 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer III, A.G.3
  • 29
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: a plausible model
    • Monod J., Wyman J., and Changeux J.P. 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
  • 31
    • 0019821957 scopus 로고
    • Binding of high affinity heparin to antithrombin III. Stopped-flow kinetic studies of the binding interaction
    • Olson S.T., Srinivasan K.R., Bjork I., and Shore J.D. Binding of high affinity heparin to antithrombin III. Stopped-flow kinetic studies of the binding interaction. J. Biol. Chem. 256 (1981) 11073-11079
    • (1981) J. Biol. Chem. , vol.256 , pp. 11073-11079
    • Olson, S.T.1    Srinivasan, K.R.2    Bjork, I.3    Shore, J.D.4
  • 32
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • Ota N., and Agard D.A. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. 351 (2005) 345-354
    • (2005) J. Mol. Biol. , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 33
    • 1642276423 scopus 로고    scopus 로고
    • Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition
    • Peterson F.C., Penkert R.R., Volkman B.F., and Prehoda K.E. Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Mol. Cell 13 (2004) 665-676
    • (2004) Mol. Cell , vol.13 , pp. 665-676
    • Peterson, F.C.1    Penkert, R.R.2    Volkman, B.F.3    Prehoda, K.E.4
  • 34
    • 0030772973 scopus 로고    scopus 로고
    • Characterization of the interactions between PDZ domains of the protein-tyrosine phosphatase PTPL1 and the carboxyl-terminal tail of Fas
    • Saras J., Engström U., Góñez L.J., and Heldin C.H. Characterization of the interactions between PDZ domains of the protein-tyrosine phosphatase PTPL1 and the carboxyl-terminal tail of Fas. J. Biol. Chem. 272 (1997) 20979-20981
    • (1997) J. Biol. Chem. , vol.272 , pp. 20979-20981
    • Saras, J.1    Engström, U.2    Góñez, L.J.3    Heldin, C.H.4
  • 35
    • 2342604895 scopus 로고    scopus 로고
    • A PDZ switch for a cellular stress response
    • Schlieker C., Mogk A., and Bukau B. A PDZ switch for a cellular stress response. Cell 117 (2004) 417-419
    • (2004) Cell , vol.117 , pp. 417-419
    • Schlieker, C.1    Mogk, A.2    Bukau, B.3
  • 36
    • 0031969090 scopus 로고    scopus 로고
    • A continuous-flow capillary mixing method to monitor reactions on the microsecond time scale
    • Shastry M.C.R., Luck S.D., and Roder H. A continuous-flow capillary mixing method to monitor reactions on the microsecond time scale. Biophys. J. 74 (1998) 2714-2721
    • (1998) Biophys. J. , vol.74 , pp. 2714-2721
    • Shastry, M.C.R.1    Luck, S.D.2    Roder, H.3
  • 38
    • 0036219167 scopus 로고    scopus 로고
    • Improving the quality of protein structures derived by NMR spectroscopy
    • Spronk C.A., Linge J.P., Hilbers C.W., and Vuister G.W. Improving the quality of protein structures derived by NMR spectroscopy. J. Biomol. NMR 22 (2002) 281-289
    • (2002) J. Biomol. NMR , vol.22 , pp. 281-289
    • Spronk, C.A.1    Linge, J.P.2    Hilbers, C.W.3    Vuister, G.W.4
  • 39
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel G.M., Lockless S.W., Wall M.A., and Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10 (2003) 59-69
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 40
    • 32344434479 scopus 로고    scopus 로고
    • The changing landscape of protein allostery
    • Swain J.F., and Gierasch L.M. The changing landscape of protein allostery. Curr. Opin. Struct. Biol. 16 (2006) 102-108
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 102-108
    • Swain, J.F.1    Gierasch, L.M.2
  • 41
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • Tobi D., and Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA 102 (2005) 18908-18913
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 42
  • 43
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 291 (2001) 2429-2433
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 44
    • 0025398721 scopus 로고
    • WHAT IF: a molecular modeling and drug design program
    • 29
    • Vriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56 29
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 45
    • 1642493671 scopus 로고    scopus 로고
    • A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL
    • Walma T., Aelen J., Nabuurs S.B., Oostendorp M., van den Berk L., Hendriks W., and Vuister G.W. A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL. Structure 12 (2004) 11-20
    • (2004) Structure , vol.12 , pp. 11-20
    • Walma, T.1    Aelen, J.2    Nabuurs, S.B.3    Oostendorp, M.4    van den Berk, L.5    Hendriks, W.6    Vuister, G.W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.