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Volumn 89, Issue 1, 2005, Pages 14-21

Functional dynamics of PDZ binding domains: A normal-mode analysis

Author keywords

[No Author keywords available]

Indexed keywords

PDZ PROTEIN;

EID: 23244447873     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.055004     Document Type: Article
Times cited : (65)

References (40)
  • 1
    • 0037155199 scopus 로고    scopus 로고
    • PDZ domains: Structural modules for protein complex assembly
    • Hung, A. Y., and M. Sheng. 2002. PDZ domains: structural modules for protein complex assembly. J. Biol. Chem. 277:5699-5102.
    • (2002) J. Biol. Chem. , vol.277 , pp. 5699-15102
    • Hung, A.Y.1    Sheng, M.2
  • 2
    • 0034916230 scopus 로고    scopus 로고
    • PDZ domains and the organization of supramolecular complexes
    • Sheng, M., and C. Sala. 2001. PDZ domains and the organization of supramolecular complexes. Annu. Rev. Neurosci. 24:1-29.
    • (2001) Annu. Rev. Neurosci. , vol.24 , pp. 1-29
    • Sheng, M.1    Sala, C.2
  • 3
    • 0037493100 scopus 로고    scopus 로고
    • Organization of signaling complexes by PDZ-domain scaffold proteins
    • Zhang, M., and W. Wang. 2003. Organization of signaling complexes by PDZ-domain scaffold proteins. Acc. Chem. Res. 36:530-538.
    • (2003) Acc. Chem. Res. , vol.36 , pp. 530-538
    • Zhang, M.1    Wang, W.2
  • 4
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson, T., and P. Nash. 2003. Assembly of cell regulatory systems through protein interaction domains. Science. 300:445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 5
    • 0033462127 scopus 로고    scopus 로고
    • The organization of INAD-signaling complexes by a multivalent PDZ domain protein in Drosophila photoreceptor cells ensures sensitivity and speed of signaling
    • Tsunoda, S., and C. S. Zuker. 1999. The organization of INAD-signaling complexes by a multivalent PDZ domain protein in Drosophila photoreceptor cells ensures sensitivity and speed of signaling. Cell Calcium. 26:165-171.
    • (1999) Cell Calcium , vol.26 , pp. 165-171
    • Tsunoda, S.1    Zuker, C.S.2
  • 7
    • 0033617473 scopus 로고    scopus 로고
    • Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex
    • Hillier, B. J., K. S. Christopherson, K. E. Prehoda, D. S. Bredt, and W. A. Lim. 1999. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science. 284:812-815.
    • (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
  • 8
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes, E. J., C. J. Der, and A. L. Lee. 2004. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol. 335:1105-1115.
    • (2004) J. Mol. Biol. , vol.335 , pp. 1105-1115
    • Fuentes, E.J.1    Der, C.J.2    Lee, A.L.3
  • 9
    • 0035957014 scopus 로고    scopus 로고
    • The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin
    • Frauenfelder, H., B. H. McMahon, R. H. Austin, K. Chu, and J. T. Groves. 2001. The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl. Acad. Sci. USA. 98:2370-2374.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 2370-2374
    • Frauenfelder, H.1    McMahon, B.H.2    Austin, R.H.3    Chu, K.4    Groves, J.T.5
  • 10
    • 0034127361 scopus 로고    scopus 로고
    • Collective protein dynamics in relation to function
    • Berendsen, H. J., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 165-169
    • Berendsen, H.J.1    Hayward, S.2
  • 11
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kem, D., and E. R. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13:748-757.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 748-757
    • Kem, D.1    Zuiderweg, E.R.2
  • 12
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt, M., C. Sander, and P. S. Stem. 1985. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181:423-447.
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stem, P.S.3
  • 13
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 14
    • 0020488742 scopus 로고
    • Collective variable description of small-amplitude conformational fluctuations in a globular protein
    • Noguti, T., and N. Go. 1982. Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature. 296:776-778.
    • (1982) Nature , vol.296 , pp. 776-778
    • Noguti, T.1    Go, N.2
  • 15
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 16
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen, K. 1998. Analysis of domain motions by approximate normal mode calculations. Proteins. 33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 17
    • 0033557178 scopus 로고    scopus 로고
    • Analysis of domain motions in large proteins
    • Hinsen, K., A. Thomas, and M. J. Field. 1999. Analysis of domain motions in large proteins. Proteins. 34:369-382.
    • (1999) Proteins , vol.34 , pp. 369-382
    • Hinsen, K.1    Thomas, A.2    Field, M.J.3
  • 19
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 2:173-181.
    • (1997) Fold. Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 20
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • Doruker, P., R. L. Jemigan, and I. Bahar. 2002. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:119-127.
    • (2002) J. Comput. Chem. , vol.23 , pp. 119-127
    • Doruker, P.1    Jemigan, R.L.2    Bahar, I.3
  • 21
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • Marques, O., and Y. H. Sanejouand. 1995. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins. 23:557-560.
    • (1995) Proteins , vol.23 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.H.2
  • 22
    • 0029791008 scopus 로고    scopus 로고
    • Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding
    • Sanejouand, Y. H. 1996. Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding. Protein Eng. 9:671-677.
    • (1996) Protein Eng. , vol.9 , pp. 671-677
    • Sanejouand, Y.H.1
  • 23
    • 3242883858 scopus 로고    scopus 로고
    • On the potential of normal-mode analysis for solving difficult molecular-replacement problems
    • Suhre, K., and Y. H. Sanejouand. 2004. On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr. D Biol. Crystallogr. 60:796-799.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 796-799
    • Suhre, K.1    Sanejouand, Y.H.2
  • 24
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 25
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama, F., and Y. H. Sanejouand. 2001. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14:1-6.
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 26
    • 0036077875 scopus 로고    scopus 로고
    • Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
    • Delarue, M., and Y. H. Sanejouand. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J. Mol. Biol. 320:1011-1024.
    • (2002) J. Mol. Biol. , vol.320 , pp. 1011-1024
    • Delarue, M.1    Sanejouand, Y.H.2
  • 27
    • 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., A. Lee, J. Lewis, E. Kim, M. Sheng, and R. MacKinnon. 1996. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell. 85:1067-1076.
    • (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
  • 29
    • 0036301446 scopus 로고    scopus 로고
    • Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions
    • Kozlov, G., D. Banville, K. Gehring, and I. Ekiel. 2002. Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions. J. Mol. Biol. 320:813-820.
    • (2002) J. Mol. Biol. , vol.320 , pp. 813-820
    • Kozlov, G.1    Banville, D.2    Gehring, K.3    Ekiel, I.4
  • 30
    • 0034646395 scopus 로고    scopus 로고
    • Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor
    • Kozlov, G., K. Gehring, and I. Ekiel. 2000. Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor. Biochemistry. 39:2572-2580.
    • (2000) Biochemistry , vol.39 , pp. 2572-2580
    • Kozlov, G.1    Gehring, K.2    Ekiel, I.3
  • 32
    • 84893482610 scopus 로고
    • Solution for best rotation to relate 2 sets of vectors
    • Kabsch, W. 1976. Solution for best rotation to relate 2 sets of vectors. Acta Crystallogr. A. 32:922-923.
    • (1976) Acta Crystallogr. A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 33
    • 0028360307 scopus 로고
    • The contribution of vibrational entropy to molecular association. The dimerization of insulin
    • Tidor, B., and M. Karplus. 1994. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J. Mol. Biol. 238:405-414.
    • (1994) J. Mol. Biol. , vol.238 , pp. 405-414
    • Tidor, B.1    Karplus, M.2
  • 34
    • 2442543557 scopus 로고    scopus 로고
    • Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
    • Micheletti, C., P. Carloni, and A. Maritan. 2004. Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models. Proteins. 55:635-645.
    • (2004) Proteins , vol.55 , pp. 635-645
    • Micheletti, C.1    Carloni, P.2    Maritan, A.3
  • 35
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park, B., and M. Levitt. 1996. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258:367-392.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 36
    • 0030711616 scopus 로고    scopus 로고
    • Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21
    • Ma, J., and M. Karplus. 1997. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc. Natl. Acad. Sci. USA. 94:11905-11910.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 11905-11910
    • Ma, J.1    Karplus, M.2
  • 37
    • 0141792364 scopus 로고    scopus 로고
    • Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T↔R2 transition
    • Xu, C., D. Tobi, and I. Bahar. 2003. Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T↔R2 transition. J. Mol. Biol. 333:153-168.
    • (2003) J. Mol. Biol. , vol.333 , pp. 153-168
    • Xu, C.1    Tobi, D.2    Bahar, I.3
  • 38
    • 0037070181 scopus 로고    scopus 로고
    • PDZ domains: Evolving classification
    • Bezprozvanny, I., and A. Maximov. 2002. PDZ domains: evolving classification. FEBS Lett. 512:347-349.
    • (2002) FEBS Lett. , vol.512 , pp. 347-349
    • Bezprozvanny, I.1    Maximov, A.2
  • 39
    • 0000053123 scopus 로고    scopus 로고
    • Protein flexibility in solution and in crystals
    • Eastman, P., M. Pellegrini, and S. Doniach. 1999. Protein flexibility in solution and in crystals. J. Chem. Phys. 110:10141-10152.
    • (1999) J. Chem. Phys. , vol.110 , pp. 10141-10152
    • Eastman, P.1    Pellegrini, M.2    Doniach, S.3
  • 40
    • 0021658956 scopus 로고
    • Allostery without conformational change. A plausible model
    • Cooper, A., and D. T. Dryden. 1984. Allostery without conformational change. A plausible model. Eur. Biophys. J. 11:103-109.
    • (1984) Eur. Biophys. J. , vol.11 , pp. 103-109
    • Cooper, A.1    Dryden, D.T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.