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Volumn 90, Issue 8, 2006, Pages 2796-2807

Simulation-based methods for interpreting x-ray data from lipid bilayers

Author keywords

[No Author keywords available]

Indexed keywords

DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID;

EID: 33646170214     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.075697     Document Type: Article
Times cited : (198)

References (42)
  • 1
    • 0018786933 scopus 로고
    • Temperature and compositional dependence of the structure of hydrated dimyristoyl lecithin
    • Janiak, M. J., D. M. Small, and G. G. Shipley. 1979. Temperature and compositional dependence of the structure of hydrated dimyristoyl lecithin. J. Biol. Chem. 254:6068-6078.
    • (1979) J. Biol. Chem. , vol.254 , pp. 6068-6078
    • Janiak, M.J.1    Small, D.M.2    Shipley, G.G.3
  • 2
    • 0023057572 scopus 로고
    • Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers
    • McIntosh, T. J., and S. A. Simon. 1986. Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers. Biochemistry. 25:4948-4952.
    • (1986) Biochemistry , vol.25 , pp. 4948-4952
    • McIntosh, T.J.1    Simon, S.A.2
  • 4
    • 0025964363 scopus 로고
    • Fluid bilayer structure determination by the combined use of x-ray and neutron-diffraction II. Composition-space refinement method
    • Wiener, M. C., and S. H. White. 1991. Fluid bilayer structure determination by the combined use of x-ray and neutron-diffraction II. Composition-space refinement method. Biophys. J. 59:174-185.
    • (1991) Biophys. J. , vol.59 , pp. 174-185
    • Wiener, M.C.1    White, S.H.2
  • 6
    • 22144486884 scopus 로고    scopus 로고
    • Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using x-ray scattering from oriented multilamellar arrays and from unilameller vesicles
    • Kučerka, N., Y. Liu, N. Chu, H. I. Petrache, S. Tristram-Nagle, and J. F. Nagle. 2005. Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using x-ray scattering from oriented multilamellar arrays and from unilameller vesicles. Biophys. J. 88:2626-2637.
    • (2005) Biophys. J. , vol.88 , pp. 2626-2637
    • Kučerka, N.1    Liu, Y.2    Chu, N.3    Petrache, H.I.4    Tristram-Nagle, S.5    Nagle, J.F.6
  • 7
    • 37649031391 scopus 로고    scopus 로고
    • Diffuse scattering provides material parameters and electron density profiles of biomembranes
    • Liu, Y. F., and J. F. Nagle. 2004. Diffuse scattering provides material parameters and electron density profiles of biomembranes. Phys. Rev. E. 69:040901.
    • (2004) Phys. Rev. E , vol.69 , pp. 040901
    • Liu, Y.F.1    Nagle, J.F.2
  • 8
    • 0024616834 scopus 로고
    • Structure of the fully hydrated gel phase of dipalmitoylphosphatidylcholine
    • Wiener, M. C., R. M. Suter, and J. F. Nagle. 1989. Structure of the fully hydrated gel phase of dipalmitoylphosphatidylcholine. Biophys. J. 55:315-325.
    • (1989) Biophys. J. , vol.55 , pp. 315-325
    • Wiener, M.C.1    Suter, R.M.2    Nagle, J.F.3
  • 9
    • 0343621506 scopus 로고    scopus 로고
    • Submolecular organization of DMPA in surface monolayers: Beyond the two-layer model
    • Schalke, M., P. Kruger, M. Weygand, and M. Losche. 2000. Submolecular organization of DMPA in surface monolayers: beyond the two-layer model. Biochim. Biophys. Acta. 1464:113-126.
    • (2000) Biochim. Biophys. Acta , vol.1464 , pp. 113-126
    • Schalke, M.1    Kruger, P.2    Weygand, M.3    Losche, M.4
  • 10
    • 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
  • 11
    • 0242498757 scopus 로고    scopus 로고
    • Interpretation of small angle x-ray measurements guided by molecular dynamics simulations of lipid bilayers
    • Sachs, J. N., H. I. Petrache, and T. B. Woolf. 2003. Interpretation of small angle x-ray measurements guided by molecular dynamics simulations of lipid bilayers. Chem. Phys. Lipids. 126:211-223.
    • (2003) Chem. Phys. Lipids , vol.126 , pp. 211-223
    • Sachs, J.N.1    Petrache, H.I.2    Woolf, T.B.3
  • 12
    • 21244462687 scopus 로고    scopus 로고
    • Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach
    • Benz, R. W., F. Castro-Roman, 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-Roman, F.2    Tobias, D.J.3    White, S.H.4
  • 14
    • 15744368593 scopus 로고    scopus 로고
    • An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
    • Klauda, J. B., B. R. Brooks, A. D. MacKerell Jr., R. M. Venable, and R. W. Pastor. 2005. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J. Phys. Chem. B. 109:5300-5311.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 5300-5311
    • Klauda, J.B.1    Brooks, B.R.2    MacKerell Jr., A.D.3    Venable, R.M.4    Pastor, R.W.5
  • 15
    • 33751157933 scopus 로고
    • Solvent-induced forces between two hydrophilic groups
    • Durell, S. R., B. R. Brooks, and A. Bennaim. 1994. Solvent-induced forces between two hydrophilic groups. J. Phys. Chem. 98:2198-2202.
    • (1994) J. Phys. Chem. , vol.98 , pp. 2198-2202
    • Durell, S.R.1    Brooks, B.R.2    Bennaim, A.3
  • 17
    • 1642455952 scopus 로고    scopus 로고
    • Pressure-based long-range correction for Lennard-Jones interactions in molecular dynamics simulations: Application to alkanes and interfaces
    • Lagüe, P., R. W. Pastor, and B. R. Brooks. 2004. Pressure-based long-range correction for Lennard-Jones interactions in molecular dynamics simulations: application to alkanes and interfaces. J. Phys. Chem. B. 108:363-368.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 363-368
    • Lagüe, P.1    Pastor, R.W.2    Brooks, B.R.3
  • 18
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An NLog(N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an NLog(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 19
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 20
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 21
    • 0000397037 scopus 로고
    • A study of solid and liquid carbon tetrafluoride using the constant pressure molecular-dynamics technique
    • Nose, S., and M. L. Klein. 1983. A study of solid and liquid carbon tetrafluoride using the constant pressure molecular-dynamics technique. J. Chem. Phys. 78:6928-6939.
    • (1983) J. Chem. Phys. , vol.78 , pp. 6928-6939
    • Nose, S.1    Klein, M.L.2
  • 22
    • 36749107785 scopus 로고
    • Molecular-dynamics simulations at constant pressure and/or temperature
    • Andersen, H. C. 1980. Molecular-dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72:2384-2393.
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 23
    • 21644455058 scopus 로고    scopus 로고
    • Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time
    • de Vries, A. H., I. Chandrasekhar, W. F. van Gunsteren, and P. H. Hunenberger. 2005. Molecular dynamics simulations of phospholipid bilayers: influence of artificial periodicity, system size, and simulation time. J. Phys. Chem. B. 109:11643-11652.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 11643-11652
    • De Vries, A.H.1    Chandrasekhar, I.2    Van Gunsteren, W.F.3    Hunenberger, P.H.4
  • 24
    • 0031268384 scopus 로고    scopus 로고
    • Computer simulation of a DPPC phospholipid bilayer: Structural changes as a function of molecular surface area
    • Feller, S. E., R. M. Venable, and R. W. Pastor. 1997. Computer simulation of a DPPC phospholipid bilayer: structural changes as a function of molecular surface area. Langmuir. 13:6555-6561.
    • (1997) Langmuir , vol.13 , pp. 6555-6561
    • Feller, S.E.1    Venable, R.M.2    Pastor, R.W.3
  • 25
    • 84980073071 scopus 로고
    • X-ray scattering factors computed from numerical Hartee-Fock wave functions
    • Cromer, D., and J. Mann. 1968. X-ray scattering factors computed from numerical Hartee-Fock wave functions. Acta Crystallogr. A. 24:321-324.
    • (1968) Acta Crystallogr. A , vol.24 , pp. 321-324
    • Cromer, D.1    Mann, J.2
  • 26
    • 0030933013 scopus 로고    scopus 로고
    • Determination of component volumes of lipid bilayers from simulations
    • Petrache, H. I., S. E. Feller, and J. F. Nagle. 1997. Determination of component volumes of lipid bilayers from simulations. Biophys. J. 72:2237-2242.
    • (1997) Biophys. J. , vol.72 , pp. 2237-2242
    • Petrache, H.I.1    Feller, S.E.2    Nagle, J.F.3
  • 27
    • 0031820877 scopus 로고    scopus 로고
    • Phospholipid component volumes: Determination and application to bilayer structure calculations
    • Armen, R. S., O. D. Uitto, and S. E. Feller. 1998. Phospholipid component volumes: determination and application to bilayer structure calculations. Biophys. J. 75:734-744.
    • (1998) Biophys. J. , vol.75 , pp. 734-744
    • Armen, R.S.1    Uitto, O.D.2    Feller, S.E.3
  • 28
    • 0024280716 scopus 로고
    • Structure of fully hydrated bilayer dispersions
    • Nagle, J. F., and M. C. Wiener. 1988. Structure of fully hydrated bilayer dispersions. Biochim. Biophys. Acta. 942:1-10.
    • (1988) Biochim. Biophys. Acta , vol.942 , pp. 1-10
    • Nagle, J.F.1    Wiener, M.C.2
  • 29
    • 0036923942 scopus 로고    scopus 로고
    • Structure of gel phase DMPC determined by x-ray diffraction
    • Tristram-Nagle, S., Y. F. Liu, J. Legleiter, and J. F. Nagle. 2002. Structure of gel phase DMPC determined by x-ray diffraction. Biophys. J. 83:3324-3335.
    • (2002) Biophys. J. , vol.83 , pp. 3324-3335
    • Tristram-Nagle, S.1    Liu, Y.F.2    Legleiter, J.3    Nagle, J.F.4
  • 30
    • 0023658631 scopus 로고
    • Steric repulsion between phosphatidylcholine bilayers
    • McIntosh, T. J., A. D. Magid, and S. A. Simon. 1987. Steric repulsion between phosphatidylcholine bilayers. Biochemistry. 26:7325-7332.
    • (1987) Biochemistry , vol.26 , pp. 7325-7332
    • McIntosh, T.J.1    Magid, A.D.2    Simon, S.A.3
  • 31
    • 0000035913 scopus 로고    scopus 로고
    • Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density
    • Jorgensen, W. L., and C. Jenson. 1998. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: seeking temperatures of maximum density. J. Comput. Chem. 19:1179-1186.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1179-1186
    • Jorgensen, W.L.1    Jenson, C.2
  • 32
    • 36449007043 scopus 로고
    • Computer-simulation of liquid/liquid interfaces. II. Surface- tension area dependence of a bilayer and monolayer
    • Feller, S. E., Y. H. Zhang, and R. W. Pastor. 1995. Computer-simulation of liquid/liquid interfaces. II. surface- tension area dependence of a bilayer and monolayer. J. Chem. Phys. 103:10267-10276.
    • (1995) J. Chem. Phys. , vol.103 , pp. 10267-10276
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3
  • 33
    • 28444481767 scopus 로고    scopus 로고
    • A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose
    • Skibinsky, A., R. M. Venable, and R. W. Pastor. 2005. A molecular dynamics study of the response of lipid bilayers and monolayers to trehalose. Biophys. J. 89:4111-4121.
    • (2005) Biophys. J. , vol.89 , pp. 4111-4121
    • Skibinsky, A.1    Venable, R.M.2    Pastor, R.W.3
  • 34
    • 0000868022 scopus 로고
    • Computer-simulation of liquid/liquid interfaces. I. Theory and application to octane/water
    • Zhang, Y. H., S. E. Feller, B. R. Brooks, and R. W. Pastor. 1995. Computer-simulation of liquid/liquid interfaces. I. Theory and application to octane/water. J. Chem. Phys. 103:10252-10266.
    • (1995) J. Chem. Phys. , vol.103 , pp. 10252-10266
    • Zhang, Y.H.1    Feller, S.E.2    Brooks, B.R.3    Pastor, R.W.4
  • 35
    • 0029737564 scopus 로고    scopus 로고
    • What is the surface pension of a lipid bilayer membrane?
    • Jähnig, F. 1996. What is the surface pension of a lipid bilayer membrane? Biophys. J. 71:1348-1349.
    • (1996) Biophys. J. , vol.71 , pp. 1348-1349
    • Jähnig, F.1
  • 36
    • 0029767694 scopus 로고    scopus 로고
    • On simulating lipid bilayers with an applied surface tension: Periodic boundary conditions and undulations
    • Feller, S. E., and R. W. Pastor. 1996. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys. J. 71:1350-1355.
    • (1996) Biophys. J. , vol.71 , pp. 1350-1355
    • Feller, S.E.1    Pastor, R.W.2
  • 37
    • 0030838404 scopus 로고    scopus 로고
    • Renormalization of the tension and area expansion modulus in fluid membranes
    • Marsh, D. 1997. Renormalization of the tension and area expansion modulus in fluid membranes. Biophys. J. 73:865-869.
    • (1997) Biophys. J. , vol.73 , pp. 865-869
    • Marsh, D.1
  • 38
    • 0033932839 scopus 로고    scopus 로고
    • Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
    • Lindahl, E., and O. Edholm. 2000. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J. 79:426-433.
    • (2000) Biophys. J. , vol.79 , pp. 426-433
    • Lindahl, E.1    Edholm, O.2
  • 39
    • 0035812110 scopus 로고    scopus 로고
    • Effect of undulations on surface tension in simulated bilayers
    • Marrink, S. J., and A. E. Mark. 2001. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B. 105:6122-6127.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6122-6127
    • Marrink, S.J.1    Mark, A.E.2
  • 40
    • 0000951252 scopus 로고    scopus 로고
    • Effect of electrostatic force truncation on interfacial and transport properties of water
    • Feller, S. E., R. W. Pastor, A. Rojnuckarin, S. Bogusz, and B. R. Brooks. 1996. Effect of electrostatic force truncation on interfacial and transport properties of water. J. Phys. Chem. 100:17011-17020.
    • (1996) J. Phys. Chem. , vol.100 , pp. 17011-17020
    • Feller, S.E.1    Pastor, R.W.2    Rojnuckarin, A.3    Bogusz, S.4    Brooks, B.R.5
  • 41
    • 0141704114 scopus 로고    scopus 로고
    • A simple polarizable model of water based on classical Drude oscillators
    • Lamoureux, G., A. D. MacKerell, and B. Roux. 2003. A simple polarizable model of water based on classical Drude oscillators. J. Chem. Phys. 119:5185-5197.
    • (2003) J. Chem. Phys. , vol.119 , pp. 5185-5197
    • Lamoureux, G.1    MacKerell, A.D.2    Roux, B.3


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