메뉴 건너뛰기




Volumn 73, Issue 4, 1997, Pages 1699-1716

Molecular dynamics study of free energy profiles for organic cations in gramicidin A channels

Author keywords

[No Author keywords available]

Indexed keywords

CATION; CATION CHANNEL; FORMAMIDINE; GRAMICIDIN A; GUANIDINE; METHYLAMMONIUM; SOLVENT; WATER;

EID: 0030808398     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78202-X     Document Type: Article
Times cited : (19)

References (56)
  • 2
    • 0000346708 scopus 로고
    • Gramicidin a transmembrane ion-channel. Three-dimensional structure reconstruction based on NMR spectroscopy and energy refinement
    • Arseniev, A. S., A. L. Lomize, I. L. Barsukov, and V. F. Bystrov. 1986. Gramicidin A transmembrane ion-channel. Three-dimensional structure reconstruction based on NMR spectroscopy and energy refinement. Biol. Membr. 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
    • 0016172553 scopus 로고
    • Temperature-dependent properties of gramicidin a channels
    • Bamberg, E., and P. Läuger. 1974. Temperature-dependent properties of gramicidin A channels. Biochim. Biophys. Acta. 367:127-133.
    • (1974) Biochim. Biophys. Acta , vol.367 , pp. 127-133
    • Bamberg, E.1    Läuger, P.2
  • 4
    • 0026778201 scopus 로고
    • Amino acid substitution and ion channel function. Model-dependent conclusions
    • Becker, M. D., R. E. Koeppe, II, and O. S. Andersen. 1992. Amino acid substitution and ion channel function. Model-dependent conclusions. Biophys. J. 62:25-27.
    • (1992) Biophys. J. , vol.62 , pp. 25-27
    • Becker, M.D.1    Koeppe R.E. II2    Andersen, O.S.3
  • 7
    • 0027533833 scopus 로고
    • The use of physical methods in determining gramicidin channel structure and function
    • Busath, D. D. 1993. The use of physical methods in determining gramicidin channel structure and function. Annu. Rev. Physiol. 55:473-501.
    • (1993) Annu. Rev. Physiol. , vol.55 , pp. 473-501
    • Busath, D.D.1
  • 8
    • 0039040716 scopus 로고
    • Guanidinium as a probe of the gramicidin channel interior
    • A. Pullman, J. Jortner, and B. Pullman, editors. Kluwer Academic Publishers, Dordrecht, Boston, and London
    • Busath, D., G. Hemsley, T. Bridal, M. Pear, K. Gaffney, and M. Karplus. 1988. Guanidinium as a probe of the gramicidin channel interior. In Transport through Membranes: Carriers, Channels and Pumps. A. Pullman, J. Jortner, and B. Pullman, editors. Kluwer Academic Publishers, Dordrecht, Boston, and London. 187-201.
    • (1988) Transport Through Membranes: Carriers, Channels and Pumps , pp. 187-201
    • Busath, D.1    Hemsley, G.2    Bridal, T.3    Pear, M.4    Gaffney, K.5    Karplus, M.6
  • 9
    • 0028108503 scopus 로고
    • A molecular dynamics study of gating in dioxolane-linked gramicidin A channels
    • Crouzy, S., T. B. Woolf, and B. Roux. 1994. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys. J. 67: 1370-1386.
    • (1994) Biophys. J. , vol.67 , pp. 1370-1386
    • Crouzy, S.1    Woolf, T.B.2    Roux, B.3
  • 10
    • 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
  • 12
    • 0021070747 scopus 로고
    • Ionic selectivity revisited: The role of kinetic and equilibrium processes in ion permeation through channels
    • Eisenman, G., and R. Horn. 1983. Ionic selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Mol. Biol. 767:197-225.
    • (1983) J. Mol. Biol. , vol.767 , pp. 197-225
    • Eisenman, G.1    Horn, R.2
  • 13
    • 1842676074 scopus 로고
    • Further studies on ion selectivity
    • M. Kessler, L. Clark, D. Lubbers, I. Silver, and W. Simon, editors. Urban and Schwarzenberg, Munich, Berlin, and Vienna
    • Eisenman, G., S. Krasne, and S. Ciani. 1976. Further studies on ion selectivity. In Ion and Enzyme Electrodes in Medicine and in Biology. M. Kessler, L. Clark, D. Lubbers, I. Silver, and W. Simon, editors. Urban and Schwarzenberg, Munich, Berlin, and Vienna. 3-22.
    • (1976) Ion and Enzyme Electrodes in Medicine and in Biology , pp. 3-22
    • Eisenman, G.1    Krasne, S.2    Ciani, S.3
  • 14
    • 0004028236 scopus 로고
    • Energy barriers in ionic channels: Data for gramicidin A interpreted using a single-file (3B4S″) model having 3 barriers separating 4 sites
    • G. Spach, editor. Elsevier North-Holland Biomedical Press, Amsterdam
    • Eisenman, G., and J. P. Sandblom. 1983. Energy barriers in ionic channels: data for gramicidin A interpreted using a single-file (3B4S″) model having 3 barriers separating 4 sites. In Physical Chemistry of Transmembrane Ion Motions. G. Spach, editor. Elsevier North-Holland Biomedical Press, Amsterdam. 329-347.
    • (1983) Physical Chemistry of Transmembrane Ion Motions , pp. 329-347
    • Eisenman, G.1    Sandblom, J.P.2
  • 15
    • 0023985917 scopus 로고
    • + in gramicidin a in the presence of water. Problem of the ion selectivity of the channel
    • + in gramicidin A in the presence of water. Problem of the ion selectivity of the channel. J. Biomol. Struct. Dyn. 5:1111-1125.
    • (1988) J. Biomol. Struct. Dyn. , vol.5 , pp. 1111-1125
    • Etchebest, C.1    Pullman, A.2
  • 16
    • 0021173195 scopus 로고
    • +. Influence of the flexibility of the ethanolamine end chain on the profiles
    • +. Influence of the flexibility of the ethanolamine end chain on the profiles. FEBS Lett. 173:301-306.
    • (1984) FEBS Lett. , vol.173 , pp. 301-306
    • Etchebest, C.1    Ranganathan, S.2    Pullman, A.3
  • 17
    • 0002933759 scopus 로고
    • Some applications of modern rate theory to physiological systems
    • Eyring, H., R. Lumry, and J. W. Woodbury. 1949. Some applications of modern rate theory to physiological systems. Record Chem. Prog. 10: 100-114.
    • (1949) Record Chem. Prog. , vol.10 , pp. 100-114
    • Eyring, H.1    Lumry, R.2    Woodbury, J.W.3
  • 18
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson, M., and B. Honig. 1988. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct. Funct. Genet. 4:7-18.
    • (1988) Proteins Struct. Funct. Genet. , vol.4 , pp. 7-18
    • Gilson, M.1    Honig, B.2
  • 19
    • 84988087911 scopus 로고
    • Calculating electrostatic interactions in bio-molecules: Method and error assessment
    • Gilson, M., K. Sharp, and B. Honig. 1988. Calculating electrostatic interactions in bio-molecules: method and error assessment. J. Comput. Chem. 9:327-335.
    • (1988) J. Comput. Chem. , vol.9 , pp. 327-335
    • Gilson, M.1    Sharp, K.2    Honig, B.3
  • 21
    • 85030304303 scopus 로고
    • Free energy profile for small organic cations in gramicidin A channel with umbrella sampling and perturbation dynamics
    • Hao, Y., and D. Busath. 1995. Free energy profile for small organic cations in gramicidin A channel with umbrella sampling and perturbation dynamics. Biophys. J. 68:A151.
    • (1995) Biophys. J. , vol.68
    • Hao, Y.1    Busath, D.2
  • 22
    • 85030304772 scopus 로고    scopus 로고
    • Free energy profiles for organic cations in gramicidin A channels
    • Hao, Y., and D. D. Busath. 1996. Free energy profiles for organic cations in gramicidin A channels. Biophys. J. 70:A80.
    • (1996) Biophys. J. , vol.70
    • Hao, Y.1    Busath, D.D.2
  • 23
    • 0025847306 scopus 로고
    • Small iminium ions block gramicidin channels in lipid bilayers
    • Hemsley, G., and D. Busath. 1991. Small iminium ions block gramicidin channels in lipid bilayers. Biophys. J. 59:901-907.
    • (1991) Biophys. J. , vol.59 , pp. 901-907
    • Hemsley, G.1    Busath, D.2
  • 25
    • 33845282559 scopus 로고
    • Microscopic approaches to ion transport through transmembrane channels. The model system gramicidin
    • Jordan, P. C. 1987. Microscopic approaches to ion transport through transmembrane channels. The model system gramicidin. J. Phys. Chem. 91:6582-6591.
    • (1987) J. Phys. Chem. , vol.91 , pp. 6582-6591
    • Jordan, P.C.1
  • 26
    • 0025000888 scopus 로고
    • Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study
    • Jordan, P. C. 1990. Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study. Biophys. J. 58:1133-1156.
    • (1990) Biophys. J. , vol.58 , pp. 1133-1156
    • Jordan, P.C.1
  • 28
    • 0030183359 scopus 로고    scopus 로고
    • Macromolecualar structural elucidation with solid state NMR derived orientational constraints
    • Ketchum, R. R., K.-C. Lee, S. Huo, and T. A. Cross. 1996. Macromolecualar structural elucidation with solid state NMR derived orientational constraints. J. Biomol. NMR. 8:1-14.
    • (1996) J. Biomol. NMR , vol.8 , pp. 1-14
    • Ketchum, R.R.1    Lee, K.-C.2    Huo, S.3    Cross, T.A.4
  • 30
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • Klapper, I., R. Hagstrom, R. Fine, K. Sharp, and B. Honig. 1986. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct. Funct. Genet. 1:47-59.
    • (1986) Proteins Struct. Funct. Genet. , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 32
    • 0015788893 scopus 로고
    • Ion transport through pores. A rate-theory analysis
    • Läuger, P. 1973. Ion transport through pores. A rate-theory analysis. Biochim. Biophys. Acta. 311:423-441.
    • (1973) Biochim. Biophys. Acta , vol.311 , pp. 423-441
    • Läuger, P.1
  • 33
    • 0020104695 scopus 로고
    • Comparison of Nernst-Planck and reaction-rate models for multiply occupied channels
    • Levitt, D. G. 1982. Comparison of Nernst-Planck and reaction-rate models for multiply occupied channels. Biophys. J. 37:575-587.
    • (1982) Biophys. J. , vol.37 , pp. 575-587
    • Levitt, D.G.1
  • 34
    • 0026011790 scopus 로고
    • General continuum theory for multiion channel. I. Theory
    • Levitt, D. G. 1991. General continuum theory for multiion channel. I. Theory. Biophys. J. 59:271-277.
    • (1991) Biophys. J. , vol.59 , pp. 271-277
    • Levitt, D.G.1
  • 36
    • 84986505827 scopus 로고
    • Validation of the general purpose Quanta 3.2/CHARMm Force Field
    • Momany, F. A., and R. Rone. 1992. Validation of the general purpose Quanta 3.2/CHARMm Force Field. J. Comp. Chem. 13:888-900.
    • (1992) J. Comp. Chem. , vol.13 , pp. 888-900
    • Momany, F.A.1    Rone, R.2
  • 37
    • 0015499163 scopus 로고
    • Ion transfer across lipid membranes in the presence of gramicidin A. II. The ion selectivity
    • Myers, V. B., and D. A. Haydon. 1972. Ion transfer across lipid membranes in the presence of gramicidin A. II. The ion selectivity. Biochim. Biophys. Acta. 274:313-322.
    • (1972) Biochim. Biophys. Acta , vol.274 , pp. 313-322
    • Myers, V.B.1    Haydon, D.A.2
  • 38
    • 0014575043 scopus 로고
    • Nonlinear electrical effects in lipid bilayer membranes. II. Integration of the generalized Nernst-Planck equations
    • Neumcke, B., and P. Läuger. 1969. Nonlinear electrical effects in lipid bilayer membranes. II. Integration of the generalized Nernst-Planck equations. Biophys. J. 9:1160-1170.
    • (1969) Biophys. J. , vol.9 , pp. 1160-1170
    • Neumcke, B.1    Läuger, P.2
  • 40
    • 0001060458 scopus 로고
    • A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution
    • Patey, G. N., and J. P. Valeau. 1975. A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution. J. Chem. Phys. 63:2334-2339.
    • (1975) J. Chem. Phys. , vol.63 , pp. 2334-2339
    • Patey, G.N.1    Valeau, J.P.2
  • 41
    • 0343034576 scopus 로고
    • Free energy profile for iminium transport by gramicidin: Guanidinium vs. formamidinium
    • Pear, M., and D. Busath. 1990. Free energy profile for iminium transport by gramicidin: guanidinium vs. formamidinium. Abstract. In Proceedings of the 10th International Biophysics Congress. P5.5.7.
    • (1990) Proceedings of the 10th International Biophysics Congress , pp. 557
    • Pear, M.1    Busath, D.2
  • 43
    • 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
  • 44
    • 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
  • 45
    • 0027232024 scopus 로고
    • Ion transport in the gramicidin channel: Free energy of the solvated right-handed dimer in a model membrane
    • Roux, B., and M. Karplus. 1993. Ion transport in the gramicidin channel: free energy of the solvated right-handed dimer in a model membrane. J. Am. Chem. Soc. 115:3250-3260.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3250-3260
    • Roux, B.1    Karplus, M.2
  • 46
    • 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
  • 48
    • 0027200325 scopus 로고
    • The permeation properties of small organic cations in gramicidin A channels
    • Seoh, S-A., and D. Busath. 1993a. The permeation properties of small organic cations in gramicidin A channels. Biophys. J. 64:1017-1028.
    • (1993) Biophys. J. , vol.64 , pp. 1017-1028
    • Seoh, S.-A.1    Busath, D.2
  • 49
    • 0027420654 scopus 로고
    • Formamidinium-induced dimer stabilization and flicker block behavior in homo- and heterodimer channels formed by gramicidin A and N-acetyl gramicidin A
    • Seoh, S-A., and D. Busath. 1993b. Formamidinium-induced dimer stabilization and flicker block behavior in homo- and heterodimer channels formed by gramicidin A and N-acetyl gramicidin A. Biophys. J. 65: 1817-1827.
    • (1993) Biophys. J. , vol.65 , pp. 1817-1827
    • Seoh, S.-A.1    Busath, D.2
  • 50
    • 0029053366 scopus 로고
    • Gramicidin tryptophans mediate formamidinium-induced channel stabilization
    • Seoh, S-A., and D. D. Busath. 1995. Gramicidin tryptophans mediate formamidinium-induced channel stabilization. Biophys. J. 68: 2271-2279.
    • (1995) Biophys. J. , vol.68 , pp. 2271-2279
    • Seoh, S.-A.1    Busath, D.D.2
  • 53
    • 85030305939 scopus 로고
    • Three dimensional structure of gramicidin in SDS micelles
    • Tucker, W. A., T. G. Fletcher, J. F. Hinton, and G. Harms. 1992. Three dimensional structure of gramicidin in SDS micelles. Biophys. J. 61: A525.
    • (1992) Biophys. J. , vol.61
    • Tucker, W.A.1    Fletcher, T.G.2    Hinton, J.F.3    Harms, G.4
  • 54
    • 0026747636 scopus 로고
    • Gramicidin channel selectivity: Molecular mechanics calculations for formamidinium, guanidinium, and acetamidinium
    • Turano, B., M. Pear, and D. Busath. 1992. Gramicidin channel selectivity: molecular mechanics calculations for formamidinium, guanidinium, and acetamidinium. Biophys. J. 63:152-161.
    • (1992) Biophys. J. , vol.63 , pp. 152-161
    • Turano, B.1    Pear, M.2    Busath, D.3
  • 55
    • 0018759138 scopus 로고
    • Ion transport in the simplest single-file pore
    • Urban, B. W., and S. B. Hladky. 1979. Ion transport in the simplest single-file pore. Biochim. Biophys. Acta. 554:410-429.
    • (1979) Biochim. Biophys. Acta , vol.554 , pp. 410-429
    • Urban, B.W.1    Hladky, S.B.2
  • 56
    • 0005187795 scopus 로고
    • On the molecular structure of the gramicidin transmembrane channel
    • A. N. Martanosi, editor. Plenum, New York
    • Urry, D. W. 1984. On the molecular structure of the gramicidin transmembrane channel. In The Enzymes of Biological Membranes, 2nd ed, Vol. 1. A. N. Martanosi, editor. Plenum, New York. 229-257.
    • (1984) The Enzymes of Biological Membranes, 2nd Ed , vol.1 , pp. 229-257
    • Urry, D.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.