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Volumn 71, Issue 6, 1996, Pages 3177-3185

Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMIDE; CHLORIDE ION; GRAMICIDIN; HYDROGEN; POTASSIUM ION;

EID: 0029731562     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79511-5     Document Type: Article
Times cited : (94)

References (46)
  • 1
    • 0026471029 scopus 로고
    • Molecular determinants of channel function
    • Andersen, O. S., and R. E. Koeppe II. 1992. Molecular determinants of channel function. Physiol. Rev. 72:S89.
    • (1992) Physiol. Rev. , vol.72
    • Andersen, O.S.1    Koeppe II, R.E.2
  • 2
    • 0344796204 scopus 로고
    • Ion water interaction potential derived from free energy perturbation simulations
    • Åqvist, J. 1990. Ion water interaction potential derived from free energy perturbation simulations. J. Phys. Chem. 94:8021-8024.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8021-8024
    • Åqvist, J.1
  • 3
    • 0000688340 scopus 로고
    • Dielectric properties of alkyl amides. II. Liquid dielectric constant and loss
    • Bass, S. J., W. I. Nathan, R. M. Meighan, and R. H. Cole. 1964. Dielectric properties of alkyl amides. II. Liquid dielectric constant and loss. J Phys. Chem. 68:509-515.
    • (1964) J Phys. Chem. , vol.68 , pp. 509-515
    • Bass, S.J.1    Nathan, W.I.2    Meighan, R.M.3    Cole, R.H.4
  • 4
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system. Solvent boundary potential for computer simulations
    • Beglov, D., and B. Roux. 1994. Finite representation of an infinite bulk system. Solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 5
    • 84890021933 scopus 로고
    • The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors
    • Boys, S. F., and F. Bernardi. 1970. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 19:553-566.
    • (1970) Mol. Phys. , vol.19 , pp. 553-566
    • Boys, S.F.1    Bernardi, F.2
  • 7
    • 0024280869 scopus 로고
    • Structure and function of voltage-sensitive ion channels
    • Catterall, W. A. 1988. Structure and function of voltage-sensitive ion channels. Science. 242:50-61.
    • (1988) Science , vol.242 , pp. 50-61
    • Catterall, W.A.1
  • 8
    • 84971074097 scopus 로고
    • Solvation of ions. XIX. Thermodynamic properties for transfer of single ions between protic and dipolar aprotic solvents
    • Cox, B. G., G. R. Hedwig, A. J. Parker, and D. W. Watts. 1974. Solvation of ions. XIX. Thermodynamic properties for transfer of single ions between protic and dipolar aprotic solvents. Aust. J. Chem. 27:477-501.
    • (1974) Aust. J. Chem. , vol.27 , pp. 477-501
    • Cox, B.G.1    Hedwig, G.R.2    Parker, A.J.3    Watts, D.W.4
  • 9
    • 0030050164 scopus 로고    scopus 로고
    • A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: The origin of cation selectivity
    • Dorman, V., M. B. Partenskii, and P. C. Jordan. 1996. A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity. Biophys. J. 70:121-134.
    • (1996) Biophys. J. , vol.70 , pp. 121-134
    • Dorman, V.1    Partenskii, M.B.2    Jordan, P.C.3
  • 10
    • 73049154846 scopus 로고
    • Cation selective electrodes and their mode of operation
    • Eisenman, G. 1962. Cation selective electrodes and their mode of operation. Biophys. J. Supp. 2: 259-323.
    • (1962) Biophys. J. Supp. , vol.2 , pp. 259-323
    • Eisenman, G.1
  • 11
    • 0011766935 scopus 로고
    • Ab initio study of hydrated chloride ion complexes: Evidence for polarization effect and nonadditivity
    • Foresman, J. B., and C. L. Brooks, III. 1987. Ab initio study of hydrated chloride ion complexes: evidence for polarization effect and nonadditivity. J. Chem. Phys. 87:5892-5894.
    • (1987) J. Chem. Phys. , vol.87 , pp. 5892-5894
    • Foresman, J.B.1    Brooks III, C.L.2
  • 12
    • 0001060947 scopus 로고
    • In-crystals polarizabilities of alkali and halide ions
    • Fowler, P. W., and P. A. Madden. 1984. In-crystals polarizabilities of alkali and halide ions. Phys. Rev. B. 29:1035-1042.
    • (1984) Phys. Rev. B , vol.29 , pp. 1035-1042
    • Fowler, P.W.1    Madden, P.A.2
  • 14
    • 0026656037 scopus 로고
    • Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic
    • Galzi, J. L., A. Devillers-Thiery, N. Hussy, S. Bertrand, J. P. Changeux, and D. Bertrand. 1992. Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic. Nature. 359:500-505.
    • (1992) Nature , vol.359 , pp. 500-505
    • Galzi, J.L.1    Devillers-Thiery, A.2    Hussy, N.3    Bertrand, S.4    Changeux, J.P.5    Bertrand, D.6
  • 15
    • 0001500532 scopus 로고
    • A new algorithm for obtaining contracted basis set from gaussian type functions
    • Gianolio, L., R. Pavani, and E. Clementi. 1978. A new algorithm for obtaining contracted basis set from gaussian type functions. Gaz. Chim. It. 108:181-205.
    • (1978) Gaz. Chim. It. , vol.108 , pp. 181-205
    • Gianolio, L.1    Pavani, R.2    Clementi, E.3
  • 16
    • 0026517122 scopus 로고
    • Calcium channel characteristics conferred on the sodium channel by single mutations
    • Heineman, S. H., H. Terlau, W. Stühmer, K. Imoto, and S. Numa. 1992. Calcium channel characteristics conferred on the sodium channel by single mutations. Nature. 356:441-443.
    • (1992) Nature , vol.356 , pp. 441-443
    • Heineman, S.H.1    Terlau, H.2    Stühmer, W.3    Imoto, K.4    Numa, S.5
  • 19
    • 0002889583 scopus 로고
    • Molecular force field and structure of water: Recent microwave results
    • Hirota, E., R. Sugisaki, C. J. Nielsen, and G. O. Sorensen. 1974. Molecular force field and structure of water: recent microwave results. J. Mol. Spectrosc. 53:62-76.
    • (1974) J. Mol. Spectrosc. , vol.53 , pp. 62-76
    • Hirota, E.1    Sugisaki, R.2    Nielsen, C.J.3    Sorensen, G.O.4
  • 21
    • 20644431615 scopus 로고
    • Theory of solution of molecules containing widely separated charges with application to zwiterions
    • Kirkwood, J. G. 1934. Theory of solution of molecules containing widely separated charges with application to zwiterions. J. Chem. Phys. 2:351.
    • (1934) J. Chem. Phys. , vol.2 , pp. 351
    • Kirkwood, J.G.1
  • 22
    • 0001584003 scopus 로고
    • Molecular structure of n-methylacetamide as studied by gas electron diffraction
    • Kitano, M., T. Fukuyama, and K. Kuchitsu. 1973. Molecular structure of n-methylacetamide as studied by gas electron diffraction. Bull. Chem. Soc. Jpn. 46:384-387.
    • (1973) Bull. Chem. Soc. Jpn. , vol.46 , pp. 384-387
    • Kitano, M.1    Fukuyama, T.2    Kuchitsu, K.3
  • 23
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. A. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 24
    • 0000332299 scopus 로고
    • Microwave spectrum, structure, dipole moment and quadrupole coupling constants of formamide
    • Kurland, R. J., and E. B. Wilson. 1957. Microwave spectrum, structure, dipole moment and quadrupole coupling constants of formamide. J. Chem. Phys. 27:585-590.
    • (1957) J. Chem. Phys. , vol.27 , pp. 585-590
    • Kurland, R.J.1    Wilson, E.B.2
  • 25
    • 0029028781 scopus 로고
    • A structural motif for the voltage-gated potassium channel pore
    • Lipkind, G. M., and H. A. Fozzard. 1995. A structural motif for the voltage-gated potassium channel pore. Proc. Natl. Acad. Sci. USA. 92:9215-9219.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 9215-9219
    • Lipkind, G.M.1    Fozzard, H.A.2
  • 27
    • 0010803605 scopus 로고
    • Dielectric properties of alkyl amides. I. Moments and polarization in benzene solution
    • Meighan, R. M., and R. H. Cole. 1964. Dielectric properties of alkyl amides. I. Moments and polarization in benzene solution. J. Phys. Chem. 68:503-508.
    • (1964) J. Phys. Chem. , vol.68 , pp. 503-508
    • Meighan, R.M.1    Cole, R.H.2
  • 28
    • 0345588922 scopus 로고
    • The polarizability of a closed-shell core of an atomic system by an outer electron. II. Evaluation of the polarizabilities from observed spectra
    • Öpik, U. 1967. The polarizability of a closed-shell core of an atomic system by an outer electron. II. Evaluation of the polarizabilities from observed spectra. Proc. Phys. Soc. Lond. 92:566-572.
    • (1967) Proc. Phys. Soc. Lond. , vol.92 , pp. 566-572
    • Öpik, U.1
  • 29
    • 0000662331 scopus 로고
    • + in the gramicidin channel
    • + in the gramicidin channel. Chem. Phys. Lett. 212:231-240.
    • (1993) Chem. Phys. Lett. , vol.212 , pp. 231-240
    • Roux, B.1
  • 30
    • 0007839690 scopus 로고
    • Theory of transport in ion channels: From molecular dynamics simulations to experiments
    • J. Goodfellow, editor. VCH, Weinheim
    • Roux, B. 1995. Theory of transport in ion channels: from molecular dynamics simulations to experiments. In Computer Simulation in Molecular Biology. J. Goodfellow, editor. VCH, Weinheim. 132-169.
    • (1995) Computer Simulation in Molecular Biology , pp. 132-169
    • Roux, B.1
  • 31
    • 0025882246 scopus 로고
    • Ion transport in a gramicidin-like channel: Structure and thermodynamics
    • Roux, B., and M. Karplus. 1991a. Ion transport in a gramicidin-like channel: structure and thermodynamics. Biophys. J. 59:961-981.
    • (1991) Biophys. J. , vol.59 , pp. 961-981
    • Roux, B.1    Karplus, M.2
  • 32
    • 33748583013 scopus 로고
    • Ion transport in a gramicidin-like channel: Dynamics and mobility
    • Roux, B., and M. Karplus. 1991b. Ion transport in a gramicidin-like channel: dynamics and mobility. J. Phys. Chem. 95:4856-4868.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4856-4868
    • Roux, B.1    Karplus, M.2
  • 33
    • 0028321565 scopus 로고
    • Molecular dynamics simulations of the gramicidin channel
    • Roux, B., and M. Karplus. 1994. Molecular dynamics simulations of the gramicidin channel. Annu. Rev. Biomol. Struct. Dyn. 23:731-761.
    • (1994) Annu. Rev. Biomol. Struct. Dyn. , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 34
    • 84986469514 scopus 로고
    • Potential energy function for cations-peptides interactions: An ab initio study
    • Roux, B., and M. Karplus. 1995. Potential energy function for cations-peptides interactions: an ab initio study. J. Comp. Chem. 16:690-704.
    • (1995) J. Comp. Chem. , vol.16 , pp. 690-704
    • Roux, B.1    Karplus, M.2
  • 35
    • 0028918454 scopus 로고
    • Ion transport in the gramicidin channel: Molecular dynamics study of single and double occupancy
    • Roux, B., and M. Karplus. 1991a. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys. J. 68:876-892.
    • (1991) Biophys. J. , vol.68 , pp. 876-892
    • Roux, B.1    Karplus, M.2
  • 36
    • 0000763912 scopus 로고
    • Molecular basis for the Born model of ion solvation
    • Roux, B., H. A. Yu, and M. Karplus. 1990. Molecular basis for the Born model of ion solvation. J. Phys. Chem. 94:4683-4688.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4683-4688
    • Roux, B.1    Yu, H.A.2    Karplus, M.3
  • 37
    • 33646940952 scopus 로고
    • Numerical Integration of the cartesian equation of motions 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 equation of motions of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Chem. 23: 327-341.
    • (1977) J. Comp. Chem. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 38
    • 0028233952 scopus 로고
    • Structural basis of ion channel permeation and selectivity
    • Sather, W. A., J. Yang, and R. W. Tsien. 1994. Structural basis of ion channel permeation and selectivity. Curr. Opin. Neurobiol. 4:313-323.
    • (1994) Curr. Opin. Neurobiol. , vol.4 , pp. 313-323
    • Sather, W.A.1    Yang, J.2    Tsien, R.W.3
  • 39
    • 0023320530 scopus 로고
    • Why is gramicidin valence selective? A theoretical study
    • Sung, S. S., and P. C. Jordan. 1987. Why is gramicidin valence selective? A theoretical study. Biophys. J. 51:661-672.
    • (1987) Biophys. J. , vol.51 , pp. 661-672
    • Sung, S.S.1    Jordan, P.C.2
  • 40
    • 84986436997 scopus 로고
    • Theoretical conformation analysis of the gramicidin A transmembrane channel. II. Energetics of helical states of the channel
    • Urry, D. W., and C. M. Venkatachalam. 1984. Theoretical conformation analysis of the gramicidin A transmembrane channel. II. Energetics of helical states of the channel. J. Comput. Chem. 5:64-71.
    • (1984) J. Comput. Chem. , vol.5 , pp. 64-71
    • Urry, D.W.1    Venkatachalam, C.M.2
  • 42
    • 0005867244 scopus 로고
    • Gaussian basis set for molecular wavefunctions containing third-row atoms
    • Wachters, A. J. H. 1970. Gaussian basis set for molecular wavefunctions containing third-row atoms. J. Chem. Phys. 52:1033-1036.
    • (1970) J. Chem. Phys. , vol.52 , pp. 1033-1036
    • Wachters, A.J.H.1
  • 43
    • 0024281633 scopus 로고
    • The gramicidin pore: Crystal structure of a cesium complex
    • Wallace, B. A., and K. Ravikumar. 1988. The gramicidin pore: crystal structure of a cesium complex. Science. 241:182-187.
    • (1988) Science , vol.241 , pp. 182-187
    • Wallace, B.A.1    Ravikumar, K.2
  • 44
    • 0028020035 scopus 로고
    • Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
    • Woolf, T. B., and B. Roux. 1994. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc. Natl. Acad. Sci. USA. 91:11631-11635.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 11631-11635
    • Woolf, T.B.1    Roux, B.2
  • 45
    • 0030038849 scopus 로고    scopus 로고
    • Structure, energetics and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer
    • Woolf, T. B., and B. Roux. 1996. Structure, energetics and dynamics of lipid-protein interactions: a molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Protein Struct. Fund. Genet. 24:92-114.
    • (1996) Protein Struct. Fund. Genet. , vol.24 , pp. 92-114
    • Woolf, T.B.1    Roux, B.2
  • 46
    • 9044236053 scopus 로고
    • Structure and dynamics of the sidechains of gramicidin in a DMPC bilayer
    • G. Wipff, editor. Kluwer Academic Publishers, Dordrecht
    • Woolf, T. B., J. Deshamais, and B. Roux. 1994. Structure and dynamics of the sidechains of gramicidin in a DMPC bilayer. In NATO ASI Series: Computational Approaches in Supramolecular Chemistry, Vol. 426. G. Wipff, editor. Kluwer Academic Publishers, Dordrecht. 519-531.
    • (1994) NATO ASI Series: Computational Approaches in Supramolecular Chemistry , vol.426 , pp. 519-531
    • Woolf, T.B.1    Deshamais, J.2    Roux, B.3


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