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Volumn 91, Issue 10, 2006, Pages 3617-3629

Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ARGON; DIOLEOYLPHOSPHATIDYLCHOLINE; MELITTIN;

EID: 33751230498     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.084483     Document Type: Article
Times cited : (17)

References (40)
  • 2
    • 0031824356 scopus 로고    scopus 로고
    • Structure and interactions of fully hydrated dioleoylphosphatidylcholine bilayers
    • Tristram-Nagle, S., H. I. Petrache, and J. F. Nagle. 1998. Structure and interactions of fully hydrated dioleoylphosphatidylcholine bilayers. Biophys. J. 75:917-925.
    • (1998) Biophys. J. , vol.75 , pp. 917-925
    • Tristram-Nagle, S.1    Petrache, H.I.2    Nagle, J.F.3
  • 3
    • 85051972100 scopus 로고
    • Determination of the structure of fluid lipid bilayer membranes
    • E. A. Disalvo and S. A. Simon, editors. CRC Press. Boca Raton, FL
    • White, S. H., and M. C. Wiener. 1995. Determination of the structure of fluid lipid bilayer membranes. In Permeability and Stability of Lipid Bilayers. E. A. Disalvo and S. A. Simon, editors. CRC Press. Boca Raton, FL. 1-19.
    • (1995) Permeability and Stability of Lipid Bilayers , pp. 1-19
    • White, S.H.1    Wiener, M.C.2
  • 4
    • 0026011502 scopus 로고
    • Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution
    • Wiener, M. C., and S. H. White. 1991. Fluid bilayer structure determination by the combined use of x-ray and neutron diffraction. I. Fluid bilayer models and the limits of resolution. Biophys. J. 59:162-173.
    • (1991) Biophys. J. , vol.59 , pp. 162-173
    • Wiener, M.C.1    White, S.H.2
  • 5
    • 0019398052 scopus 로고
    • Low-angle X-ray diffraction
    • E. Grell, editor. Springer-Verlag. Berlin, Germany
    • Franks, N. P., and Y. K. Levine. 1981. Low-angle X-ray diffraction. In Membrane Spectroscopy. E. Grell, editor. Springer-Verlag. Berlin, Germany. 437-487.
    • (1981) Membrane Spectroscopy , pp. 437-487
    • Franks, N.P.1    Levine, Y.K.2
  • 6
    • 0026729232 scopus 로고
    • Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure
    • Wiener, M. C., and S. H. White. 1992. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. Biophys. J. 61:434-447.
    • (1992) Biophys. J. , vol.61 , pp. 434-447
    • Wiener, M.C.1    White, S.H.2
  • 7
    • 21244462687 scopus 로고    scopus 로고
    • Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach
    • Benz, R. W., F. Castro-Román, D. J. Tobias, and S. H. White. 2005. Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. Biophys. J. 88:805-817.
    • (2005) Biophys. J. , vol.88 , pp. 805-817
    • Benz, R.W.1    Castro-Román, F.2    Tobias, D.J.3    White, S.H.4
  • 8
    • 0018280201 scopus 로고
    • A direct method for determination of membrane electron density profiles on an absolute scale
    • Franks, N. P., T. Arunachalam, and E. Caspi. 1978. A direct method for determination of membrane electron density profiles on an absolute scale. Nature. 276:530-532.
    • (1978) Nature , vol.276 , pp. 530-532
    • Franks, N.P.1    Arunachalam, T.2    Caspi, E.3
  • 9
    • 0025819980 scopus 로고
    • Transbilayer distribution of bromine in fluid bilayers containing a specifically brominated analog of dioleoylphosphatidylcholine
    • Wiener, M. C., and S. H. White. 1991. Transbilayer distribution of bromine in fluid bilayers containing a specifically brominated analog of dioleoylphosphatidylcholine. Biochemistry. 30:6997-7008.
    • (1991) Biochemistry , vol.30 , pp. 6997-7008
    • Wiener, M.C.1    White, S.H.2
  • 10
    • 0017927954 scopus 로고
    • Neutron diffraction studies on selectively deuterated phospholipid bilayers
    • Büldt, G., H. U. Gally, A. Seelig, J. Seelig, and G. Zaccai. 1978. Neutron diffraction studies on selectively deuterated phospholipid bilayers. Nature. 271:182-184.
    • (1978) Nature , vol.271 , pp. 182-184
    • Büldt, G.1    Gally, H.U.2    Seelig, A.3    Seelig, J.4    Zaccai, G.5
  • 11
    • 0026048378 scopus 로고
    • Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. I. Scaling of neutron data and the distribution of double-bonds and water
    • Wiener, M. C., G. I. King, and S. H. White. 1991. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. I. Scaling of neutron data and the distribution of double-bonds and water. Biophys. J. 60:568-576.
    • (1991) Biophys. J. , vol.60 , pp. 568-576
    • Wiener, M.C.1    King, G.I.2    White, S.H.3
  • 12
    • 0026683431 scopus 로고
    • Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. II. Distribution and packing of terminal methyl groups
    • Wiener, M. C., and S. H. White. 1992. Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. II. Distribution and packing of terminal methyl groups. Biophys. J. 61:428-433.
    • (1992) Biophys. J. , vol.61 , pp. 428-433
    • Wiener, M.C.1    White, S.H.2
  • 13
    • 0024558250 scopus 로고
    • The nature of the hydrophobic binding of small peptides at the bilayer interface: Implications for the insertion of transbilayer helices
    • Jacobs, R. E., and S. H. White. 1989. The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices. Biochemistry. 28:3421-3437.
    • (1989) Biochemistry , vol.28 , pp. 3421-3437
    • Jacobs, R.E.1    White, S.H.2
  • 14
    • 0031848843 scopus 로고    scopus 로고
    • Interaction of substance P with phospholipid bilayers: A neutron diffraction study
    • Bradshaw, J. P., S. M. A. Davies, and T. Hauss. 1998. Interaction of substance P with phospholipid bilayers: a neutron diffraction study. Biophys. J. 75:889-895.
    • (1998) Biophys. J. , vol.75 , pp. 889-895
    • Bradshaw, J.P.1    Davies, S.M.A.2    Hauss, T.3
  • 15
    • 0033516703 scopus 로고    scopus 로고
    • An amphipathic α-helix at a membrane interface: A structural study using a novel x-ray diffraction method
    • Hristova, K., W. C. Wimley, V. K. Mishra, G. M. Anantharamaiah, J. P. Segrest, and S. H. White. 1999. An amphipathic α-helix at a membrane interface: A structural study using a novel x-ray diffraction method. J. Mol. Biol. 290:99-117.
    • (1999) J. Mol. Biol. , vol.290 , pp. 99-117
    • Hristova, K.1    Wimley, W.C.2    Mishra, V.K.3    Anantharamaiah, G.M.4    Segrest, J.P.5    White, S.H.6
  • 16
    • 0035144532 scopus 로고    scopus 로고
    • Structure, location, and lipid perturbations of melittin at the membrane interface
    • Hristova, K., C. E. Dempsey, and S. H. White. 2001. Structure, location, and lipid perturbations of melittin at the membrane interface. Biophys. J. 80:801-811.
    • (2001) Biophys. J. , vol.80 , pp. 801-811
    • Hristova, K.1    Dempsey, C.E.2    White, S.H.3
  • 17
    • 0030000521 scopus 로고    scopus 로고
    • Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints
    • Bassolino-Klimas, D., R. Tejero, S. R. Krystek, W. J. Metzler, G. T. Montelione, and R. E. Bruccoleri. 1996. Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints. Protein Sci. 5:593-603.
    • (1996) Protein Sci. , vol.5 , pp. 593-603
    • Bassolino-Klimas, D.1    Tejero, R.2    Krystek, S.R.3    Metzler, W.J.4    Montelione, G.T.5    Bruccoleri, R.E.6
  • 18
    • 0000870109 scopus 로고
    • Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin
    • Brünger, A. T., G. M. Clore, A. M. Gronenborn, and M. Karplus. 1986. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. USA. 83:3801-3805.
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 3801-3805
    • Brünger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Karplus, M.4
  • 20
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • Park, S., F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten. 2003. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J. Chem. Phys. 119:3559-3566.
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-Araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 21
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. 1995. The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun. 91:275-282.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 22
    • 0035277126 scopus 로고    scopus 로고
    • Extension to the weighted histogram analysis methods: Combining umbrella sampling with free energy calculations
    • Souaille, M., and B. Roux. 2001. Extension to the weighted histogram analysis methods: combining umbrella sampling with free energy calculations. Comput. Phys. Commun. 135:40-57.
    • (2001) Comput. Phys. Commun. , vol.135 , pp. 40-57
    • Souaille, M.1    Roux, B.2
  • 25
    • 0002062192 scopus 로고    scopus 로고
    • An empirical potential energy function for phospholipids: Criteria for parameter optimization and applications
    • K. M. Merz, Jr., and B. Roux, editors. Birkhäuser. Boston, MA
    • Schlenkrich, M., J. Brickmann, A. D. MacKerell, Jr., and M. Karplus. 1996. An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In Biological Membranes. K. M. Merz, Jr., and B. Roux, editors. Birkhäuser. Boston, MA. 31-81.
    • (1996) Biological Membranes , pp. 31-81
    • Schlenkrich, M.1    Brickmann, J.2    MacKerell Jr., A.D.3    Karplus, M.4
  • 26
    • 0030844208 scopus 로고    scopus 로고
    • Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: Parameterization and comparison with diffraction studies
    • Feller, S. E., D. X. Yin, R. W. Pastor, and A. D. MacKerell, Jr. 1997. Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophys. J. 73:2269-2279.
    • (1997) Biophys. J. , vol.73 , pp. 2269-2279
    • Feller, S.E.1    Yin, D.X.2    Pastor, R.W.3    MacKerell Jr., A.D.4
  • 27
    • 0034250744 scopus 로고    scopus 로고
    • An improved empirical potential energy function for molecular simulations of phospholipids
    • Feller, S. E., and A. D. MacKerell, Jr. 2000. An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B. 104:7510-7515.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7510-7515
    • Feller, S.E.1    MacKerell Jr., A.D.2
  • 29
    • 0028867364 scopus 로고
    • Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer
    • Tu, K., D. J. Tobias, and M. L. Klein. 1995. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer. Biophys. J. 69:2558-2562.
    • (1995) Biophys. J. , vol.69 , pp. 2558-2562
    • Tu, K.1    Tobias, D.J.2    Klein, M.L.3
  • 30
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation: The Langevin piston method
    • Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys. , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.2    Pastor, R.W.3    Brooks, B.R.4
  • 32
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman, M., and B. J. Berne. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97:1990-2001.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.J.2
  • 33
    • 84963146276 scopus 로고
    • Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
    • Grubmüller, H., H. Heller, A. Windemuth, and K. Schulten. 1991. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6:121-142.
    • (1991) Mol. Simul. , vol.6 , pp. 121-142
    • Grubmüller, H.1    Heller, H.2    Windemuth, A.3    Schulten, K.4
  • 35
    • 0035201782 scopus 로고    scopus 로고
    • Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration
    • Mashl, R. J., H. L. Scott, S. Subramaniam, and E. Jokobsson. 2001. Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration. Biophys. J. 81:3005-3015.
    • (2001) Biophys. J. , vol.81 , pp. 3005-3015
    • Mashl, R.J.1    Scott, H.L.2    Subramaniam, S.3    Jokobsson, E.4
  • 36
    • 0011613265 scopus 로고    scopus 로고
    • Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane
    • Bernèche, S., M. Nina, and B. Roux. 1998. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys. J. 75:1603-1618.
    • (1998) Biophys. J. , vol.75 , pp. 1603-1618
    • Bernèche, S.1    Nina, M.2    Roux, B.3
  • 37
    • 0001183580 scopus 로고    scopus 로고
    • Melittin at a membrane/water interface: Effects on water orientation and water penetration
    • Bachar, M., and O. M. Becker. 1999. Melittin at a membrane/water interface: effects on water orientation and water penetration. J. Chem. Phys. 111:8672-8685.
    • (1999) J. Chem. Phys. , vol.111 , pp. 8672-8685
    • Bachar, M.1    Becker, O.M.2
  • 38
    • 0034091671 scopus 로고    scopus 로고
    • Protein-induced membrane disorder: A molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer
    • Bachar, M., and O. M. Becker. 2000. Protein-induced membrane disorder: a molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer. Biophys. J. 78:1359-1375.
    • (2000) Biophys. J. , vol.78 , pp. 1359-1375
    • Bachar, M.1    Becker, O.M.2
  • 39
    • 0002691613 scopus 로고    scopus 로고
    • Adsorption of melittin to a lipid bilayer: A molecular dynamics study
    • Lin, J.-H., and A. Baumgärtner. 2000. Adsorption of melittin to a lipid bilayer: a molecular dynamics study. J. Mol. Liquids. 84:89-98.
    • (2000) J. Mol. Liquids , vol.84 , pp. 89-98
    • Lin, J.-H.1    Baumgärtner, A.2
  • 40
    • 0031980119 scopus 로고    scopus 로고
    • Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: Effect of hydration
    • Hristova, K., and S. H. White. 1998. Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: effect of hydration. Biophys. J. 74:2419-2433.
    • (1998) Biophys. J. , vol.74 , pp. 2419-2433
    • Hristova, K.1    White, S.H.2


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