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Volumn 1697, Issue 1-2, 2004, Pages 289-300

Structure, dynamics and interaction with kinase targets: Computer simulations of calmodulin

Author keywords

Calmodulin; CaM; FRET; Kinase; MLCK; Molecular dynamics simulation; Myosin light chain kinase; Poisson Boltzmann equation; Protein peptide interaction; Quasi harmonic entropy calculation; smMLCK; Smooth muscle MLCK

Indexed keywords

CALCIUM; CALMODULIN; MYOSIN LIGHT CHAIN KINASE; PEPTIDE; SOLVENT;

EID: 1542358827     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2003.11.032     Document Type: Conference Paper
Times cited : (59)

References (61)
  • 1
    • 0029149085 scopus 로고
    • Molecular and structural basis of target recognition by calmodulin
    • Crivici A., Ikura M. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24:1995;85-116.
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 85-116
    • Crivici, A.1    Ikura, M.2
  • 3
    • 0024213513 scopus 로고
    • Structure of calmodulin refined to 2.2 Å resolution
    • Babu Y.S., Bugg C.E., Cook W.J. Structure of calmodulin refined to 2.2 Å resolution. J. Mol. Biol. 204:1988;191-204.
    • (1988) J. Mol. Biol. , vol.204 , pp. 191-204
    • Babu, Y.S.1    Bugg, C.E.2    Cook, W.J.3
  • 4
    • 0025719432 scopus 로고
    • Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-Å resolution
    • Taylor D.A., Sack J.S., Maune J.F., Beckingham K., Quiocho F.A. Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-Å resolution. J. Biol. Chem. 266:1991;21375-21380.
    • (1991) J. Biol. Chem. , vol.266 , pp. 21375-21380
    • Taylor, D.A.1    Sack, J.S.2    Maune, J.F.3    Beckingham, K.4    Quiocho, F.A.5
  • 7
    • 0026794065 scopus 로고
    • Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex
    • Meador W.E., Means A.R., Quiocho F.A. Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex. Science. 257:1992;1251-1255.
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 8
    • 0029160568 scopus 로고
    • Calcium-induced conformational transition revealed by the solution structure of apo calmodulin
    • Zhang M., Tanaka M., Ikura T.M. Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat. Struct. Biol. 2:1995;758-767.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 758-767
    • Zhang, M.1    Tanaka, M.2    Ikura, T.M.3
  • 10
    • 0026536335 scopus 로고
    • Solution structure of a calmodulin-target peptide complex by multidimensional NMR
    • Ikura M., Clore M., Gronenborn A.M., Zhu G., Klee C.B., Bax A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 256:1992;632-638.
    • (1992) Science , vol.256 , pp. 632-638
    • Ikura, M.1    Clore, M.2    Gronenborn, A.M.3    Zhu, G.4    Klee, C.B.5    Bax, A.6
  • 11
    • 0023845141 scopus 로고
    • Comparison of the crystal and solution structures of calmodulin and troponin C
    • Heidorn D.B., Trewhella J. Comparison of the crystal and solution structures of calmodulin and troponin C. Biochemistry. 27:1988;909-915.
    • (1988) Biochemistry , vol.27 , pp. 909-915
    • Heidorn, D.B.1    Trewhella, J.2
  • 12
    • 0025996973 scopus 로고
    • 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy
    • 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. Biochemistry. 30:1991;9216-9228.
    • (1991) Biochemistry , vol.30 , pp. 9216-9228
    • Ikura, M.1    Spera, S.2    Barbato, G.3    Kay, L.E.4    Krinks, M.5    Bax, A.6
  • 13
    • 0026748968 scopus 로고
    • 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
    • 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible. Biochemistry. 31:1992;5269-5278.
    • (1992) Biochemistry , vol.31 , pp. 5269-5278
    • Barbato, G.1    Ikura, M.2    Kay, L.E.3    Pastor, R.W.4    Bax, A.5
  • 14
    • 0028232698 scopus 로고
    • Resolution of structural changes associated with calcium activation of calmodulin using frequency domain fluorescence spectroscopy
    • Yao Y., Schoeneich C., Squier T.C. Resolution of structural changes associated with calcium activation of calmodulin using frequency domain fluorescence spectroscopy. Biochemistry. 33:1994;7797-7810.
    • (1994) Biochemistry , vol.33 , pp. 7797-7810
    • Yao, Y.1    Schoeneich, C.2    Squier, T.C.3
  • 15
    • 0033592317 scopus 로고    scopus 로고
    • Calcium-dependent structural coupling between opposing globular domains of calmodulin involves the central helix
    • Sun H., Yin D., Squier T.C. Calcium-dependent structural coupling between opposing globular domains of calmodulin involves the central helix. Biochemistry. 38:1999;12266-12279.
    • (1999) Biochemistry , vol.38 , pp. 12266-12279
    • Sun, H.1    Yin, D.2    Squier, T.C.3
  • 17
    • 0028956081 scopus 로고
    • The energetics and dynamics of molecular recognition by calmodulin
    • Ehrhardt M.R., Urbauer J.L., Wand A.J. The energetics and dynamics of molecular recognition by calmodulin. Biochemistry. 34:1995;2731-2738.
    • (1995) Biochemistry , vol.34 , pp. 2731-2738
    • Ehrhardt, M.R.1    Urbauer, J.L.2    Wand, A.J.3
  • 18
    • 0033988897 scopus 로고    scopus 로고
    • Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex
    • Lee A.L., Kinnear S.A., Wand A.J. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat. Struct. Biol. 7:2000;72-77.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 72-77
    • Lee, A.L.1    Kinnear, S.A.2    Wand, A.J.3
  • 19
    • 0029731735 scopus 로고    scopus 로고
    • Localization of unique functional determinants in the calmodulin lobes of individual EF hands
    • Persechini A., Stemmer P.A., Ohashi I. Localization of unique functional determinants in the calmodulin lobes of individual EF hands. J. Biol. Chem. 271:1996;32217-32225.
    • (1996) J. Biol. Chem. , vol.271 , pp. 32217-32225
    • Persechini, A.1    Stemmer, P.A.2    Ohashi, I.3
  • 22
    • 0025148992 scopus 로고
    • Use of DNA sequence and mutant analyses and antisense oligonucleotides to examine the molecular basis of nonmuscle myosin light chain kinase autoinhibition, calmodulin recognition, and activity
    • Shoemaker M.O., Lau W., Shattuck R.L., Kwiatkowski A.P., Matrisian P.E., Guerra-Santos L., Wilson E., Lukas T.J., Van Eldrik L.J., Watterson D.M. Use of DNA sequence and mutant analyses and antisense oligonucleotides to examine the molecular basis of nonmuscle myosin light chain kinase autoinhibition, calmodulin recognition, and activity. J. Cell Biol. 111:1990;1107-1125.
    • (1990) J. Cell Biol. , vol.111 , pp. 1107-1125
    • Shoemaker, M.O.1    Lau, W.2    Shattuck, R.L.3    Kwiatkowski, A.P.4    Matrisian, P.E.5    Guerra-Santos, L.6    Wilson, E.7    Lukas, T.J.8    Van Eldrik, L.J.9    Watterson, D.M.10
  • 23
    • 0028784853 scopus 로고
    • Role of the N-terminal region of the skeletal muscle myosin light chain kinase target sequence in its interaction with calmodulin
    • Findlay W.A., Gradwell M.W., Bayley P.M. Role of the N-terminal region of the skeletal muscle myosin light chain kinase target sequence in its interaction with calmodulin. Protein Sci. 4:1995;2375-2382.
    • (1995) Protein Sci. , vol.4 , pp. 2375-2382
    • Findlay, W.A.1    Gradwell, M.W.2    Bayley, P.M.3
  • 24
    • 0022549779 scopus 로고
    • Calmodulin binding domains: Characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase
    • Lukas T.J., Burgess W.H., Prendergast F.G., Lau W., Watterson D.M. Calmodulin binding domains: characterization of a phosphorylation and calmodulin binding site from myosin light chain kinase. Biochemistry. 25:1986;1458-1464.
    • (1986) Biochemistry , vol.25 , pp. 1458-1464
    • Lukas, T.J.1    Burgess, W.H.2    Prendergast, F.G.3    Lau, W.4    Watterson, D.M.5
  • 25
    • 0028965961 scopus 로고
    • Recovery of native structure by calcium binding site mutants of calmodulin upon binding of sm-MLCK target peptide
    • Findlay W.A., Martin S.R., Beckingham K., Bayley P.M. Recovery of native structure by calcium binding site mutants of calmodulin upon binding of sm-MLCK target peptide. Biochemistry. 34:1995;2087-2094.
    • (1995) Biochemistry , vol.34 , pp. 2087-2094
    • Findlay, W.A.1    Martin, S.R.2    Beckingham, K.3    Bayley, P.M.4
  • 26
    • 0031567108 scopus 로고    scopus 로고
    • Energetics of target peptide recognition by calmodulin: A calorimetric study
    • Wintrode P.L., Privalov P.L. Energetics of target peptide recognition by calmodulin: a calorimetric study. J. Mol. Biol. 266:1997;1050-1062.
    • (1997) J. Mol. Biol. , vol.266 , pp. 1050-1062
    • Wintrode, P.L.1    Privalov, P.L.2
  • 27
    • 0035958004 scopus 로고    scopus 로고
    • Energetics of target peptide binding by calmodulin reveals different modes of binding
    • Brockx R.D., Lopez M.M., Vogel H.J., Makhatadze G.I. Energetics of target peptide binding by calmodulin reveals different modes of binding. J. Biol. Chem. 276:2001;14083-14091.
    • (2001) J. Biol. Chem. , vol.276 , pp. 14083-14091
    • Brockx, R.D.1    Lopez, M.M.2    Vogel, H.J.3    Makhatadze, G.I.4
  • 29
    • 0026599780 scopus 로고
    • Molecular dynamics simulations of calmodulin in the extended and in a bent conformation
    • Vorherr T., Kessler O., Mark A., Carafoli E. Molecular dynamics simulations of calmodulin in the extended and in a bent conformation. Eur. J. Biochem. 204:1992;913-937.
    • (1992) Eur. J. Biochem. , vol.204 , pp. 913-937
    • Vorherr, T.1    Kessler, O.2    Mark, A.3    Carafoli, E.4
  • 32
    • 0035029050 scopus 로고    scopus 로고
    • Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin
    • Vigil D., Gallagher S.C., Trewhella J., Garcia A.E. Functional dynamics of the hydrophobic cleft in the N-domain of calmodulin. Biophys. J. 80:2001;2082-2092.
    • (2001) Biophys. J. , vol.80 , pp. 2082-2092
    • Vigil, D.1    Gallagher, S.C.2    Trewhella, J.3    Garcia, A.E.4
  • 33
    • 0028124954 scopus 로고
    • Investigating the high affinity and low sequence specificity of calmodulin binding to its targets
    • Afshar A., Caves L.S.D., Guimard L., Hubbard R.E., Calas B., Grassy G., Haiech J. Investigating the high affinity and low sequence specificity of calmodulin binding to its targets. J. Mol. Biol. 244:1994;554-571.
    • (1994) J. Mol. Biol. , vol.244 , pp. 554-571
    • Afshar, A.1    Caves, L.S.D.2    Guimard, L.3    Hubbard, R.E.4    Calas, B.5    Grassy, G.6    Haiech, J.7
  • 34
    • 0036250080 scopus 로고    scopus 로고
    • Molecular dynamics simulations of calcium-free calmodulin in solution
    • Yang C., Kuczera K. Molecular dynamics simulations of calcium-free calmodulin in solution. J. Biomol. Struct. Dyn. 19:2002;801-820.
    • (2002) J. Biomol. Struct. Dyn. , vol.19 , pp. 801-820
    • Yang, C.1    Kuczera, K.2
  • 35
    • 0034761290 scopus 로고    scopus 로고
    • Structure and dynamics of calcium-activated calmodulin in solution
    • Yang C., Jas G.S., Kuczera K. Structure and dynamics of calcium-activated calmodulin in solution. J. Biomol. Struct. Dyn. 19:2001;247-271.
    • (2001) J. Biomol. Struct. Dyn. , vol.19 , pp. 247-271
    • Yang, C.1    Jas, G.S.2    Kuczera, K.3
  • 36
    • 0036805880 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a calmodulin-peptide complex in solution
    • Yang C., Kuczera K. Molecular dynamics simulations of a calmodulin-peptide complex in solution. J. Biomol. Struct. Dyn. 20:2002;179-197.
    • (2002) J. Biomol. Struct. Dyn. , vol.20 , pp. 179-197
    • Yang, C.1    Kuczera, K.2
  • 40
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
    • Sagui C., Darden T.A. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 28:1999;155-179.
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 155-179
    • Sagui, C.1    Darden, T.A.2
  • 41
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the cartesian equations of motion with constraints: molecular dynamics of n-alkanes. J. Comp. Physiol. 23:1977;327-341.
    • (1977) J. Comp. Physiol. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 42
    • 0000577041 scopus 로고
    • Nonlinear dynamics of proteins
    • Garcia A.E. Nonlinear dynamics of proteins. Phys. Rev. Lett. 68:1992;2696-2699.
    • (1992) Phys. Rev. Lett. , vol.68 , pp. 2696-2699
    • Garcia, A.E.1
  • 44
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I., Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J. Chem. Phys. 115:2001;6289-6292.
    • (2001) J. Chem. Phys. , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 45
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and application
    • Sharp K.A., Honig B. Electrostatic interactions in macromolecules: theory and application. Annu. Rev. Biophys. Biophys. Chem. 19:1990;301.
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301
    • Sharp, K.A.1    Honig, B.2
  • 46
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 268:1995;1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 47
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • Simonson T., Brunger A. Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment. J. Phys. Chem. 98:1994;4683-4694.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4683-4694
    • Simonson, T.1    Brunger, A.2
  • 48
    • 0000435390 scopus 로고    scopus 로고
    • Comparison of continuum and explicit models of solvation: Potential of mean force for alanine dipeptide
    • Marrone T.J., Gilson M.K., McCammon J.A. Comparison of continuum and explicit models of solvation: potential of mean force for alanine dipeptide. J. Phys. Chem. 100:1996;1439-1441.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1439-1441
    • Marrone, T.J.1    Gilson, M.K.2    McCammon, J.A.3
  • 52
    • 0036234027 scopus 로고    scopus 로고
    • Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized born model and with explicit water
    • Xia B., Tsui V., Case D.A., Dyson H.J., Wright P.E. Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized born model and with explicit water. J. Biomol. NMR. 22:2002;317-331.
    • (2002) J. Biomol. NMR , vol.22 , pp. 317-331
    • Xia, B.1    Tsui, V.2    Case, D.A.3    Dyson, H.J.4    Wright, P.E.5
  • 53
    • 0029969392 scopus 로고    scopus 로고
    • Oxidative modification of a carboxyl-terminal vicinal methionine in calmodulin by peroxide inhibits calmodulin-dependent activation of the plasma-membrane Ca-ATPase
    • Yao Y., Yin D., Jas G., Kuczera K., Williams T.D., Schöneich C., Squier T.C. Oxidative modification of a carboxyl-terminal vicinal methionine in calmodulin by peroxide inhibits calmodulin-dependent activation of the plasma-membrane Ca-ATPase. Biochemistry. 35:1996;2767-2787.
    • (1996) Biochemistry , vol.35 , pp. 2767-2787
    • Yao, Y.1    Yin, D.2    Jas, G.3    Kuczera, K.4    Williams, T.D.5    Schöneich, C.6    Squier, T.C.7
  • 54
    • 0034059865 scopus 로고    scopus 로고
    • Sensitivity of carboxyl-terminus methionines in calmodulin isoforms to oxidation by HO modulates the ability to activate the plasma membrane ca-ATPase
    • Yin D., Kuczera K., Squier T.C. Sensitivity of carboxyl-terminus methionines in calmodulin isoforms to oxidation by HO modulates the ability to activate the plasma membrane ca-ATPase. Chem. Res. Toxicol. 13:2000;103-110.
    • (2000) Chem. Res. Toxicol. , vol.13 , pp. 103-110
    • Yin, D.1    Kuczera, K.2    Squier, T.C.3
  • 55
    • 0034669358 scopus 로고    scopus 로고
    • Diastereoselective protein methionine oxidation by reactive oxygen species and diastereoselective repair by methionine sulfoxide reductase
    • Sharov V.S., Schoeneich C.S. Diastereoselective protein methionine oxidation by reactive oxygen species and diastereoselective repair by methionine sulfoxide reductase. Free Radic. Biol. Med. 29:2000;986-994.
    • (2000) Free Radic. Biol. Med. , vol.29 , pp. 986-994
    • Sharov, V.S.1    Schoeneich, C.S.2
  • 56
    • 0033605726 scopus 로고    scopus 로고
    • Surface exposure of the methionine sidechains of calmodulin in solution. a nitroxide spin label and two-dimensional NMR study
    • Yuan T., Ouyang H., Vogel H.J. Surface exposure of the methionine sidechains of calmodulin in solution. a nitroxide spin label and two-dimensional NMR study. J. Biol. Chem. 274:1999;8411-8420.
    • (1999) J. Biol. Chem. , vol.274 , pp. 8411-8420
    • Yuan, T.1    Ouyang, H.2    Vogel, H.J.3
  • 57
    • 0024745871 scopus 로고
    • The price of lost freedom: Entropy of biomolecular complex formation
    • Finkelstein A.V., Janin J. The price of lost freedom: entropy of biomolecular complex formation. Protein Eng. 3:1989;1-3.
    • (1989) Protein Eng. , vol.3 , pp. 1-3
    • Finkelstein, A.V.1    Janin, J.2
  • 58
    • 0024279165 scopus 로고
    • The central helix of calmodulin functions as a flexible tether
    • Persechini A., Kretsinger R.H. The central helix of calmodulin functions as a flexible tether. J. Biol. Chem. 263:1988;12175-12178.
    • (1988) J. Biol. Chem. , vol.263 , pp. 12175-12178
    • Persechini, A.1    Kretsinger, R.H.2
  • 60
    • 0030945196 scopus 로고    scopus 로고
    • Sequence motifs for calmodulin recognition
    • Rhoads A.R., Friedberg F. Sequence motifs for calmodulin recognition. FASEB J. 11:1997;331-340.
    • (1997) FASEB J. , vol.11 , pp. 331-340
    • Rhoads, A.R.1    Friedberg, F.2
  • 61
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1


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