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Volumn 91, Issue 8, 2006, Pages 2768-2777

Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN; METHIONINE; MYOSIN LIGHT CHAIN KINASE; PROTEIN; PROTEIN M13; UNCLASSIFIED DRUG;

EID: 33749519366     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.086611     Document Type: Article
Times cited : (41)

References (58)
  • 1
    • 31944434700 scopus 로고    scopus 로고
    • Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: Two ways to promote multifunctionality
    • Ikura, M., and J. B. Ames. 2006. Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality. Proc. Natl. Acad. Sci. USA. 103:1159-1164.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1159-1164
    • Ikura, M.1    Ames, J.B.2
  • 2
    • 0037022309 scopus 로고    scopus 로고
    • Calcium signaling: A tale for all seasons
    • Carafoli, E. 2002. Calcium signaling: a tale for all seasons. Proc. Natl. Acad. Sci. USA. 99:1115-1122.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1115-1122
    • Carafoli, E.1
  • 3
    • 0029189946 scopus 로고
    • Calcium-binding proteins 1: EF-hands
    • Kawasaki, H., and R. H. Kretsinger. 1995. Calcium-binding proteins 1: EF-hands. Protein Profile. 2:297-490.
    • (1995) Protein Profile , vol.2 , pp. 297-490
    • Kawasaki, H.1    Kretsinger, R.H.2
  • 4
    • 0025159272 scopus 로고
    • How calmodulin binds its targets: Sequence independent recognition of amphiphilic α-helices
    • O'Neil, K. T., and W. F. DeGrado. 1990. How calmodulin binds its targets: sequence independent recognition of amphiphilic α-helices. Trends Biochem. Sci. 15:59-64.
    • (1990) Trends Biochem. Sci. , vol.15 , pp. 59-64
    • O'Neil, K.T.1    DeGrado, W.F.2
  • 5
    • 0029149085 scopus 로고
    • Molecular and structural basis of target recognition by calmodulin
    • Crivici, A., and M. Ikura. 1995. Molecular and structural basis of target recognition by calmodulin. Annu. Rev. Biophys. Biomol. Struct. 24:85-116.
    • (1995) Annu. Rev. Biophys. Biomol. Struct. , vol.24 , pp. 85-116
    • Crivici, A.1    Ikura, M.2
  • 7
    • 0037155689 scopus 로고    scopus 로고
    • Calmodulin in action: Diversity in target recognition and activation mechanisms
    • Hoeflich, K. P., and M. Ikura. 2002. Calmodulin in action: diversity in target recognition and activation mechanisms. Cell. 108:739-742.
    • (2002) Cell , vol.108 , pp. 739-742
    • Hoeflich, K.P.1    Ikura, M.2
  • 8
    • 0026536335 scopus 로고
    • Solution structure of a calmodulin-target peptide complex by multidimensional NMR
    • Ikura, M., G. M. Clore, A. M. Gronenborn, G. Zhu, C. B. Klee, and A. Bax. 1992. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science. 256:632-638.
    • (1992) Science , vol.256 , pp. 632-638
    • Ikura, M.1    Clore, G.M.2    Gronenborn, A.M.3    Zhu, G.4    Klee, C.B.5    Bax, A.6
  • 9
    • 0028176721 scopus 로고
    • The effect of met → leu mutations on calmodulin's ability to activate cyclic nucleotide phosphodiesterase
    • Zhang, M., M. Li, J. H. Wang, and H. J. Vogel. 1994. The effect of met → leu mutations on calmodulin's ability to activate cyclic nucleotide phosphodiesterase. J. Biol. Chem. 269:15546-15552.
    • (1994) J. Biol. Chem. , vol.269 , pp. 15546-15552
    • Zhang, M.1    Li, M.2    Wang, J.H.3    Vogel, H.J.4
  • 10
    • 4744372036 scopus 로고    scopus 로고
    • Systematic delineation of a calmodulin peptide interaction
    • Hultschig, C., H. J. Hecht, and R. Frank. 2004. Systematic delineation of a calmodulin peptide interaction. J. Mol. Biol. 343:559-568.
    • (2004) J. Mol. Biol. , vol.343 , pp. 559-568
    • Hultschig, C.1    Hecht, H.J.2    Frank, R.3
  • 11
    • 0344392711 scopus 로고    scopus 로고
    • Exploring the origins of binding specificity through the computational redesign of calmodulin
    • Shifman, J. M., and S. L. Mayo. 2003. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc. Natl. Acad. Sci. USA. 100:13274-13279.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13274-13279
    • Shifman, J.M.1    Mayo, S.L.2
  • 12
    • 0029803672 scopus 로고    scopus 로고
    • Methionine to glutamine substitutions in the C-terminal domain of calmodulin impair the activation of three protein kinases
    • Chin, D., and A. R. Means. 1996. Methionine to glutamine substitutions in the C-terminal domain of calmodulin impair the activation of three protein kinases. J. Biol. Chem. 271:30465-30471.
    • (1996) J. Biol. Chem. , vol.271 , pp. 30465-30471
    • Chin, D.1    Means, A.R.2
  • 13
    • 0032055830 scopus 로고    scopus 로고
    • Activation of calcineurin and smooth muscle myosin light chain kinase by Met-to-Leu mutants of calmodulin
    • Edwards, R. A., M. P. Walsh, C. Sutherland, and H. J. Vogel. 1998. Activation of calcineurin and smooth muscle myosin light chain kinase by Met-to-Leu mutants of calmodulin. Biochem. J. 331:149-152.
    • (1998) Biochem. J. , vol.331 , pp. 149-152
    • Edwards, R.A.1    Walsh, M.P.2    Sutherland, C.3    Vogel, H.J.4
  • 14
    • 0031567108 scopus 로고    scopus 로고
    • Energetics of target peptide recognition by calmodulin: A calorimetric study
    • Wintrode, P. L., and P. L. Privalov. 1997. Energetics of target peptide recognition by calmodulin: a calorimetric study. J. Mol. Biol. 266:1050-1062.
    • (1997) J. Mol. Biol. , vol.266 , pp. 1050-1062
    • Wintrode, P.L.1    Privalov, P.L.2
  • 15
    • 0033988897 scopus 로고    scopus 로고
    • Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex
    • Lee, A. L., S. A. Kinnear, and A. J. Wand. 2000. Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex. Nat. Struct. Biol. 7:72-77.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 72-77
    • Lee, A.L.1    Kinnear, S.A.2    Wand, A.J.3
  • 16
    • 0033986595 scopus 로고    scopus 로고
    • May the driving force be with you - Whatever it is
    • Cavanagh, J., and M. Akke. 2000. May the driving force be with you - whatever it is. Nat. Struct. Biol. 7:11-13.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 11-13
    • Cavanagh, J.1    Akke, M.2
  • 17
    • 0037457815 scopus 로고    scopus 로고
    • Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics
    • Prabhu, N. V., A. L. Lee, A. J. Wand, and K. A. Sharp. 2003. Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry. 42:562-570.
    • (2003) Biochemistry , vol.42 , pp. 562-570
    • Prabhu, N.V.1    Lee, A.L.2    Wand, A.J.3    Sharp, K.A.4
  • 19
    • 0028305218 scopus 로고
    • Activation of myosin light chain kinase and nitric oxide synthase activities by calmodulin fragments
    • Persechini, A., K. McMillan, and P. Leakey. 1994. Activation of myosin light chain kinase and nitric oxide synthase activities by calmodulin fragments. J. Biol. Chem. 269:16148-16154.
    • (1994) J. Biol. Chem. , vol.269 , pp. 16148-16154
    • Persechini, A.1    McMillan, K.2    Leakey, P.3
  • 20
    • 33646476301 scopus 로고    scopus 로고
    • Reconstitution of calmodulin from domains and subdomains: Influence of target peptide
    • Shuman, C. F., R. Jiji, K. S. Kerfeldt, and S. Linse. 2006. Reconstitution of calmodulin from domains and subdomains: influence of target peptide. J. Mol. Biol. 358:870-881.
    • (2006) J. Mol. Biol. , vol.358 , pp. 870-881
    • Shuman, C.F.1    Jiji, R.2    Kerfeldt, K.S.3    Linse, S.4
  • 22
    • 0041810451 scopus 로고    scopus 로고
    • Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics
    • Iannuzzi, M., A. Laio, and M. Parrinello. 2003. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys. Rev. Lett. 90:238-302.
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 238-302
    • Iannuzzi, M.1    Laio, A.2    Parrinello, M.3
  • 23
    • 3543055345 scopus 로고    scopus 로고
    • A minimum free energy reaction path for the e2 reaction between fluoro ethane and a fluoride ion
    • Ensing, B., A. Laio, F. L. Gervasio, M. Parrinello, and M. L. Klein. 2004. A minimum free energy reaction path for the e2 reaction between fluoro ethane and a fluoride ion. J. Am. Chem. Soc. 126:9492-9493.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 9492-9493
    • Ensing, B.1    Laio, A.2    Gervasio, F.L.3    Parrinello, M.4    Klein, M.L.5
  • 24
    • 14744276066 scopus 로고    scopus 로고
    • Flexible docking in solution using metadynamics
    • Gervasio, F. L., A. Laio, and M. Parrinello. 2005. Flexible docking in solution using metadynamics. J. Am. Chem. Soc. 127:2600-2607.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 2600-2607
    • Gervasio, F.L.1    Laio, A.2    Parrinello, M.3
  • 25
    • 21244439384 scopus 로고    scopus 로고
    • The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge
    • Branduardi, D., F. L. Gervasio, A. Cavalli, M. Recanatini, and M. Parrinello. 2005. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J. Am. Chem. Soc. 127:9147-9155.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9147-9155
    • Branduardi, D.1    Gervasio, F.L.2    Cavalli, A.3    Recanatini, M.4    Parrinello, M.5
  • 27
    • 0019182299 scopus 로고
    • Activation of skeletal muscle myosin light chain kinase by calcium(2+) and calmodulin
    • Blumenthal, D. K., and J. T. Stull. 1980. Activation of skeletal muscle myosin light chain kinase by calcium(2+) and calmodulin. Biochemistry. 19:5608-5614.
    • (1980) Biochemistry , vol.19 , pp. 5608-5614
    • Blumenthal, D.K.1    Stull, J.T.2
  • 28
    • 0019962812 scopus 로고
    • Effects of pH, ionic strength, and temperature on activation by calmodulin and catalytic activity of myosin light chain kinase
    • Blumenthal, D. K., and J. T. Stull. 1982. Effects of pH, ionic strength, and temperature on activation by calmodulin and catalytic activity of myosin light chain kinase. Biochemistry. 21:2386-2391.
    • (1982) Biochemistry , vol.21 , pp. 2386-2391
    • Blumenthal, D.K.1    Stull, J.T.2
  • 29
    • 0028965961 scopus 로고
    • Recovery of native structure by calcium binding site mutants of calmodulin upon binding of sk-MLCK target peptides
    • Findlay, W. A., S. R. Martin, K. Beckingham, and P. M. Bayley. 1995. Recovery of native structure by calcium binding site mutants of calmodulin upon binding of sk-MLCK target peptides. Biochemistry. 34:2087-2094.
    • (1995) Biochemistry , vol.34 , pp. 2087-2094
    • Findlay, W.A.1    Martin, S.R.2    Beckingham, K.3    Bayley, P.M.4
  • 30
    • 0026794065 scopus 로고
    • Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex
    • Meador, W. E., A. R. Means, and F. A. Quiocho. 1992. Target enzyme recognition by calmodulin: 2.4 Å structure of a calmodulin-peptide complex. Science. 257:1251-1255.
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 31
    • 0028956081 scopus 로고
    • The energetics and dynamics of molecular recognition by calmodulin
    • Ehrhardt, M. R., J. L. Urbauer, and A. J. Wand. 1995. The energetics and dynamics of molecular recognition by calmodulin. Biochemistry. 34:2731-2738.
    • (1995) Biochemistry , vol.34 , pp. 2731-2738
    • Ehrhardt, M.R.1    Urbauer, J.L.2    Wand, A.J.3
  • 32
    • 0034635461 scopus 로고    scopus 로고
    • 2+ binding and energy coupling in the calmodulin-myosin light chain kinase complex
    • 2+ binding and energy coupling in the calmodulin-myosin light chain kinase complex. J. Biol. Chem. 275:4199-4204.
    • (2000) J. Biol. Chem. , vol.275 , pp. 4199-4204
    • Persechini, A.1    Kano, K.2    Stemmer, P.L.3
  • 33
    • 1542358827 scopus 로고    scopus 로고
    • Structure, dynamics and interaction with kinase targets: Computer simulations of calmodulin
    • Yang, C., G. S. Jas, and K. Kuczera. 2004. Structure, dynamics and interaction with kinase targets: computer simulations of calmodulin. Biochim. Biophys. Acta. 1697:289-300.
    • (2004) Biochim. Biophys. Acta , vol.1697 , pp. 289-300
    • Yang, C.1    Jas, G.S.2    Kuczera, K.3
  • 34
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder, J. W., and D. A. Case. 2003. Force fields for protein simulations. Adv. Prot. Chem. 66:27-85.
    • (2003) Adv. Prot. Chem. , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 39
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna, G., D. Tobias, and M. Klein. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.1    Tobias, D.2    Klein, M.3
  • 40
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 41
    • 11544327705 scopus 로고
    • Solvation dynamics for an ion pair in a polar solvent: Time-dependent fluorescence and photochemical charge transfer
    • Carter, E. A., and J. T. Hynes. 1991. Solvation dynamics for an ion pair in a polar solvent: time-dependent fluorescence and photochemical charge transfer. J. Chem. Phys. 94:5961-5979.
    • (1991) J. Chem. Phys. , vol.94 , pp. 5961-5979
    • Carter, E.A.1    Hynes, J.T.2
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 43
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:4546-4559.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 44
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
    • Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104:4559-4570.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 45
    • 0033620360 scopus 로고    scopus 로고
    • 13C NMR relaxation techniques for the study of protein methyl group dynamics in solution
    • 13C NMR relaxation techniques for the study of protein methyl group dynamics in solution. J. Am. Chem. Soc. 121:2891-2902.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 2891-2902
    • Lee, A.1    Flynn, P.2    Wand, A.3
  • 47
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. Van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7:306-317.
    • (2001) J. Mol. Mod. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 48
    • 0035742163 scopus 로고    scopus 로고
    • The VMD-XPLOR visualization package for NMR structure refinement
    • Schwieters, C. D., and G. M. Clore. 2001. The VMD-XPLOR visualization package for NMR structure refinement. J. Magn. Res. 149:239-244.
    • (2001) J. Magn. Res. , vol.149 , pp. 239-244
    • Schwieters, C.D.1    Clore, G.M.2
  • 50
    • 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. 31:5269-5278.
    • (1992) Biochemistry , vol.31 , pp. 5269-5278
    • Barbato, G.1    Ikura, M.2    Kay, L.E.3    Pastor, R.W.4    Bax, A.5
  • 51
    • 0141506108 scopus 로고    scopus 로고
    • Protein Ligand Database (PLD): Additional understanding of the nature and specificity of protein-ligand complexes
    • Puvanendrampillai, D., and J. B. O. Mitchell. 2003. Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics. 19:1856-1857.
    • (2003) Bioinformatics , vol.19 , pp. 1856-1857
    • Puvanendrampillai, D.1    Mitchell, J.B.O.2
  • 53
    • 28644432411 scopus 로고    scopus 로고
    • Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study
    • Fiorin, G., R. R. Biekofsky, A. Pastore, and P. Carloni. 2005. Unwinding the helical linker of calcium-loaded calmodulin: a molecular dynamics study. Proteins. 61:829-839.
    • (2005) Proteins , vol.61 , pp. 829-839
    • Fiorin, G.1    Biekofsky, R.R.2    Pastore, A.3    Carloni, P.4
  • 54
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • Cheatham, T. E., P. Cieplak III, and P. A. Kollman. 1999. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16:845-862.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham, T.E.1    Cieplak III, P.2    Kollman, P.A.3
  • 55
    • 0036250080 scopus 로고    scopus 로고
    • Molecular dynamics simulations of calcium-free calmodulin in solution
    • Yang, C., and K. Kuczera. 2002. Molecular dynamics simulations of calcium-free calmodulin in solution. J. Biomol. Struct. Dyn. 19:801-819.
    • (2002) J. Biomol. Struct. Dyn. , vol.19 , pp. 801-819
    • Yang, C.1    Kuczera, K.2
  • 56
    • 33644557736 scopus 로고    scopus 로고
    • Binding of phosphinate and phosphonate inhibitors to aspartic proteases: A first-principles study
    • Vidossich, P., and P. Carloni. 2006. Binding of phosphinate and phosphonate inhibitors to aspartic proteases: a first-principles study. J. Phys. Chem. B. 110:1437-1442.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 1437-1442
    • Vidossich, P.1    Carloni, P.2
  • 57
    • 0035958004 scopus 로고    scopus 로고
    • Energetics of target peptide binding by calmodulin reveals different modes of binding
    • Brokx, R. D., M. M. Lopez, H. J. Vogel, and G. I. Makhatadze. 2001. Energetics of target peptide binding by calmodulin reveals different modes of binding. J. Biol. Chem. 276:14083-14091.
    • (2001) J. Biol. Chem. , vol.276 , pp. 14083-14091
    • Brokx, R.D.1    Lopez, M.M.2    Vogel, H.J.3    Makhatadze, G.I.4


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