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Volumn 71, Issue 1, 1996, Pages 19-39

Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; GRAMICIDIN A; WATER;

EID: 0030011088     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79211-1     Document Type: Article
Times cited : (263)

References (63)
  • 1
    • 0025823857 scopus 로고
    • Proton conductance by the gramicidin water wire
    • Akeson, M., and D. W. Deamer. 1991. Proton conductance by the gramicidin water wire. Biophys. J. 60:101-109.
    • (1991) Biophys. J. , vol.60 , pp. 101-109
    • Akeson, M.1    Deamer, D.W.2
  • 3
    • 0021892874 scopus 로고
    • 1H-NMR study of gramicidin-A transmembrane ion channel. Head-to-head right-handed, single stranded helices
    • 1H-NMR study of gramicidin-A transmembrane ion channel. Head-to-head right-handed, single stranded helices. FEBS Lett. 186:168-174.
    • (1985) FEBS Lett. , vol.186 , pp. 168-174
    • Arseniev, A.S.1    Bystrov, V.F.2    Ivanov, T.V.3    Ovchinnikov, Y.A.4
  • 4
    • 0000044605 scopus 로고
    • A quantum molecular-dynamics study of proton-transfer reactions along asymmetrical hydrogen bonds in solution
    • Azzouz, H., and D. Borgis. 1992. A quantum molecular-dynamics study of proton-transfer reactions along asymmetrical hydrogen bonds in solution. J. Chem. Phys. 98:7361-7374.
    • (1992) J. Chem. Phys. , vol.98 , pp. 7361-7374
    • Azzouz, H.1    Borgis, D.2
  • 5
    • 25944434685 scopus 로고
    • Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes
    • Bala, P., B. Lesyng, and J. A. McCammon. 1994. Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes. Chem. Phys. 180:271-285.
    • (1994) Chem. Phys. , vol.180 , pp. 271-285
    • Bala, P.1    Lesyng, B.2    McCammon, J.A.3
  • 6
    • 0002775934 scopus 로고
    • Interaction models for water in relation to proteins hydration
    • B. Pullman, editor. Reidel, Dordrecht
    • Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to proteins hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht. 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 8
    • 0026332339 scopus 로고
    • Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base
    • Cao, Y., G. Váró, M. Chang, B. Ni, R. Needleman, and J. K. Lanyi. 1991. Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base. Biochemistry. 30:10972-10979.
    • (1991) Biochemistry , vol.30 , pp. 10972-10979
    • Cao, Y.1    Váró, G.2    Chang, M.3    Ni, B.4    Needleman, R.5    Lanyi, J.K.6
  • 9
    • 8944255166 scopus 로고
    • Theory of quantum processes in liquids
    • D. Levesque, J. P. Hansen and J. Zinn-Justin, editors. Elsevier, Amsterdam
    • Chandler, D. 1990. Theory of quantum processes in liquids. In Les Houches, Session LI, 1989. Liquids, Freezing and Glass Transition. D. Levesque, J. P. Hansen and J. Zinn-Justin, editors. Elsevier, Amsterdam. 1-101.
    • (1990) Les Houches, Session LI, 1989. Liquids, Freezing and Glass Transition , pp. 1-101
    • Chandler, D.1
  • 10
    • 33645931176 scopus 로고
    • Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids
    • Chandler, D., and P. G. Wolynes. 1980. Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids. J. Chem. Phys. 74:4078-4095.
    • (1980) J. Chem. Phys. , vol.74 , pp. 4078-4095
    • Chandler, D.1    Wolynes, P.G.2
  • 12
    • 0025895720 scopus 로고
    • Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels
    • Chiu, S.-W., E. Jakobsson, S. Subramaniam, and J. A. McCammon. 1991. Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys. J. 60:273-285.
    • (1991) Biophys. J. , vol.60 , pp. 273-285
    • Chiu, S.-W.1    Jakobsson, E.2    Subramaniam, S.3    McCammon, J.A.4
  • 13
    • 0027466002 scopus 로고
    • The nature of ion and water barrier crossings in a simulated ion channel
    • Chiu, S.-W., J. A. Novotny, and E. Jakobsson. 1993. The nature of ion and water barrier crossings in a simulated ion channel. Biophys. J. 64: 98-108.
    • (1993) Biophys. J. , vol.64 , pp. 98-108
    • Chiu, S.-W.1    Novotny, J.A.2    Jakobsson, E.3
  • 14
    • 0024375490 scopus 로고
    • Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study
    • Chiu, S.-W., S. Subramaniam, E. Jakobsson, and J. A. McCammon. 1989. Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophys. J. 56:253-261.
    • (1989) Biophys. J. , vol.56 , pp. 253-261
    • Chiu, S.-W.1    Subramaniam, S.2    Jakobsson, E.3    McCammon, J.A.4
  • 15
    • 0023429474 scopus 로고
    • Proton permeation of lipid bilayers
    • Deamer, D. W. 1987. Proton permeation of lipid bilayers. J. Bioenerg. Biomembr. 19:457-479.
    • (1987) J. Bioenerg. Biomembr. , vol.19 , pp. 457-479
    • Deamer, D.W.1
  • 16
    • 0011703877 scopus 로고
    • n (A = N, O, F, P, S, and Cl)
    • n (A = N, O, F, P, S, and Cl). J. Phys. Chem. 92:2874-2880.
    • (1988) J. Phys. Chem. , vol.92 , pp. 2874-2880
    • Del Bene, J.E.1
  • 17
    • 0022592151 scopus 로고
    • The gramicidin A channel: Energetics and structural characteristics of the progression of a sodium ion in the presence of water
    • Etchebest, C., and A. Pullman. 1986a. The gramicidin A channel: energetics and structural characteristics of the progression of a sodium ion in the presence of water. J. Biomol. Struct. Dyn. 3:805-825.
    • (1986) J. Biomol. Struct. Dyn. , vol.3 , pp. 805-825
    • Etchebest, C.1    Pullman, A.2
  • 18
    • 0001619956 scopus 로고
    • + in the presence of water with inclusion of the flexibility of the ethanolamine tail
    • + in the presence of water with inclusion of the flexibility of the ethanolamine tail. FEBS Lett. 204:261-265.
    • (1986) FEBS Lett. , vol.204 , pp. 261-265
    • Etchebest, C.1    Pullman, A.2
  • 20
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field, M. J., P. A. Bash, and M. Karplus. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem. 11:700-733.
    • (1990) J. Comp. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 21
    • 0019795013 scopus 로고
    • The gramicidin A channel: A review of its permeability characteristics with special reference to the single-file aspect of transport
    • Finkelstein, A., and O. S. Andersen. 1981. The gramicidin A channel: a review of its permeability characteristics with special reference to the single-file aspect of transport. J. Membr. Biol. 59:155-171.
    • (1981) J. Membr. Biol. , vol.59 , pp. 155-171
    • Finkelstein, A.1    Andersen, O.S.2
  • 22
  • 23
    • 0027125907 scopus 로고
    • A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
    • Gao, J., and X. Xia. 1992. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. Science. 258: 631-635.
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.1    Xia, X.2
  • 24
    • 33644930396 scopus 로고
    • Ab initio studies of hydrogen bonding of N-methylacetamide: Structure, cooperativity, and internal rotational barriers
    • Guo, H., and M. Karplus. 1992. Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers. J. Phys. Chem. 96:7273-7287.
    • (1992) J. Phys. Chem. , vol.96 , pp. 7273-7287
    • Guo, H.1    Karplus, M.2
  • 26
    • 0015499206 scopus 로고
    • Ion transfer across lipid membranes in the presence of gramicidin A
    • Hladky, S. B., and D. A. Haydon. 1972. Ion transfer across lipid membranes in the presence of gramicidin A. Biochim. Biophys. Acta. 274: 294-312.
    • (1972) Biochim. Biophys. Acta , vol.274 , pp. 294-312
    • Hladky, S.B.1    Haydon, D.A.2
  • 27
    • 0026009213 scopus 로고
    • Stable submolecular folding units in a non-compact form of cytochrome c
    • Jeng, M.-F., and S. W. Englander. 1991. Stable submolecular folding units in a non-compact form of cytochrome c. J. Mol. Biol. 221:1045-1061.
    • (1991) J. Mol. Biol. , vol.221 , pp. 1045-1061
    • Jeng, M.-F.1    Englander, S.W.2
  • 28
    • 0025000888 scopus 로고
    • Ion-water and ion-polypeptide correlations in a gramicidin-like channel
    • Jordan, P. C. 1990. Ion-water and ion-polypeptide correlations in a gramicidin-like channel. Biophys. J. 58:1133-1156.
    • (1990) Biophys. J. , vol.58 , pp. 1133-1156
    • Jordan, P.C.1
  • 30
    • 0027360175 scopus 로고
    • High-resolution conformation of gramicidin A in lipid bilayer by solid-state nmr
    • Ketchem, R. R., W. Hu, and T. A. Cross. 1993. High-resolution conformation of gramicidin A in lipid bilayer by solid-state nmr. Science. 261:1457-1460.
    • (1993) Science , vol.261 , pp. 1457-1460
    • Ketchem, R.R.1    Hu, W.2    Cross, T.A.3
  • 32
    • 0000657978 scopus 로고
    • Proton conduction in linear hydrogen-bonded systems
    • Knapp, E.-W., K. Schulten, and Z. Schulten. 1980. Proton conduction in linear hydrogen-bonded systems. Chem. Phys. 46:215-229.
    • (1980) Chem. Phys. , vol.46 , pp. 215-229
    • Knapp, E.-W.1    Schulten, K.2    Schulten, Z.3
  • 33
    • 11744318071 scopus 로고
    • Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interaction and potential energy surfaces
    • Komatsuzaki, T., and I. Ohmine. 1994. Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interaction and potential energy surfaces. Chem. Phys. 180:239-269.
    • (1994) Chem. Phys. , vol.180 , pp. 239-269
    • Komatsuzaki, T.1    Ohmine, I.2
  • 35
    • 21344493167 scopus 로고
    • Activation free energy for proton transfer in solution
    • Laria, D., G. Ciccotti, M. Ferrario, and R. Kapral. 1994. Activation free energy for proton transfer in solution. Chem. Phys. 180:181-189.
    • (1994) Chem. Phys. , vol.180 , pp. 181-189
    • Laria, D.1    Ciccotti, G.2    Ferrario, M.3    Kapral, R.4
  • 36
    • 0001244822 scopus 로고
    • Kinetics of movements in narrow pores
    • Levitt, D. G. 1984. Kinetics of movements in narrow pores. Curr. Top. Membr. Transp. 21:181-197.
    • (1984) Curr. Top. Membr. Transp. , vol.21 , pp. 181-197
    • Levitt, D.G.1
  • 37
    • 0001680162 scopus 로고
    • Calculation of quantum activation free energies for proton transfer reactions in polar solvents
    • Lobaugh, J., and G. A. Voth. 1992. Calculation of quantum activation free energies for proton transfer reactions in polar solvents. Chem. Phys. Lett. 198:311-315.
    • (1992) Chem. Phys. Lett. , vol.198 , pp. 311-315
    • Lobaugh, J.1    Voth, G.A.2
  • 38
    • 0021472805 scopus 로고
    • Structure and dynamics of ion transport through gramicidin A
    • MacKay, D. H., P. H. Berens, K. R. Wilson, and A. T. Hagler. 1984. Structure and dynamics of ion transport through gramicidin A. Biophys. J. 46:229-248.
    • (1984) Biophys. J. , vol.46 , pp. 229-248
    • MacKay, D.H.1    Berens, P.H.2    Wilson, K.R.3    Hagler, A.T.4
  • 39
    • 0022822022 scopus 로고
    • Possible allosteric significance of water structures in proteins
    • MacKay, D. H., and K. R. Wilson. 1986. Possible allosteric significance of water structures in proteins. J. Biomol. Struct. Dyn. 4:491-500.
    • (1986) J. Biomol. Struct. Dyn. , vol.4 , pp. 491-500
    • MacKay, D.H.1    Wilson, K.R.2
  • 41
    • 0000473772 scopus 로고
    • Calculation of the proton transfer rate using density matrix evolution and molecular dynamics simulations - Inclusion of the proton excited states
    • Mavri, J., and H. J. C. Berendsen. 1995. Calculation of the proton transfer rate using density matrix evolution and molecular dynamics simulations - inclusion of the proton excited states. J. Phys. Chem. 99: 12711-12717.
    • (1995) J. Phys. Chem. , vol.99 , pp. 12711-12717
    • Mavri, J.1    Berendsen, H.J.C.2
  • 42
    • 0023428452 scopus 로고
    • Theory of passive proton conductance in lipid bilayers
    • Nagle, J. F. 1987. Theory of passive proton conductance in lipid bilayers. J. Bioenerg. Biomembr. 19:413-426.
    • (1987) J. Bioenerg. Biomembr. , vol.19 , pp. 413-426
    • Nagle, J.F.1
  • 43
    • 0345613372 scopus 로고
    • Molecular mechanisms for proton transport in membranes
    • Nagle, J. F., and H. J. Morowitz. 1978. Molecular mechanisms for proton transport in membranes. Proc. Natl. Acad Sci. USA. 75:298-302.
    • (1978) Proc. Natl. Acad Sci. USA , vol.75 , pp. 298-302
    • Nagle, J.F.1    Morowitz, H.J.2
  • 44
    • 0020967882 scopus 로고
    • Hydrogen bonded chain mechanism for proton conduction and proton pumping
    • Nagle, J. F., and S. Tristam-Nagle. 1983. Hydrogen bonded chain mechanism for proton conduction and proton pumping. J. Membr. Biol. 74:1-14.
    • (1983) J. Membr. Biol. , vol.74 , pp. 1-14
    • Nagle, J.F.1    Tristam-Nagle, S.2
  • 45
    • 0028175523 scopus 로고
    • α Helical hydrophobic polypeptides form proton-selective channels in lipid bilayers
    • Oliver, A. E., and D. W. Deamer. 1994. α Helical hydrophobic polypeptides form proton-selective channels in lipid bilayers. Biophys. J. 66: 1364-1379.
    • (1994) Biophys. J. , vol.66 , pp. 1364-1379
    • Oliver, A.E.1    Deamer, D.W.2
  • 46
    • 0000214894 scopus 로고
    • Quantum effects on the structure and energy of a protonated linear chain of hydrogen-bonded water molecules
    • Pomès, R., and B. Roux. 1995. Quantum effects on the structure and energy of a protonated linear chain of hydrogen-bonded water molecules. Chem. Phys. Lett. 234:416-424.
    • (1995) Chem. Phys. Lett. , vol.234 , pp. 416-424
    • Pomès, R.1    Roux, B.2
  • 47
    • 33748662705 scopus 로고    scopus 로고
    • + translocation along a model proton wire
    • + translocation along a model proton wire. J. Phys. Chem. 100:2519-2527.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2519-2527
    • Pomès, R.1    Roux, B.2
  • 48
    • 38149146419 scopus 로고
    • Theory of proton transport along a hydrogen bond chain in an external field
    • Prokop, P., and L. Skála. 1994. Theory of proton transport along a hydrogen bond chain in an external field. Chem. Phys. Lett. 223:279-282.
    • (1994) Chem. Phys. Lett. , vol.223 , pp. 279-282
    • Prokop, P.1    Skála, L.2
  • 49
    • 0023445780 scopus 로고
    • Energy profiles in the gramicidin A channel
    • Pullman, A. 1987. Energy profiles in the gramicidin A channel. Q. Rev. Biophys. 20:173-200.
    • (1987) Q. Rev. Biophys. , vol.20 , pp. 173-200
    • Pullman, A.1
  • 50
    • 0003311012 scopus 로고
    • Theory of transport in ion channels. From molecular dynamics simulations to experiments
    • J. M. Goodfellow, editor. VCH, Weinheim, Germany
    • Roux, B. 1995. Theory of transport in ion channels. From molecular dynamics simulations to experiments. In Computer Modelling in Molecular Biology. J. M. Goodfellow, editor. VCH, Weinheim, Germany.
    • (1995) Computer Modelling in Molecular Biology
    • Roux, B.1
  • 51
    • 33748583013 scopus 로고
    • Ion transport in a gramicidin-like channel: Dynamics and mobility
    • Roux, B., and M. Karplus. 1991. 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
  • 52
    • 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. Biophys. Biomol. Struct. 23:731-761.
    • (1994) Annu. Rev. Biophys. Biomol. Struct. , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 53
    • 33845377796 scopus 로고
    • Theoretical studies of proton transfers
    • Scheiner, S. 1985. Theoretical studies of proton transfers. Acc. Chem. Res. 18:174-180.
    • (1985) Acc. Chem. Res. , vol.18 , pp. 174-180
    • Scheiner, S.1
  • 54
    • 0028693333 scopus 로고
    • Ab initio studies of hydrogen bonds: The water dimer paradigm
    • Scheiner, S. 1994. Ab initio studies of hydrogen bonds: the water dimer paradigm. Annu. Rev. Chem. Phys. 45:23-56.
    • (1994) Annu. Rev. Chem. Phys. , vol.45 , pp. 23-56
    • Scheiner, S.1
  • 55
    • 0023358088 scopus 로고
    • Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels
    • Skerra, A., and J. Brickman. 1987. Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels. Biophys. J. 51:969-976.
    • (1987) Biophys. J. , vol.51 , pp. 969-976
    • Skerra, A.1    Brickman, J.2
  • 56
    • 0001296204 scopus 로고
    • Dynamics and ensemble averages for the polarization models of molecular interactions
    • Stillinger, F. H. 1979. Dynamics and ensemble averages for the polarization models of molecular interactions. J. Chem. Phys. 71:1647-1651.
    • (1979) J. Chem. Phys. , vol.71 , pp. 1647-1651
    • Stillinger, F.H.1
  • 57
    • 36749115718 scopus 로고
    • Polarization model for water and its ionic dissociation products
    • Stillinger, F. H., and C. W. David. 1978. Polarization model for water and its ionic dissociation products. J. Chem. Phys. 69:1473-1484.
    • (1978) J. Chem. Phys. , vol.69 , pp. 1473-1484
    • Stillinger, F.H.1    David, C.W.2
  • 60
    • 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
  • 61
    • 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. Proteins Struct. Funct. Genet. 24:92-114.
    • (1996) Proteins Struct. Funct. Genet. , vol.24 , pp. 92-114
    • Woolf, T.B.1    Roux, B.2
  • 63
    • 0343852056 scopus 로고
    • Classical and quantum aspects of ferrocytochrome c
    • Zheng, C., C. F. Wong, J. A. McCammon, and P. G. Wolynes. 1989. Classical and quantum aspects of ferrocytochrome c. Chim. Scripta. 29A:171-179.
    • (1989) Chim. Scripta , vol.29 A , pp. 171-179
    • Zheng, C.1    Wong, C.F.2    McCammon, J.A.3    Wolynes, P.G.4


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