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Volumn 51, Issue 11, 2008, Pages 3081-3093

Interaction of antagonists with calmodulin: Insights from molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

BIPHENYL DERIVATIVE; CALMODULIN; CALMODULIN INHIBITOR; N (3,3 DIPHENYLPROPYL) N' [(3,4 BISBUTOXYPHENYL)ETHYL]PROPYLENEDIAMINE; TRIFLUOPERAZINE;

EID: 44949141462     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm701406e     Document Type: Article
Times cited : (7)

References (84)
  • 1
    • 0019982268 scopus 로고
    • Calmodulin: An overview
    • Cheung, W. Y. Calmodulin: An overview. FED Proc. 1982, 41, 2253-2227.
    • (1982) FED Proc , vol.41 , pp. 2253-2227
    • Cheung, W.Y.1
  • 2
    • 0346366556 scopus 로고    scopus 로고
    • Calmodulin and various ways to regulate its activity
    • Kortvely, E.; Gulya, K. Calmodulin and various ways to regulate its activity. Life Sci. 2004, 74, 1065-1070.
    • (2004) Life Sci , vol.74 , pp. 1065-1070
    • Kortvely, E.1    Gulya, K.2
  • 3
    • 0037318056 scopus 로고    scopus 로고
    • Novel aspects of calmodulin target recognition and activation
    • Vetter, S. W.; Leclerc, E. Novel aspects of calmodulin target recognition and activation. Eur. J. Biochem. 2003, 270, 404-414.
    • (2003) Eur. J. Biochem , vol.270 , pp. 404-414
    • Vetter, S.W.1    Leclerc, E.2
  • 4
    • 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. 1995, 24, 85-116.
    • (1995) Annu. Rev. Biophys. Biomol. Struct , vol.24 , pp. 85-116
    • Crivici, A.1    Ikura, M.2
  • 5
    • 0035958004 scopus 로고    scopus 로고
    • Energetics of target peptide binding by calmodulin reveals different modes of binding
    • Brokx, 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. 2001, 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
  • 7
    • 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. 2001, 80, 2082-2092.
    • (2001) Biophys. J , vol.80 , pp. 2082-2092
    • Vigil, D.1    Gallagher, S.C.2    Trewhella, J.3    Garcia, A.E.4
  • 8
    • 0027529026 scopus 로고
    • Structure of Paramecium tetraurelia calmodulin at 1.8 A resolution
    • Rao, S. T.; Wu, S.; Satyshur, K. A.; Ling, K. Y.; Kung, C.; et al. Structure of Paramecium tetraurelia calmodulin at 1.8 A resolution. Protein Sci. 1993, 2, 436-447.
    • (1993) Protein Sci , vol.2 , pp. 436-447
    • Rao, S.T.1    Wu, S.2    Satyshur, K.A.3    Ling, K.Y.4    Kung, C.5
  • 10
    • 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 1988, 27, 909-915.
    • (1988) Biochemistry , vol.27 , pp. 909-915
    • Heidorn, D.B.1    Trewhella, J.2
  • 11
    • 0026748968 scopus 로고
    • Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
    • Barbato, G.; Ikura, M.; Key, L. E.; Pastor, R. W.; Bax, A. Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible. Biochemistry 1992, 31, 5269-5278.
    • (1992) Biochemistry , vol.31 , pp. 5269-5278
    • Barbato, G.1    Ikura, M.2    Key, L.E.3    Pastor, R.W.4    Bax, A.5
  • 13
    • 44949235744 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. 2001, 80, 2082-2092.
    • (2001) J. Biomol. Struct. Dyn , vol.80 , pp. 2082-2092
    • Yang, C.1    Jas, G.S.2    Kuczera, K.3
  • 14
    • 4143151599 scopus 로고    scopus 로고
    • + -calmodulin: Evidence of interdomain coupling and structural collapse on the nanosecond timescale
    • + -calmodulin: Evidence of interdomain coupling and structural collapse on the nanosecond timescale. Biophys. J. 2004, 87, 780-791.
    • (2004) Biophys. J , vol.87 , pp. 780-791
    • Shepherd, C.M.1    Vogel, H.J.2
  • 15
    • 28644432411 scopus 로고    scopus 로고
    • Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study
    • Fiorin, G.; Biekofshy, R. R.; Pastore, A.; Carloni, P. Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study. Proteins: Struct., Funct., Genet. 2005, 61, 829-839.
    • (2005) Proteins: Struct., Funct., Genet , vol.61 , pp. 829-839
    • Fiorin, G.1    Biekofshy, R.R.2    Pastore, A.3    Carloni, P.4
  • 16
    • 0030008340 scopus 로고    scopus 로고
    • Target recognition by calmodulin: Dissecting the kinetics and affinity of interactin using short peptide sequences
    • Bayley, P. M.; Findlay, W. A.; Martin, S. R. Target recognition by calmodulin: Dissecting the kinetics and affinity of interactin using short peptide sequences. Protein Sci. 1996, 5, 1215-1228.
    • (1996) Protein Sci , vol.5 , pp. 1215-1228
    • Bayley, P.M.1    Findlay, W.A.2    Martin, S.R.3
  • 17
    • 4444253338 scopus 로고    scopus 로고
    • Calmodulin binds to and inhibits the activity of phosphoglycerate kinase
    • Myre, M. A.; O'Day, D. H. Calmodulin binds to and inhibits the activity of phosphoglycerate kinase. Biochim. Biophys. Acta 2004, 1693, 177-183.
    • (2004) Biochim. Biophys. Acta , vol.1693 , pp. 177-183
    • Myre, M.A.1    O'Day, D.H.2
  • 18
    • 0037138403 scopus 로고    scopus 로고
    • Callmodulin signaling via the IQ motif
    • Baehler, M.; Rhoads, A. Callmodulin signaling via the IQ motif. FEBS Lett. 2002, 513, 107-113.
    • (2002) FEBS Lett , vol.513 , pp. 107-113
    • Baehler, M.1    Rhoads, A.2
  • 19
    • 0030945196 scopus 로고    scopus 로고
    • Sequence motifs for calmodulin recognition
    • Rhoads, A. R.; Friedberg, F. Sequence motifs for calmodulin recognition. FASEB J. 1997, 11, 331-340.
    • (1997) FASEB J , vol.11 , pp. 331-340
    • Rhoads, A.R.1    Friedberg, F.2
  • 20
    • 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 1992, 257, 1251-1255.
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 21
    • 0019321879 scopus 로고
    • Hydrophobic region function in calmodulin-enzyme interactions
    • Tanaka, T.; Hidaka, H. Hydrophobic region function in calmodulin-enzyme interactions. J. Biol. Chem. 1980, 255, 11078-11080.
    • (1980) J. Biol. Chem , vol.255 , pp. 11078-11080
    • Tanaka, T.1    Hidaka, H.2
  • 22
    • 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. 2002, 20, 179-197.
    • (2002) J. Biomol. Struct. Dyn , vol.20 , pp. 179-197
    • Yang, C.1    Kuczera, K.2
  • 24
    • 0030066214 scopus 로고    scopus 로고
    • Homologs of idoxifene: Variation of estrogen receptor binding and calmodulin antagonism with chain length
    • Hardcastle, I. R.; Rowlands, M. G.; Grimshaw, R. M.; Houghton, J.; Jarman, M.; et al. Homologs of idoxifene: Variation of estrogen receptor binding and calmodulin antagonism with chain length. J. Med. Chem. 1996, 39, 999-1004.
    • (1996) J. Med. Chem , vol.39 , pp. 999-1004
    • Hardcastle, I.R.1    Rowlands, M.G.2    Grimshaw, R.M.3    Houghton, J.4    Jarman, M.5
  • 26
    • 0034737308 scopus 로고    scopus 로고
    • Harmat, V.; Boecskei, Z.; Naray-Szabo, G.; Bata, I.; Csutor, S. A. A new potent calmodulin antagonist with arylalkylamine structure: Crystallographic, spectroscopic and functional studies. J. Mol. Biol. 2000, 297, 747-755.
    • Harmat, V.; Boecskei, Z.; Naray-Szabo, G.; Bata, I.; Csutor, S. A. A new potent calmodulin antagonist with arylalkylamine structure: Crystallographic, spectroscopic and functional studies. J. Mol. Biol. 2000, 297, 747-755.
  • 27
    • 0022927779 scopus 로고
    • Binding of trifluoperazine and fluorene-containing compounds to calmodulin and adducts
    • Jackson, A. E.; Puett, D. Binding of trifluoperazine and fluorene-containing compounds to calmodulin and adducts. Biochem. Pharmacol. 1986, 35, 4395-4400.
    • (1986) Biochem. Pharmacol , vol.35 , pp. 4395-4400
    • Jackson, A.E.1    Puett, D.2
  • 28
    • 0025101653 scopus 로고
    • Trifluoperazine binding to porcine brain calmodulin and skeletal muscle troponin C
    • Massom, L.; Lee, H.; Jarrett, H. W. Trifluoperazine binding to porcine brain calmodulin and skeletal muscle troponin C. Biochemistry 1990, 29, 671-681.
    • (1990) Biochemistry , vol.29 , pp. 671-681
    • Massom, L.1    Lee, H.2    Jarrett, H.W.3
  • 30
    • 0022374897 scopus 로고
    • Effects of trifluoperazine on calcium binding by calmodulin. A microcalorimetric study
    • Tanokura, M.; Yamada, K. Effects of trifluoperazine on calcium binding by calmodulin. A microcalorimetric study. J. Biol. Chem. 1985, 260, 8680-8682.
    • (1985) J. Biol. Chem , vol.260 , pp. 8680-8682
    • Tanokura, M.1    Yamada, K.2
  • 31
    • 0017701494 scopus 로고
    • Binding of trifluoperazine to the calcium-dependent activator of cyclic nucleotide phosphodiesterase
    • Levin, R. M.; Weiis, B. Binding of trifluoperazine to the calcium-dependent activator of cyclic nucleotide phosphodiesterase. Mol. Pharmacol. 1977, 13, 690-697.
    • (1977) Mol. Pharmacol , vol.13 , pp. 690-697
    • Levin, R.M.1    Weiis, B.2
  • 32
    • 0028558882 scopus 로고
    • Drug binding by calmodulin: Crystal structure of calmodulin-trifluoperazine complex
    • Cook, W. J.; Walter, L. J.; Walter, M. R. Drug binding by calmodulin: Crystal structure of calmodulin-trifluoperazine complex. Biochemistry 1994, 33, 15259-15265.
    • (1994) Biochemistry , vol.33 , pp. 15259-15265
    • Cook, W.J.1    Walter, L.J.2    Walter, M.R.3
  • 34
    • 0035115805 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the calmodulin-trifluoperazine complex in aqueous solution
    • Yamaotsu, N.; Suga, M.; Hirono, S. Molecular dynamics simulation of the calmodulin-trifluoperazine complex in aqueous solution. Biopolymers 2001, 58, 410-421.
    • (2001) Biopolymers , vol.58 , pp. 410-421
    • Yamaotsu, N.1    Suga, M.2    Hirono, S.3
  • 35
    • 2542586266 scopus 로고    scopus 로고
    • Molecular basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations
    • Rizzon, R. C.; Toba, S.; Kuntz, I. D. Molecular basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations. J. Med. Chem. 2004, 47, 3065-3074.
    • (2004) J. Med. Chem , vol.47 , pp. 3065-3074
    • Rizzon, R.C.1    Toba, S.2    Kuntz, I.D.3
  • 36
    • 4444270810 scopus 로고    scopus 로고
    • The role of electrostatic interactions in calmodulin-peptide complex formation
    • Andre, I.; Kesvatera, T.; Jonsson, B.; Akerfeld, K. S.; Linse, S. The role of electrostatic interactions in calmodulin-peptide complex formation. Biophys. J. 2004, 87, 1929-1938.
    • (2004) Biophys. J , vol.87 , pp. 1929-1938
    • Andre, I.1    Kesvatera, T.2    Jonsson, B.3    Akerfeld, K.S.4    Linse, S.5
  • 37
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
    • Froloff, N.; Windemuth, A.; Honig, B. On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions. Protein Sci. 1997, 6, 1293-1301.
    • (1997) Protein Sci , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 38
    • 4744338722 scopus 로고    scopus 로고
    • Ladbury, J., E.; Williams, M. A. The extended interface: Measuring nonlocal effects in biomolecular interactions. Curr. Opin. Struct. Biol. 2004, 14, 562-569.
    • Ladbury, J., E.; Williams, M. A. The extended interface: Measuring nonlocal effects in biomolecular interactions. Curr. Opin. Struct. Biol. 2004, 14, 562-569.
  • 40
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus, M.; Kuriyan, J. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6679-6685.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 41
    • 33747451719 scopus 로고    scopus 로고
    • Binding and interaction of dinitroanilines with apicomplexan and kinetoplastid -tubulin
    • Mitra, A.; Sept, D. Binding and interaction of dinitroanilines with apicomplexan and kinetoplastid -tubulin. J. Med. Chem. 2006, 49, 5226-5231.
    • (2006) J. Med. Chem , vol.49 , pp. 5226-5231
    • Mitra, A.1    Sept, D.2
  • 42
    • 27444442315 scopus 로고    scopus 로고
    • Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists
    • Ivanov, A. A.; Baskin, I. I.; Palyulin, V. A.; Piccagli, L.; Baraldi, P. G.; et al. Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists. J. Med. Chem. 2005, 48, 6813-6820.
    • (2005) J. Med. Chem , vol.48 , pp. 6813-6820
    • Ivanov, A.A.1    Baskin, I.I.2    Palyulin, V.A.3    Piccagli, L.4    Baraldi, P.G.5
  • 43
    • 3042533277 scopus 로고    scopus 로고
    • Possible involvement of collective domain movement int he catalytic reaction of soluble epoxide hydrolase
    • Schiott, B. Possible involvement of collective domain movement int he catalytic reaction of soluble epoxide hydrolase. Int. J. Quantum Chem. 2004, 99, 61-69.
    • (2004) Int. J. Quantum Chem , vol.99 , pp. 61-69
    • Schiott, B.1
  • 44
    • 0035895423 scopus 로고    scopus 로고
    • Binding free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
    • Archontis, G.; Simonson, T.; Karplus, M. Binding free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. J. Mol. Biol. 2001, 306, 307-327.
    • (2001) J. Mol. Biol , vol.306 , pp. 307-327
    • Archontis, G.1    Simonson, T.2    Karplus, M.3
  • 45
    • 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 1992, 257, 1251-1255.
    • (1992) Science , vol.257 , pp. 1251-1255
    • Meador, W.E.1    Means, A.R.2    Quiocho, F.A.3
  • 46
    • 0037165139 scopus 로고    scopus 로고
    • Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
    • Drum, C. L.; Yan, S. Z.; Bard, J.; Shen, Y. Q.; Lu, D. Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. Nature 2002, 415, 396-402.
    • (2002) Nature , vol.415 , pp. 396-402
    • Drum, C.L.1    Yan, S.Z.2    Bard, J.3    Shen, Y.Q.4    Lu, D.5
  • 47
    • 12244306922 scopus 로고    scopus 로고
    • Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins
    • Shen, Y. Q.; Lee, Y. S.; Soelaiman, S.; Bergson, P.; Lu, D.; et al. Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins. EMBO J. 2002, 21, 6721-6732.
    • (2002) EMBO J , vol.21 , pp. 6721-6732
    • Shen, Y.Q.1    Lee, Y.S.2    Soelaiman, S.3    Bergson, P.4    Lu, D.5
  • 48
    • 0032512626 scopus 로고    scopus 로고
    • Solution structure of calmodulin-W-7 complex: The basis of diversity in molecular recognition
    • Osawa, M.; Swindells, M. B.; Tanikawa, J.; Tanaka, T.; Mase, T.; et al. Solution structure of calmodulin-W-7 complex: The basis of diversity in molecular recognition. J. Mol. Biol. 1998, 276, 165-176.
    • (1998) J. Mol. Biol , vol.276 , pp. 165-176
    • Osawa, M.1    Swindells, M.B.2    Tanikawa, J.3    Tanaka, T.4    Mase, T.5
  • 49
    • 2242474818 scopus 로고    scopus 로고
    • Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: Studies of the kinase activation mechanism
    • Clapperton, J. A.; Martin, S. R.; Smerdon, S. J.; Gamblin, S. J.; Bayley, P. M. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: Studies of the kinase activation mechanism. Biochemistry 2002, 41, 14669-14679.
    • (2002) Biochemistry , vol.41 , pp. 14669-14679
    • Clapperton, J.A.1    Martin, S.R.2    Smerdon, S.J.3    Gamblin, S.J.4    Bayley, P.M.5
  • 50
    • 0037453258 scopus 로고    scopus 로고
    • Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxyloase to calmodulin
    • Yap, K. L.; Yuan, T.; Mal, T. K.; Vogel, H. J.; Ikura, M. Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxyloase to calmodulin. J. Mol. Biol. 2003, 328, 193-204.
    • (2003) J. Mol. Biol , vol.328 , pp. 193-204
    • Yap, K.L.1    Yuan, T.2    Mal, T.K.3    Vogel, H.J.4    Ikura, M.5
  • 52
    • 3142662017 scopus 로고    scopus 로고
    • Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate
    • Guo, Q.; Shen, Y.; Zhukovskaya, N. L.; Florian, J.; Tang, W. J. Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate. J. Biol. Chem. 2004, 279, 29427-29435.
    • (2004) J. Biol. Chem , vol.279 , pp. 29427-29435
    • Guo, Q.1    Shen, Y.2    Zhukovskaya, N.L.3    Florian, J.4    Tang, W.J.5
  • 53
    • 22144464877 scopus 로고    scopus 로고
    • Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: Residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family
    • Contessa, G. M.; Orsale, M.; Melino, S.; Torre, V.; Paci, M.; Desideri, A.; Cicero, D. O. Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: Residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family. J. Biomol. NMR 2005, 31, 185-199.
    • (2005) J. Biomol. NMR , vol.31 , pp. 185-199
    • Contessa, G.M.1    Orsale, M.2    Melino, S.3    Torre, V.4    Paci, M.5    Desideri, A.6    Cicero, D.O.7
  • 54
    • 14844324990 scopus 로고    scopus 로고
    • The structure of the complex of calmodulin with KAR-2: A novel mode of binding explains the unique pharmacology of the drug
    • Horvath, I.; Harmat, V.; Perczel, A.; Palfi, V.; Nyitrai, L.; Nagy, A.; Hlavanda, E.; Naray-Szabo, G.; Ovadi, J. The structure of the complex of calmodulin with KAR-2: A novel mode of binding explains the unique pharmacology of the drug. J. Biol. Chem. 2005, 280, 8266-8274.
    • (2005) J. Biol. Chem , vol.280 , pp. 8266-8274
    • Horvath, I.1    Harmat, V.2    Perczel, A.3    Palfi, V.4    Nyitrai, L.5    Nagy, A.6    Hlavanda, E.7    Naray-Szabo, G.8    Ovadi, J.9
  • 56
    • 0026536335 scopus 로고
    • Solution structure of a calmodulin-target peptide complex by multidimensional NMR
    • Ikura, M.; Clore, G. M.; Gronenborn, A. M.; Zhu, G.; Klee, C. B.; Bax, A. Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science 1992, 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
  • 57
    • 33749246223 scopus 로고    scopus 로고
    • Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode
    • Maximciuc, A. A.; Putkey, J. A.; Shamoo, Y.; Mackenzie, K. R. Complex of calmodulin with a ryanodine receptor target reveals a novel, flexible binding mode. Structure 2006, 14, 1547-1556.
    • (2006) Structure , vol.14 , pp. 1547-1556
    • Maximciuc, A.A.1    Putkey, J.A.2    Shamoo, Y.3    Mackenzie, K.R.4
  • 59
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization and dynamics calculations
    • Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; et al. CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
    • (1983) J. Comput. Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Olafson, B.D.3    States, D.J.4    Swaminathan, S.5
  • 62
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N.; MacKerell, J. A. D. All-atom empirical force field for nucleic acids: Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 2000, 21, 86-104.
    • (2000) J. Comput. Chem , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, J.A.D.2
  • 63
    • 0000999989 scopus 로고    scopus 로고
    • Combined ab initio/empirical approach for the optimization of Lennard-Jones parameters
    • Yin, D.; MacKerell, J. A. D. Combined ab initio/empirical approach for the optimization of Lennard-Jones parameters. J. Comput. Chem. 1998, 19, 334-348.
    • (1998) J. Comput. Chem , vol.19 , pp. 334-348
    • Yin, D.1    MacKerell, J.A.D.2
  • 64
    • 0034625269 scopus 로고    scopus 로고
    • High performance computational chemistry: An overview of NWChem a distributed parallel application
    • Kendall, R. A.; Apra, E.; Bernholdt, D. E.; Bylaska, E. J.; Dupuis, M., et al. High performance computational chemistry: An overview of NWChem a distributed parallel application. Comput. Phys. Commun. 2000, 128, 260-283.
    • (2000) Comput. Phys. Commun , vol.128 , pp. 260-283
    • Kendall, R.A.1    Apra, E.2    Bernholdt, D.E.3    Bylaska, E.J.4    Dupuis, M.5
  • 65
    • 44949100893 scopus 로고    scopus 로고
    • Apra, E.; Windus, T. L.; Straatsma, T. P.; Bylaska, E. J.; de Jong, W. NWChem, 4.7 ed.; Pacific Northwest National Laboratory: Richland, WA.
    • Apra, E.; Windus, T. L.; Straatsma, T. P.; Bylaska, E. J.; de Jong, W. NWChem, 4.7 ed.; Pacific Northwest National Laboratory: Richland, WA.
  • 66
    • 10644250257 scopus 로고
    • Inhomogeneous electron gas
    • Hohenberg, P.; Kohn, W. Inhomogeneous electron gas. Phys. Rev. 1964, 136, B864-B887.
    • (1964) Phys. Rev , vol.136
    • Hohenberg, P.1    Kohn, W.2
  • 67
    • 0042113153 scopus 로고
    • Self-consistent equations including exchange and correlation effects
    • Sham, L. J. Self-consistent equations including exchange and correlation effects. Phys. Rev. 1965, 140, A1133-A1138.
    • (1965) Phys. Rev , vol.140
    • Sham, L.J.1
  • 68
    • 0030218597 scopus 로고    scopus 로고
    • Density functional theory of electronic structure
    • Kohn, W.; Becke, A. D.; Parr, R. G. Density functional theory of electronic structure. J. Phys. Chem. 1996, 100, 12974-12980.
    • (1996) J. Phys. Chem , vol.100 , pp. 12974-12980
    • Kohn, W.1    Becke, A.D.2    Parr, R.G.3
  • 69
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 70
    • 0005744966 scopus 로고
    • Compact effective potentials and efficient shared-exponent basis sets for the first- and second-row atoms
    • Stevens, W. J.; Basch, H.; Krauss, M. Compact effective potentials and efficient shared-exponent basis sets for the first- and second-row atoms. J. Chem. Phys. 1984, 81, 6026-6033.
    • (1984) J. Chem. Phys , vol.81 , pp. 6026-6033
    • Stevens, W.J.1    Basch, H.2    Krauss, M.3
  • 71
    • 84986513567 scopus 로고    scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
    • Breneman, C. M.; Wiberg, K. B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 2004, 11, 361-373.
    • (2004) J. Comput. Chem , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 73
    • 0037645333 scopus 로고    scopus 로고
    • 1.0 ed, Ludwig-Maximilians Universität, München; Theoretical Biophysics Group, Institute for Medical Optics: München
    • Grubmuller, H. SOLVATE, 1.0 ed.; Ludwig-Maximilians Universität, München; Theoretical Biophysics Group, Institute for Medical Optics: München.
    • SOLVATE
    • Grubmuller, H.1
  • 74
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion for a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 1977, 23, 327-341.
    • (1977) J. Comp. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 76
    • 12744260687 scopus 로고    scopus 로고
    • R-state hemoglobin bound to heterotropic effectors: Models of the DPG, IHP, and RSR13 binding sites
    • Laberge, M. K. I.; Yonetani, T.; Fidy, J. R-state hemoglobin bound to heterotropic effectors: models of the DPG, IHP, and RSR13 binding sites. FEBS Lett. 2005, 579, 627-632.
    • (2005) FEBS Lett , vol.579 , pp. 627-632
    • Laberge, M.K.I.1    Yonetani, T.2    Fidy, J.3
  • 77
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. Constant pressure molecular dynamics simulation: The Langevin piston method. J. Chem. Phys. 1995, 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
  • 78
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I. K.; Thornton, J. M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 1994, 238, 777-793.
    • (1994) J. Mol. Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 79
    • 0020698476 scopus 로고
    • Dynamics of proteins: Elements and function
    • Karplus, M.; McCammon, J. A. Dynamics of proteins: elements and function. Annu. Rev. Biochem. 1983, 52, 263-300.
    • (1983) Annu. Rev. Biochem , vol.52 , pp. 263-300
    • Karplus, M.1    McCammon, J.A.2
  • 80
    • 22144482668 scopus 로고    scopus 로고
    • Fluctuations and correlations in crystalline protein dynamics: A simulation analysis of staphylococcal nuclease
    • Meinhold, L.; Smith, J. C. Fluctuations and correlations in crystalline protein dynamics: A simulation analysis of staphylococcal nuclease. Biophys. J. 2005, 88, 2554-2563.
    • (2005) Biophys. J , vol.88 , pp. 2554-2563
    • Meinhold, L.1    Smith, J.C.2
  • 81
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
    • Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem. B. 2001, 105, 6507-6514.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 82
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface for both molecules and geometric objects: Application to the finite difference Poisson-Boltzmann method
    • Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: application to the finite difference Poisson-Boltzmann method. J. Comput. Chem. 2002, 23, 128-137.
    • (2002) J. Comput. Chem , vol.23 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 83
    • 0023280069 scopus 로고
    • Calculations of electrostatic potentials in an enzyme active site
    • Gilson, M.; Honig, B. Calculations of electrostatic potentials in an enzyme active site. Nature 1987, 330, 84-86.
    • (1987) Nature , vol.330 , pp. 84-86
    • Gilson, M.1    Honig, B.2
  • 84
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls, A.; Honig, B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 1991, 12, 435-445.
    • (1991) J. Comput. Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2


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