메뉴 건너뛰기




Volumn 71, Issue 3, 1996, Pages 1172-1178

Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A

Author keywords

[No Author keywords available]

Indexed keywords

GRAMICIDIN A; ION CHANNEL; WATER;

EID: 0029775587     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79321-9     Document Type: Article
Times cited : (101)

References (44)
  • 1
    • 11744384413 scopus 로고
    • The Grötthus mechanism
    • Agmon. N. 1995. The Grötthus mechanism. Chem. Phys. Lett. 244: 456-462.
    • (1995) Chem. Phys. Lett. , vol.244 , pp. 456-462
    • Agmon, N.1
  • 4
    • 4243553426 scopus 로고
    • Density functional exchange-energy approximation with correct asymptotic behavior
    • Becke, A. D. 1988. Density functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A. 38:3098-3100.
    • (1988) Phys. Rev. A. , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 5
    • 0026778201 scopus 로고
    • Amino acid substitutions and ion channel function: Model-dependent conclusions
    • Becker, M. D., R. E. Koeppe II, and O. S. Andersen. 1992. Amino acid substitutions 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 II, R.E.2    Andersen, O.S.3
  • 6
    • 0027293465 scopus 로고
    • Influence of the nature of the aromatic side-chain on the conductance of the channel of linear gramicidin: Study of a series of 9,11,13,15-Tyr(O-protected) derivatives
    • Benamar, D., P. Daumas, Y. Trudelle, B. Calas, R. Bennes, F. Heitz. 1993. Influence of the nature of the aromatic side-chain on the conductance of the channel of linear gramicidin: study of a series of 9,11,13,15-Tyr(O-protected) derivatives. Eur. Biophys. J. 22:145-150.
    • (1993) Eur. Biophys. J. , vol.22 , pp. 145-150
    • Benamar, D.1    Daumas, P.2    Trudelle, Y.3    Calas, B.4    Bennes, R.5    Heitz, F.6
  • 7
    • 0026332339 scopus 로고
    • Water is required for proton transport 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 transport 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
  • 8
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car, R., and M. Parrinello. 1985. Unified approach for molecular dynamics and density-functional theory. Phys. Rev. Lett. 55:2471-2474.
    • (1985) Phys. Rev. Lett. , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 9
    • 0025895720 scopus 로고
    • Time correlation analysis of simulated water motion in flexible and rigid gramicidin channels
    • Chiu, S. W., L. K. Nicholson, 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    Nicholson, L.K.2    Subramaniam, S.3    McCammon, J.A.4
  • 10
    • 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
  • 11
    • 0005384356 scopus 로고
    • Nobel Lecture: The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis
    • Deisenhofer, J., and H. Michel. 1989. Nobel Lecture: the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. EMBO. J. 8:2149-2170.
    • (1989) EMBO. J. , vol.8 , pp. 2149-2170
    • Deisenhofer, J.1    Michel, H.2
  • 12
    • 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
  • 13
    • 33646900958 scopus 로고
    • Proton mobility in water at high temperatures and pressures
    • Franck, E. U., D. Hartmann, and F. Hensel. 1965. Proton mobility in water at high temperatures and pressures. Disc. Faraday Soc. 39:200-206.
    • (1965) Disc. Faraday Soc. , vol.39 , pp. 200-206
    • Franck, E.U.1    Hartmann, D.2    Hensel, F.3
  • 14
    • 0025292355 scopus 로고
    • Model for the structure for bacteriorhodopsin based on high resolution cryo-microscopy
    • Henderson, R., J. M. Baldwin, T. A. Ceska, F. Zemlin, E. Beckmann, and K. H. Downing. 1990. Model for the structure for bacteriorhodopsin based on high resolution cryo-microscopy. J. Mol. Biol. 213:899-929.
    • (1990) J. Mol. Biol. , vol.213 , pp. 899-929
    • Henderson, R.1    Baldwin, J.M.2    Ceska, T.A.3    Zemlin, F.4    Beckmann, E.5    Downing, K.H.6
  • 15
    • 0028787147 scopus 로고
    • Tryptophan hydrogen bonding and electric dipole moments: Functional roles in the gramicidin channel and implications for membrane proteins
    • Hu, W., and T. A. Cross. 1995. Tryptophan hydrogen bonding and electric dipole moments: functional roles in the gramicidin channel and implications for membrane proteins. Biochemistry. 34:14147-14155.
    • (1995) Biochemistry , vol.34 , pp. 14147-14155
    • Hu, W.1    Cross, T.A.2
  • 16
    • 16444375810 scopus 로고
    • The performance of a family of density functional methods
    • Johnson, B., P. M. W. Gill, and J. A. Pople. 1993. The performance of a family of density functional methods. J. Chem. Phys. 98:5612-5626.
    • (1993) J. Chem. Phys. , vol.98 , pp. 5612-5626
    • Johnson, B.1    Gill, P.M.W.2    Pople, J.A.3
  • 18
    • 0001432987 scopus 로고
    • Ion thermochemistry and solvation from gas phase equilibria
    • Kebarle, P. 1977. Ion thermochemistry and solvation from gas phase equilibria. Annu. Rev. Phys. Chem. 28:445-476.
    • (1977) Annu. Rev. Phys. Chem. , vol.28 , pp. 445-476
    • Kebarle, P.1
  • 19
    • 0001498808 scopus 로고
    • Ab initio molecular dynamics study of hydrochloric acid in water
    • Laasonen, K., and M. L. Klein. 1994. Ab initio molecular dynamics study of hydrochloric acid in water. J. Am. Chem. Soc. 116:11620-11621.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 11620-11621
    • Laasonen, K.1    Klein, M.L.2
  • 20
    • 34247648401 scopus 로고
    • Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials
    • Laasonen, K., A. Pasquarello, R. Car, C. Lee, and D. Vanderbilt. 1993a. Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials. Phys. Rev. B. 47:10142-10153.
    • (1993) Phys. Rev. B. , vol.47 , pp. 10142-10153
    • Laasonen, K.1    Pasquarello, A.2    Car, R.3    Lee, C.4    Vanderbilt, D.5
  • 22
    • 0021733063 scopus 로고
    • Molecular dynamics simulation of cation motion in water-filled gramicidin-like pores
    • Lee, W. K., and P. C. Jordan. 1984. Molecular dynamics simulation of cation motion in water-filled gramicidin-like pores. Biophys. J. 46: 805-819.
    • (1984) Biophys. J. , vol.46 , pp. 805-819
    • Lee, W.K.1    Jordan, P.C.2
  • 23
    • 0018072320 scopus 로고
    • Number of water molecules coupled to the transport of sodium, potassium, and hydrogen ions via gramicidin, nonactin, or valinomycin
    • Levin, D. G., S. R. Elias, and J. M. Hautman. 1978. Number of water molecules coupled to the transport of sodium, potassium, and hydrogen ions via gramicidin, nonactin, or valinomycin. Biochim. Biophys. Acta. 512:436-451.
    • (1978) Biochim. Biophys. Acta. , vol.512 , pp. 436-451
    • Levin, D.G.1    Elias, S.R.2    Hautman, J.M.3
  • 24
    • 5944238344 scopus 로고    scopus 로고
    • The quantum dynamics of an excess proton in water
    • Lobaugh, J., and G. A. Voth. 1996. The quantum dynamics of an excess proton in water. J. Chem. Phys. 104:2056-2069.
    • (1996) J. Chem. Phys. , vol.104 , pp. 2056-2069
    • Lobaugh, J.1    Voth, G.A.2
  • 27
    • 33845374904 scopus 로고
    • Comparative stabilities of cationic and anionic hydrogen-bonded networks: Mixed clusters of water-methanol
    • Meot-Ner, M. J. 1986. Comparative stabilities of cationic and anionic hydrogen-bonded networks: mixed clusters of water-methanol. J. Am. Chem. Soc. 108:6189-6197.
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 6189-6197
    • Meot-Ner, M.J.1
  • 28
    • 0001356079 scopus 로고
    • Density-functional theory applied to proton transfer systems: A numerical test
    • Mijoule, C., Z. Latajka, and D. Borgis. 1993. Density-functional theory applied to proton transfer systems: a numerical test. Chem. Phys. Lett. 208:364-368.
    • (1993) Chem. Phys. Lett. , vol.208 , pp. 364-368
    • Mijoule, C.1    Latajka, Z.2    Borgis, D.3
  • 29
    • 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
  • 30
    • 0009758179 scopus 로고
    • Evaluation of the density functional approximation on the computation of hydrogen bond interactions
    • Novoa, J. J., C. Sosa. 1995. Evaluation of the density functional approximation on the computation of hydrogen bond interactions. J. Phys. Chem. 99:15837-15845.
    • (1995) J. Phys. Chem. , vol.99 , pp. 15837-15845
    • Novoa, J.J.1    Sosa, C.2
  • 31
    • 0025298852 scopus 로고
    • Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction: Elements of the proton pathway?
    • Papadopoulos, G., N. A. Dencher, G. Zaccai, and G. Buldt. 1990. Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction: elements of the proton pathway? J. Mol. Biol. 214:1519.
    • (1990) J. Mol. Biol. , vol.214 , pp. 1519
    • Papadopoulos, G.1    Dencher, N.A.2    Zaccai, G.3    Buldt, G.4
  • 32
    • 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
  • 33
    • 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
  • 34
    • 0342910044 scopus 로고
    • The gramicidin a channel: The energy profile for the single and double occupancy in a head-to-head β[stack][low]3,3[high]6,3[/stack]-helical dimer backbone
    • Pullman, A., and C. Etchebest. 1983. The gramicidin A channel: the energy profile for the single and double occupancy in a head-to-head β[stack][low]3,3[high]6,3[/stack]-helical dimer backbone. FEBS Lett. 163:199-202.
    • (1983) FEBS Lett. , vol.163 , pp. 199-202
    • Pullman, A.1    Etchebest, C.2
  • 36
    • 0025882246 scopus 로고
    • Ion transport in a model gramicidin channel: Structure and thermodynamics
    • Roux, B., and M. Karplus. 1991. Ion transport in a model gramicidin channel: structure and thermodynamics. Biophys. J. 59:961-981.
    • (1991) Biophys. J. , vol.59 , pp. 961-981
    • Roux, B.1    Karplus, M.2
  • 37
    • 0029878757 scopus 로고    scopus 로고
    • The structure and dynamics of hydronium in the ion channel gramicidin a
    • Sagnella, D. E., and G. A. Voth. 1996. The structure and dynamics of hydronium in the ion channel gramicidin A. Biophys. J. 70:2043-2051.
    • (1996) Biophys. J. , vol.70 , pp. 2043-2051
    • Sagnella, D.E.1    Voth, G.A.2
  • 38
    • 0001042824 scopus 로고
    • Gaussian density functional calculations on hydrogen bonded systems
    • Sim, F., A. St-Amant, I. Papai, and D. R. Salahub. 1992. Gaussian density functional calculations on hydrogen bonded systems. J. Am. Chem. Soc. 114:4391-4400.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 4391-4400
    • Sim, F.1    St-Amant, A.2    Papai, I.3    Salahub, D.R.4
  • 39
    • 0004155427 scopus 로고
    • W. H. Freeman and Co., New York
    • Stryer, L. 1988. Biochemistry, 3rd ed. W. H. Freeman and Co., New York. 25.
    • (1988) Biochemistry, 3rd Ed. , pp. 25
    • Stryer, L.1
  • 40
    • 0000135791 scopus 로고
    • Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
    • Tuckerman, M., K. Laasonen, M. Sprik, and M. Parrinello. 1995. Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J. Chem. Phys. 103:150-161.
    • (1995) J. Chem. Phys. , vol.103 , pp. 150-161
    • Tuckerman, M.1    Laasonen, K.2    Sprik, M.3    Parrinello, M.4
  • 41
    • 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
  • 43
    • 20544463457 scopus 로고
    • Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
    • Vanderbilt, D. 1990. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B. 41:7892-7895.
    • (1990) Phys. Rev. B. , vol.41 , pp. 7892-7895
    • Vanderbilt, D.1
  • 44
    • 0028210368 scopus 로고
    • The conformation of linear gramicidin is sequence dependent: A monolayer and infrared study
    • Van Mau, N., B. Bonnet, A. Benayad, and F. Heitz. 1994. The conformation of linear gramicidin is sequence dependent: a monolayer and infrared study. Eur. Biophys. J. 22:447-452.
    • (1994) Eur. Biophys. J. , vol.22 , pp. 447-452
    • Van Mau, N.1    Bonnet, B.2    Benayad, A.3    Heitz, F.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.