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Volumn 50, Issue 1, 2003, Pages 63-80

Ion permeation through the gramicidin channel: Atomically detailed modeling by the Stochastic Difference Equation

Author keywords

Computer simulations; Diffusion; Functional optimization; Ionic solutions; Long time dynamics; Membranes; Transport

Indexed keywords

GRAMICIDIN; LITHIUM; MEMBRANE PROTEIN; POTASSIUM; SODIUM; VALINE;

EID: 0037233422     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10256     Document Type: Article
Times cited : (20)

References (59)
  • 1
    • 0015100247 scopus 로고
    • Gramicidin A transmembrane channel. Characteristics of head-to-head dimerized. pi.L, D helices
    • Urry DW, Goodall MC, Glickson JD, Mayers DF. Gramicidin A transmembrane channel. Characteristics of head-to-head dimerized. pi.L, D helices. Proc Natl Acad Sci USA 1971;68:1907-1911.
    • (1971) Proc Natl Acad Sci USA , vol.68 , pp. 1907-1911
    • Urry, D.W.1    Goodall, M.C.2    Glickson, J.D.3    Mayers, D.F.4
  • 2
    • 0000346708 scopus 로고
    • Gramicidin-A transmembrane ion-channel-3-dimensional structure reconstruction based on NMR-spectroscopy and energy refinement
    • Arseniev AS, Lomize AL, Barsukov IL, Bystrov VF. Gramicidin-A transmembrane ion-channel-3-dimensional structure reconstruction based on NMR-spectroscopy and energy refinement. Biol Membr 1986;3:1077-1104.
    • (1986) Biol Membr , vol.3 , pp. 1077-1104
    • Arseniev, A.S.1    Lomize, A.L.2    Barsukov, I.L.3    Bystrov, V.F.4
  • 3
    • 0026471029 scopus 로고
    • Molecular determinants of channel function
    • Andersen OS, Koeppe RE II. Molecular determinants of channel function. Physiol Rev 1992;72:89-158.
    • (1992) Physiol Rev , vol.72 , pp. 89-158
    • Andersen, O.S.1    Koeppe, R.E.2
  • 4
    • 0015499206 scopus 로고
    • Ion transfer across lipid-membranes in presence of gramicidin-A. 1. Studies of unit conductance channel
    • Hladky SB, Haydon DA. Ion transfer across lipid-membranes in presence of gramicidin-A. 1. Studies of unit conductance channel. Biochim Biophys Acta 1972;274:294-312.
    • (1972) Biochim Biophys Acta , vol.274 , pp. 294-312
    • Hladky, S.B.1    Haydon, D.A.2
  • 5
    • 0032343366 scopus 로고    scopus 로고
    • Ionic channels in biological membranes: Electrostatic analysis of a natural nanotubes
    • Eisenberg RS. Ionic channels in biological membranes: electrostatic analysis of a natural nanotubes. Contemp Phys 1998;39:447-466.
    • (1998) Contemp Phys , vol.39 , pp. 447-466
    • Eisenberg, R.S.1
  • 6
    • 0033032906 scopus 로고    scopus 로고
    • A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel
    • Kurnikova MG, Coalson RD, Graf P, Nitzan A. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel. Biophys J 1999;76:642-656.
    • (1999) Biophys J , vol.76 , pp. 642-656
    • Kurnikova, M.G.1    Coalson, R.D.2    Graf, P.3    Nitzan, A.4
  • 7
    • 0043239420 scopus 로고    scopus 로고
    • Three-dimensional Poisson-Nernst-Planck theory studies: Influence of membrane electrostatics on gramicidin A channel conductance
    • Cárdenas AE, Coalson RD, Kurnikova MG. Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on gramicidin A channel conductance. Biophys J 2000;79:80-93.
    • (2000) Biophys J , vol.79 , pp. 80-93
    • Cárdenas, A.E.1    Coalson, R.D.2    Kurnikova, M.G.3
  • 8
    • 0007165005 scopus 로고    scopus 로고
    • Lynden-Bell RM, Rasaiah JC. J Chem Phys 1996;105:9266; Koneshan S, Rasaiah JC, Lynden-Bell RM, Lee SH. J Phys Chem 1998;102:4193.
    • (1996) J Chem Phys , vol.105 , pp. 9266
    • Lynden-Bell, R.M.1    Rasaiah, J.C.2
  • 10
    • 0012340894 scopus 로고
    • Free-energies for association of CS+ to 18-CROWN-6 in water - A molecular-dynamics study including counter ions
    • Dang LX. Free-energies for association of CS+ to 18-CROWN-6 in water - a molecular-dynamics study including counter ions. Chem Phys Lett 1994;227:211-214.
    • (1994) Chem Phys Lett , vol.227 , pp. 211-214
    • Dang, L.X.1
  • 11
    • 0028321565 scopus 로고
    • Molecular dynamics simulations of the gramicidin channel
    • Roux B, Karplus M. Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys 1994;23:731-761.
    • (1994) Annu Rev Biophys , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 13
    • 0034207477 scopus 로고    scopus 로고
    • Predicting function from structure using the Poisson-Nernst-Planck equations: Sodium current in the gramicidin A channel
    • Hollerbach U, Chen DP, Busath DD, Eisenberg RS. Predicting function from structure using the Poisson-Nernst-Planck equations: sodium current in the gramicidin A channel. Langmuir 2000;16:5509-5514.
    • (2000) Langmuir , vol.16 , pp. 5509-5514
    • Hollerbach, U.1    Chen, D.P.2    Busath, D.D.3    Eisenberg, R.S.4
  • 15
    • 0024375490 scopus 로고
    • Water and polypeptide conformations in the gramicidin channel: A molecular dynamics study
    • Chiu SW, Subramaniam S, Jakobsson E, McCammon JA. Water and polypeptide conformations in the gramicidin channel: a molecular dynamics study. Biophys J 1989;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
  • 16
    • 0033061633 scopus 로고    scopus 로고
    • Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex
    • Chiu SW, Subramaniam S, Jakobsson E. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. Biophys J 1999;76:1929-1938.
    • (1999) Biophys J , vol.76 , pp. 1929-1938
    • Chiu, S.W.1    Subramaniam, S.2    Jakobsson, E.3
  • 17
    • 0033037793 scopus 로고    scopus 로고
    • Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport
    • Chiu SW, Subramaniam S, Jakobsson E. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport. Biophys J 1999;76:1939-1950.
    • (1999) Biophys J , vol.76 , pp. 1939-1950
    • Chiu, S.W.1    Subramaniam, S.2    Jakobsson, E.3
  • 18
    • 33845282559 scopus 로고
    • Microscopic approaches to ion transport through transmembrane channels - The model system gramicidin
    • Jordan PC. Microscopic approaches to ion transport through transmembrane channels - the model system gramicidin. J Phys Chem 1987;91:6582-6591.
    • (1987) J Phys Chem , vol.91 , pp. 6582-6591
    • Jordan, P.C.1
  • 19
    • 0030965871 scopus 로고    scopus 로고
    • Ion-water and water-water interactions in a gramicidin like channel: Effects due to group polarizability and backbone flexibility
    • Duca KA, Jordan PC. Ion-water and water-water interactions in a gramicidin like channel: effects due to group polarizability and backbone flexibility. Biophys Chem 1997;65:123-141.
    • (1997) Biophys Chem , vol.65 , pp. 123-141
    • Duca, K.A.1    Jordan, P.C.2
  • 20
    • 0023680894 scopus 로고
    • Theoretical study of the antiparallel double-stranded helical dimer of gramicidin as an ion channel
    • Sung SS, Jordan PC. Theoretical study of the antiparallel double-stranded helical dimer of gramicidin as an ion channel. Biophys J 1988;54:519-526.
    • (1988) Biophys J , vol.54 , pp. 519-526
    • Sung, S.S.1    Jordan, P.C.2
  • 21
    • 0030995981 scopus 로고    scopus 로고
    • The binding site of sodium in the gramicidin channel. Comparison of molecular dynamics with solid-state NMR data
    • Woolf TB, Roux B. The binding site of sodium in the gramicidin channel. Comparison of molecular dynamics with solid-state NMR data. Biophys J 1997;72:1930-1945.
    • (1997) Biophys J , vol.72 , pp. 1930-1945
    • Woolf, T.B.1    Roux, B.2
  • 22
    • 0025882246 scopus 로고
    • Ion transport in a model gramicidin channel: Structure and thermodynamics
    • Roux B, Karplus M. Ion transport in a model gramicidin channel: structure and thermodynamics. Biophys J 1991;59:961-981.
    • (1991) Biophys J , vol.59 , pp. 961-981
    • Roux, B.1    Karplus, M.2
  • 23
    • 33748583013 scopus 로고
    • Ion transport in a gramicidin like channel: Dynamics and mobility
    • Roux B, Karplus M. Ion transport in a gramicidin like channel: dynamics and mobility. J Phys Chem 1991;95:4856-4868.
    • (1991) J Phys Chem , vol.95 , pp. 4856-4868
    • Roux, B.1    Karplus, M.2
  • 24
    • 0027232024 scopus 로고
    • Ion transport in the gramicidin channel: Free energy of the solvated right-handed dimer in a model membrane
    • Roux B, Karplus M. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane. J Am Chem Soc 1993;115:3250-3262.
    • (1993) J Am Chem Soc , vol.115 , pp. 3250-3262
    • Roux, B.1    Karplus, M.2
  • 25
    • 0028918454 scopus 로고
    • Ion transport in the gramicidin channel: Molecular dynamics study of single and double occupancy
    • Roux B, Prod'horn B, Karplus M. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys J 1995;68:876-892.
    • (1995) Biophys J , vol.68 , pp. 876-892
    • Roux, B.1    Prod'horn, B.2    Karplus, M.3
  • 26
    • 0029731562 scopus 로고    scopus 로고
    • Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study
    • Roux B. Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study. Biophys J 1996;71:3177-3185.
    • (1996) Biophys J , vol.71 , pp. 3177-3185
    • Roux, B.1
  • 27
    • 0030808398 scopus 로고    scopus 로고
    • Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels
    • Hao Y, Pear MR, Busath DD. Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels. Biophys J 1997;73:1699-1716.
    • (1997) Biophys J , vol.73 , pp. 1699-1716
    • Hao, Y.1    Pear, M.R.2    Busath, D.D.3
  • 28
    • 0002197305 scopus 로고    scopus 로고
    • Reaction path studies of biomolecules
    • Elber R, editor. Singapore: World Scientific
    • Elber R. Reaction path studies of biomolecules. In: Elber R, editor. Recent developments in theoretical studies of proteins. Singapore: World Scientific; 1996. p 65-136.
    • (1996) Recent Developments in Theoretical Studies of Proteins , pp. 65-136
    • Elber, R.1
  • 29
    • 0012021417 scopus 로고    scopus 로고
    • Calculation of classical trajectories with a very large time step: Formalism and numerical examples
    • Olender R, Elber R. Calculation of classical trajectories with a very large time step: formalism and numerical examples. J Chem Phys 1996;105:9299-9315.
    • (1996) J Chem Phys , vol.105 , pp. 9299-9315
    • Olender, R.1    Elber, R.2
  • 30
    • 4243691221 scopus 로고    scopus 로고
    • Yet another look at the steepest descent path
    • Olender R, Elber R. Yet another look at the steepest descent path. J Mol Struct 1997;398:63-72.
    • (1997) J Mol Struct , vol.398 , pp. 63-72
    • Olender, R.1    Elber, R.2
  • 31
    • 0012559944 scopus 로고    scopus 로고
    • Application of a stochastic path integral to the computations of an optimal path and ensembles of trajectories
    • Deuflhard HJP, Leimukhlar B, Mark AE, Reich S, Skeel RD, editors. Berlin Heidelberg: Springer Verlag
    • Elber R, Roux B, Olender R. Application of a stochastic path integral to the computations of an optimal path and ensembles of trajectories. In: Deuflhard HJP, Leimukhlar B, Mark AE, Reich S, Skeel RD, editors. Lecture Notes in Computational Science and Engineeri. Vol. 4. Berlin Heidelberg: Springer Verlag; 1999; p 263-280.
    • (1999) Lecture Notes in Computational Science and Engineering , vol.4 , pp. 263-280
    • Elber, R.1    Roux, B.2    Olender, R.3
  • 32
    • 16444370098 scopus 로고    scopus 로고
    • A stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide
    • Elber R, Meller J, Olender R. A stochastic path approach to compute atomically detailed trajectories: application to the folding of C peptide. J Phys Chem B 1999;103:899-911.
    • (1999) J Phys Chem B , vol.103 , pp. 899-911
    • Elber, R.1    Meller, J.2    Olender, R.3
  • 33
    • 0034625276 scopus 로고    scopus 로고
    • Parallel computations of molecular dynamics trajectories using the stochastic path approach
    • Zaloj V, Elber R. Parallel computations of molecular dynamics trajectories using the stochastic path approach. Comput Phys Commun 2000;128:118-127.
    • (2000) Comput Phys Commun , vol.128 , pp. 118-127
    • Zaloj, V.1    Elber, R.2
  • 34
    • 0035250027 scopus 로고    scopus 로고
    • Simulation of protein folding by reaction path annealing
    • 201
    • Eastman P, Gronbech-Jensen N, Doniach S. Simulation of protein folding by reaction path annealing. J Chem Phys 201;114:3823-3841.
    • J Chem Phys , vol.114 , pp. 3823-3841
    • Eastman, P.1    Gronbech-Jensen, N.2    Doniach, S.3
  • 35
    • 0001486087 scopus 로고
    • Dynamics and design of enzymes and inhibitors
    • Wong CF, McCammon JA. Dynamics and design of enzymes and inhibitors. J Am Chem Soc 1986;108:3830-3832.
    • (1986) J Am Chem Soc , vol.108 , pp. 3830-3832
    • Wong, C.F.1    McCammon, J.A.2
  • 36
    • 0023663097 scopus 로고
    • Computer-aided molecular design
    • McCammon JA. Computer-aided molecular design. Science 1987; 238:486-491.
    • (1987) Science , vol.238 , pp. 486-491
    • McCammon, J.A.1
  • 39
    • 0001611806 scopus 로고    scopus 로고
    • Dielectric continuum models for hydration effects on peptide conformational transitions
    • Osapay K, Young WS, Bashford D, Brooks CL, Case DA. Dielectric continuum models for hydration effects on peptide conformational transitions. J Phys Chem 1996;100:2698-2705.
    • (1996) J Phys Chem , vol.100 , pp. 2698-2705
    • Osapay, K.1    Young, W.S.2    Bashford, D.3    Brooks, C.L.4    Case, D.A.5
  • 40
    • 0029833446 scopus 로고    scopus 로고
    • Charge screening and the dielectric constant of proteins: Insights from molecular dynamics
    • Simonson Y, Brooks CL. Charge screening and the dielectric constant of proteins: insights from molecular dynamics. J Am Chem Soc 1996;118:8452-8458.
    • (1996) J Am Chem Soc , vol.118 , pp. 8452-8458
    • Simonson, Y.1    Brooks, C.L.2
  • 41
    • 0001767031 scopus 로고    scopus 로고
    • Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
    • Ferrara P, Apostolakis J, Caflisch A. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J Phys Chem B. 2000;104:5000-5010.
    • (2000) J Phys Chem B , vol.104 , pp. 5000-5010
    • Ferrara, P.1    Apostolakis, J.2    Caflisch, A.3
  • 42
    • 0001744683 scopus 로고    scopus 로고
    • Targeted molecular dynamics simulations of protein unfolding
    • Ferrar P, Apostolakis J, Caflisch A. Targeted molecular dynamics simulations of protein unfolding. J Phys Chem B 2000;104:4511-4518.
    • (2000) J Phys Chem B , vol.104 , pp. 4511-4518
    • Ferrar, P.1    Apostolakis, J.2    Caflisch, A.3
  • 43
    • 0000871204 scopus 로고
    • Multiconfiguration thermodynamic integration
    • Straatsma TP, McCammon JA. Multiconfiguration thermodynamic integration. J Chem Phys 1991;95:1175-1188.
    • (1991) J Chem Phys , vol.95 , pp. 1175-1188
    • Straatsma, T.P.1    McCammon, J.A.2
  • 45
    • 0028258175 scopus 로고
    • Molecular dynamics simulation of a phospholipid membrane
    • Egberts E, Marrink SJ, Berendsen HJC. Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J 1994;22: 423-436.
    • (1994) Eur Biophys J , vol.22 , pp. 423-436
    • Egberts, E.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 47
    • 48749148224 scopus 로고
    • Rattle: A velocity version of the SHAKE algorithm for molecular dynamics calculations
    • Andersen HC. Rattle: a velocity version of the SHAKE algorithm for molecular dynamics calculations. J Comput Phys 1983;52:24-34.
    • (1983) J Comput Phys , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 49
    • 0030197443 scopus 로고    scopus 로고
    • Effects of polarizability on the hydration of the chloride ion
    • Stuart SJ, Berne BJ. Effects of polarizability on the hydration of the chloride ion. J Phys Chem 1996;100:11934-11943.
    • (1996) J Phys Chem , vol.100 , pp. 11934-11943
    • Stuart, S.J.1    Berne, B.J.2
  • 50
    • 0000826117 scopus 로고    scopus 로고
    • Molecular dynamic study of Sn-1 and Sn-2 chain conformations in dipalmitoylphosphatidylcholine membranes
    • Smondyrev AM, Berkowitz ML. Molecular dynamic study of Sn-1 and Sn-2 chain conformations in dipalmitoylphosphatidylcholine membranes. J Chem Phys 1999;110:3981-3985.
    • (1999) J Chem Phys , vol.110 , pp. 3981-3985
    • Smondyrev, A.M.1    Berkowitz, M.L.2
  • 51
    • 0031658230 scopus 로고    scopus 로고
    • A carbon-13 nuclear magnetic resonance spectroscopic study of inter-proton pair order parameters: A new approach to study order and dynamics in phospholipid membrane systems
    • Urbina JA, Moreno B, Arnold W, Taron CH, Orlean P, Oldfield E. A carbon-13 nuclear magnetic resonance spectroscopic study of inter-proton pair order parameters: a new approach to study order and dynamics in phospholipid membrane systems. Biophys J 1998;75:1372-1383.
    • (1998) Biophys J , vol.75 , pp. 1372-1383
    • Urbina, J.A.1    Moreno, B.2    Arnold, W.3    Taron, C.H.4    Orlean, P.5    Oldfield, E.6
  • 52
    • 84986468608 scopus 로고
    • An approach to computing electrostatic charges for molecules
    • Singh UC, Kollman PA. An approach to computing electrostatic charges for molecules. J Comp Chem 1984;5:129-145.
    • (1984) J Comp Chem , vol.5 , pp. 129-145
    • Singh, U.C.1    Kollman, P.A.2
  • 53
    • 84986492477 scopus 로고
    • Atomic charges derived from semiempirical methods
    • Besler BH, Merz KM, Kollman PA. Atomic charges derived from semiempirical methods. J Comp Chem 1990;11:431-439.
    • (1990) J Comp Chem , vol.11 , pp. 431-439
    • Besler, B.H.1    Merz, K.M.2    Kollman, P.A.3
  • 54
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - The RESP model
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - the RESP model. J Phys Chem 1993;97: 10269-10280.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 56
    • 0035892155 scopus 로고    scopus 로고
    • One-step perturbation methods for solvation free energies of polar solutes
    • Pitera JW, van Gunsteren WF. One-step perturbation methods for solvation free energies of polar solutes. J Phys Chem B 2001;105: 11264-11274.
    • (2001) J Phys Chem B , vol.105 , pp. 11264-11274
    • Pitera, J.W.1    Van Gunsteren, W.F.2
  • 57
    • 0012606052 scopus 로고    scopus 로고
    • Molecular dynamics simulations of solvated ions between a membrane and metal electrodes at various electric potentials
    • 198
    • Elber R, Eisenberg RS. Molecular dynamics simulations of solvated ions between a membrane and metal electrodes at various electric potentials. Biophys J 198;74:A342-A342.
    • Biophys J , vol.74 , pp. A342
    • Elber, R.1    Eisenberg, R.S.2
  • 58
    • 0345421087 scopus 로고    scopus 로고
    • Bridging the gap between reaction pathways, long time dynamics, and calculation of rates
    • Forthcoming
    • Elber R, Ghosh A, Cárdenas A, Stern H. Bridging the gap between reaction pathways, long time dynamics, and calculation of rates. Adv Chem Phys. Forthcoming.
    • Adv Chem Phys
    • Elber, R.1    Ghosh, A.2    Cárdenas, A.3    Stern, H.4
  • 59
    • 0015499163 scopus 로고
    • Ion transfer across lipid membranes in presence of gramicidin-A. 2. Ion selectivity
    • Myers VB, Haydon DA. Ion transfer across lipid membranes in presence of gramicidin-A. 2. Ion selectivity. Biochim Biophys Acta 1972;274:313-321.
    • (1972) Biochim Biophys Acta , vol.274 , pp. 313-321
    • Myers, V.B.1    Haydon, D.A.2


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