메뉴 건너뛰기




Volumn 6, Issue 11, 1997, Pages 2336-2343

Kinase conformations: A computational study of the effect of ligand binding

Author keywords

cAMP dependent protein kinase; Conformational transition; Poisson electrostatics calculations

Indexed keywords

CYCLIC AMP DEPENDENT PROTEIN KINASE;

EID: 0030671575     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560061106     Document Type: Article
Times cited : (16)

References (52)
  • 3
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
    • Davis ME, Madura JD, Luty BA, McCammon JA. 1991. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program. Comput Phys Commun 62:187-197.
    • (1991) Comput Phys Commun , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 4
    • 0029886930 scopus 로고    scopus 로고
    • Study of global motions in proteins by weighted masses molecular dynamics: Adenylate kinase as a test case
    • Elamrani S, Berry MB Jr, GN Phillips, McCammon JA. 1996. Study of global motions in proteins by weighted masses molecular dynamics: Adenylate kinase as a test case. Proteins Struct Funct Genet 25:79-88.
    • (1996) Proteins Struct Funct Genet , vol.25 , pp. 79-88
    • Elamrani, S.1    Berry Jr., M.B.2    Phillips, G.N.3    McCammon, J.A.4
  • 5
    • 0030068480 scopus 로고    scopus 로고
    • 2 in noncrystalline environments show a subunit transition from the open to the closed conformation
    • 2 in noncrystalline environments show a subunit transition from the open to the closed conformation. Protein Sci 5:62-71.
    • (1996) Protein Sci , vol.5 , pp. 62-71
    • Garcia, A.E.1    Harman, J.G.2
  • 6
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein M, Lesk AM, Chothia C. 1994. Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1    Lesk, A.M.2    Chothia, C.3
  • 7
    • 0029066848 scopus 로고
    • Theory of electrostatic interactions in macromolecules
    • Gilson MK. 1995. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol 5:216-223.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 216-223
    • Gilson, M.K.1
  • 8
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA. 1997. The statistical-thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72:1047-1069.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 9
    • 84986439462 scopus 로고
    • Molecular dynamics simulation with a continuum electrostatic model of the solvent
    • Gilson MK, McCammon JA, Madura JD. 1995. Molecular dynamics simulation with a continuum electrostatic model of the solvent. J Comput Chem 16:1081-1095.
    • (1995) J Comput Chem , vol.16 , pp. 1081-1095
    • Gilson, M.K.1    McCammon, J.A.2    Madura, J.D.3
  • 10
    • 0030010603 scopus 로고    scopus 로고
    • Examination of an active-site electrostatic node in the cAMP-dependent protein kinase catalytic subunit
    • Grant BD, Tsigelny I, Adams JA, Taylor SS. 1996. Examination of an active-site electrostatic node in the cAMP-dependent protein kinase catalytic subunit. Protein Sci 5:1316-1324.
    • (1996) Protein Sci , vol.5 , pp. 1316-1324
    • Grant, B.D.1    Tsigelny, I.2    Adams, J.A.3    Taylor, S.S.4
  • 11
    • 0029964613 scopus 로고    scopus 로고
    • Requirement lor cAMP-PKA pathway activation by m phase-promoting factor in the transition from mitosis to interphase
    • Grieco D, Porccllini A, Avvedimento EV Gottesman ME. 1996. Requirement lor cAMP-PKA pathway activation by m phase-promoting factor in the transition from mitosis to interphase. Science 271:1718-1723.
    • (1996) Science , vol.271 , pp. 1718-1723
    • Grieco, D.1    Porccllini, A.2    Avvedimento, E.V.3    Gottesman, M.E.4
  • 12
    • 0000689085 scopus 로고
    • Predicting slow structural transitions in macromolecular systems: Conformational flooding
    • Grubmueller H. 1994. Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys Rev E 52:2893-2906.
    • (1994) Phys Rev E , vol.52 , pp. 2893-2906
    • Grubmueller, H.1
  • 13
    • 1842401817 scopus 로고    scopus 로고
    • Energy transfer methods for determining distance distributions and conformational fluctuations in proteins
    • Havel HA, ed. New York: VCH Publishers Inc.
    • Haas E. 1996. Energy transfer methods for determining distance distributions and conformational fluctuations in proteins. In: Havel HA, ed. Spectroscopic methods for determining protein structure in solution. New York: VCH Publishers Inc. pp 28-61.
    • (1996) Spectroscopic Methods for Determining Protein Structure in Solution , pp. 28-61
    • Haas, E.1
  • 14
    • 0027074883 scopus 로고
    • Domain motions in phosphoglycerate kinase: Determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transter
    • Haran G, Haas E, Szpikowska BK, Mas MT. 1992. Domain motions in phosphoglycerate kinase: Determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transter. Prof Natl Acad Sci USA 89:11764-11768.
    • (1992) Prof Natl Acad Sci USA , vol.89 , pp. 11764-11768
    • Haran, G.1    Haas, E.2    Szpikowska, B.K.3    Mas, M.T.4
  • 16
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science 268:1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 17
    • 0020647920 scopus 로고
    • Functional significance of flexibility in proteins
    • Huber R, Bennett WS. 1983. Functional significance of flexibility in proteins. Biopolymers 22:261-279.
    • (1983) Biopolymers , vol.22 , pp. 261-279
    • Huber, R.1    Bennett, W.S.2
  • 18
    • 0027186150 scopus 로고
    • Normal mode analysis of mouse epidermal growth factor: Characterization of the harmonic motion
    • Ikura T, Go N. 1993. Normal mode analysis of mouse epidermal growth factor: Characterization of the harmonic motion. Proteins Struct Funct Genet 16:423-436.
    • (1993) Proteins Struct Funct Genet , vol.16 , pp. 423-436
    • Ikura, T.1    Go, N.2
  • 20
    • 0021604916 scopus 로고
    • Mechanisms of domain closure in proteins
    • Lesk AM, Chothia C. 1984. Mechanisms of domain closure in proteins. J Mol Biol 174:175-191.
    • (1984) J Mol Biol , vol.174 , pp. 175-191
    • Lesk, A.M.1    Chothia, C.2
  • 21
    • 0031035585 scopus 로고    scopus 로고
    • Synergistic binding of nucleotides and inhibitors to cAMP-dependent protein kinase examined by acrylodan fluorescence spectroscopy
    • Lew J, Coruh N, Tsigelny I, Garrod S, Taylor SS. 1997. Synergistic binding of nucleotides and inhibitors to cAMP-dependent protein kinase examined by acrylodan fluorescence spectroscopy. J Biol Chem 272:1507-1513.
    • (1997) J Biol Chem , vol.272 , pp. 1507-1513
    • Lew, J.1    Coruh, N.2    Tsigelny, I.3    Garrod, S.4    Taylor, S.S.5
  • 22
    • 0029633152 scopus 로고
    • Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program
    • Madura JD, Briggs JM, Wade RC, Davis ME. 1995. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian dynamics program. Comput Phys Commun 91:57-95.
    • (1995) Comput Phys Commun , vol.91 , pp. 57-95
    • Madura, J.D.1    Briggs, J.M.2    Wade, R.C.3    Davis, M.E.4
  • 23
    • 85050521214 scopus 로고
    • Biological applications in electrostatic calculations and brownian dynamics simulations
    • Lipkowitz KB, Boyd DB, eds. New York: VCH Publishers Inc.
    • Madura JD, Davis ME, Gilson MK, Wade RC, Luty B, McCammon JA. 1994. Biological applications in electrostatic calculations and brownian dynamics simulations. In: Lipkowitz KB, Boyd DB, eds. Reviews in computational chemistry, vol V. New York: VCH Publishers Inc. pp 229-267.
    • (1994) Reviews in Computational Chemistry , vol.5 , pp. 229-267
    • Madura, J.D.1    Davis, M.E.2    Gilson, M.K.3    Wade, R.C.4    Luty, B.5    McCammon, J.A.6
  • 25
    • 0000435390 scopus 로고    scopus 로고
    • Comparison of continuum and explicit models of solvation: Potentials of mean force for alanine dipeptide
    • Marrone T, Gilson MK, McCammon JA. 1996. Comparison of continuum and explicit models of solvation: Potentials of mean force for alanine dipeptide. J Phys Chem 100:1439-1441.
    • (1996) J Phys Chem , vol.100 , pp. 1439-1441
    • Marrone, T.1    Gilson, M.K.2    McCammon, J.A.3
  • 27
    • 1842326248 scopus 로고    scopus 로고
    • Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling
    • Mchaourab HS, Oh KJ, Fang CJ, Hubbell WL. 1997. Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. Biochemistry 36:307-316.
    • (1997) Biochemistry , vol.36 , pp. 307-316
    • Mchaourab, H.S.1    Oh, K.J.2    Fang, C.J.3    Hubbell, W.L.4
  • 29
    • 0029937635 scopus 로고    scopus 로고
    • Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary t-like, quaternary r-like intermediate structures
    • Mouawad L, Perahia D. 1996. Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary t-like, quaternary r-like intermediate structures. J Mol Biol 258:393-410.
    • (1996) J Mol Biol , vol.258 , pp. 393-410
    • Mouawad, L.1    Perahia, D.2
  • 30
    • 0030932129 scopus 로고    scopus 로고
    • Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI (5-24) and adenosine
    • Narayana N, Cox S, Shaltiel S, Taylor SS, Xuong N. 1997a. Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI (5-24) and adenosine. Biochemistry 36:4438-4448.
    • (1997) Biochemistry , vol.36 , pp. 4438-4448
    • Narayana, N.1    Cox, S.2    Shaltiel, S.3    Taylor, S.S.4    Xuong, N.5
  • 31
    • 0031571091 scopus 로고    scopus 로고
    • A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility
    • Narayana N, Cox S, Xuong N, Ten-Eyck LF, Taylor SS. 1997b. A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility. Structure 5:921-935.
    • (1997) Structure , vol.5 , pp. 921-935
    • Narayana, N.1    Cox, S.2    Xuong, N.3    Ten-Eyck, L.F.4    Taylor, S.S.5
  • 32
    • 0027159007 scopus 로고
    • Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide
    • Olah GA, Mitchell RD, Sosnick TR, Walsh DA, Trewhella J. 1993. Solution structure of the cAMP-dependent protein kinase catalytic subunit and its contraction upon binding the protein kinase inhibitor peptide. Biochemistry 32:3649-3657.
    • (1993) Biochemistry , vol.32 , pp. 3649-3657
    • Olah, G.A.1    Mitchell, R.D.2    Sosnick, T.R.3    Walsh, D.A.4    Trewhella, J.5
  • 33
    • 0030217514 scopus 로고    scopus 로고
    • Nuclear magnetic resonance studies of biopolymer dynamics
    • Palmer AG, Williams J, McDermott A. 1996. Nuclear magnetic resonance studies of biopolymer dynamics. J Phys Chem 100:13293-13310.
    • (1996) J Phys Chem , vol.100 , pp. 13293-13310
    • Palmer, A.G.1    Williams, J.2    McDermott, A.3
  • 34
    • 1842397599 scopus 로고
    • Conformational changes in the catalytic subunit of cAMP-dependent protein kinase. a small-angle neutron scattering study in solution
    • Parello J, Timmins PA, Sowadski JM, Taylor SS. 1993. Conformational changes in the catalytic subunit of cAMP-dependent protein kinase. A small-angle neutron scattering study in solution. J Mol Biol 253:414-420.
    • (1993) J Mol Biol , vol.253 , pp. 414-420
    • Parello, J.1    Timmins, P.A.2    Sowadski, J.M.3    Taylor, S.S.4
  • 35
    • 0029374782 scopus 로고
    • Computation of low-frequency normal modes in macro-molecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin
    • Perahia D, Mouawad L. 1995. Computation of low-frequency normal modes in macro-molecules: Improvements to the method of diagonalization in a mixed basis and application to hemoglobin. Comp Chem 19:241-246.
    • (1995) Comp Chem , vol.19 , pp. 241-246
    • Perahia, D.1    Mouawad, L.2
  • 36
    • 0018606116 scopus 로고
    • Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase
    • Pickover CA, McKay DB, Engelman DM, Steitz TA. 1979. Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase. J Biol Chem 254:11323-11329.
    • (1979) J Biol Chem , vol.254 , pp. 11323-11329
    • Pickover, C.A.1    McKay, D.B.2    Engelman, D.M.3    Steitz, T.A.4
  • 38
    • 0028455053 scopus 로고
    • Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
    • Schlitter J, Engels M, Kruger P. 1994. Targeted molecular dynamics: A new approach for searching pathways of conformational transitions. J Mol Graph 12:84-89.
    • (1994) J Mol Graph , vol.12 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Kruger, P.3
  • 39
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • Simonson T, Brünger AT 1994. Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment. J Phys Chem 95:4683-4694.
    • (1994) J Phys Chem , vol.95 , pp. 4683-4694
    • Simonson, T.1    Brünger, A.T.2
  • 40
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D, Sharp KA, Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 95:1978-1988.
    • (1994) J Phys Chem , vol.95 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 41
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in protein
    • Smith KC, Honig B. 1994. Evaluation of the conformational free energies of loops in protein. Proteins Struct Funct Genet 18:119-132.
    • (1994) Proteins Struct Funct Genet , vol.18 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 42
    • 0029777433 scopus 로고    scopus 로고
    • Intermediate trapping and Laue X-ray diffraction: Potential for enzyme mechanism, dynamics, and inhibitor screening
    • Stoddard BL. 1996. Intermediate trapping and Laue X-ray diffraction: Potential for enzyme mechanism, dynamics, and inhibitor screening. Pharmacol Ther 70:216-256.
    • (1996) Pharmacol Ther , vol.70 , pp. 216-256
    • Stoddard, B.L.1
  • 43
    • 0028773477 scopus 로고
    • Three protein kinase structures define a common motif
    • Taylor SS, Radzio-Andzelm E. 1994. Three protein kinase structures define a common motif. Structure 2:345-355.
    • (1994) Structure , vol.2 , pp. 345-355
    • Taylor, S.S.1    Radzio-Andzelm, E.2
  • 44
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
    • Tomasi J, Persico M. 1994. Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem Rev 94:2027-2094.
    • (1994) Chem Rev , vol.94 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 45
    • 0020630637 scopus 로고
    • Baker's yeast adenylate kinase
    • Tomasselli AG, Noda LH. 1983. Baker's yeast adenylate kinase. Eur J Biochem 132:109-115.
    • (1983) Eur J Biochem , vol.132 , pp. 109-115
    • Tomasselli, A.G.1    Noda, L.H.2
  • 46
    • 0029152775 scopus 로고
    • Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
    • Troyer JJ, Cohen FE. 1995. Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory. Proteins Struct Funct Genet 23:97-110.
    • (1995) Proteins Struct Funct Genet , vol.23 , pp. 97-110
    • Troyer, J.J.1    Cohen, F.E.2
  • 47
    • 0030249098 scopus 로고    scopus 로고
    • Catalytic subunit of cAMP-dependent protein kinase: Electrostatic features and peptide recognition
    • Tsigelny I, Grant BD, Taylor SS, Ten-Eyck LF. 1996. Catalytic subunit of cAMP-dependent protein kinase: Electrostatic features and peptide recognition. Biopolymers 39:353-365.
    • (1996) Biopolymers , vol.39 , pp. 353-365
    • Tsigelny, I.1    Grant, B.D.2    Taylor, S.S.3    Ten-Eyck, L.F.4
  • 48
    • 0030596522 scopus 로고
    • Free energy determinants of secondary structure formation: III: β-turns and their role in protein folding
    • Yang AS, Hitz B, Honig B. 1995. Free energy determinants of secondary structure formation: III: β-turns and their role in protein folding. J Mol Biol 259:873-882.
    • (1995) J Mol Biol , vol.259 , pp. 873-882
    • Yang, A.S.1    Hitz, B.2    Honig, B.3
  • 49
    • 0029121068 scopus 로고
    • Free energy determinants of secondary structure formation: I. α-helices
    • Yang AS, Honig B. 1995. Free energy determinants of secondary structure formation: I. α-helices. J Mol Biol 252:351-365.
    • (1995) J Mol Biol , vol.252 , pp. 351-365
    • Yang, A.S.1    Honig, B.2
  • 50
    • 0017163462 scopus 로고
    • Studies on tyrosine residues in porcine muscle adenylate kinase
    • Yazawa M, Noda LH. 1976. Studies on tyrosine residues in porcine muscle adenylate kinase. J Biol Chem 251:3021-3026.
    • (1976) J Biol Chem , vol.251 , pp. 3021-3026
    • Yazawa, M.1    Noda, L.H.2
  • 51
    • 0027408171 scopus 로고
    • Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor
    • Zheng J, Knighton DR, Ten-Eyck LF, Karlsson R, Xuong NH, Taylor SS, Sowadski JM. 1993a. Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry 32:2154-2161.
    • (1993) Biochemistry , vol.32 , pp. 2154-2161
    • Zheng, J.1    Knighton, D.R.2    Ten-Eyck, L.F.3    Karlsson, R.4    Xuong, N.H.5    Taylor, S.S.6    Sowadski, J.M.7
  • 52
    • 0027429591 scopus 로고
    • Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations
    • Zheng J, Knighton DR, Xuong NH, Taylor SS, Sowadski JM, Ten-Eyck LF. 1993b. Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci 2:1559-1573.
    • (1993) Protein Sci , vol.2 , pp. 1559-1573
    • Zheng, J.1    Knighton, D.R.2    Xuong, N.H.3    Taylor, S.S.4    Sowadski, J.M.5    Ten-Eyck, L.F.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.