메뉴 건너뛰기




Volumn 2, Issue 1, 2004, Pages 27-45

Simulating the physiological phase of hydrated DPPC bilayers: The ester moiety

Author keywords

Esters; Free energy of hydration; GROMOS96; Lipids; Molecular dynamics simulation; Potential energy parameters

Indexed keywords

COMPUTER SIMULATION; ELECTRIC CHARGE; FREE ENERGY; HYDRATION; LIPIDS; MOLECULAR DYNAMICS; SHRINKAGE; VAN DER WAALS FORCES;

EID: 3042772967     PISSN: 1539445X     EISSN: None     Source Type: Journal    
DOI: 10.1081/SMTS-120030764     Document Type: Article
Times cited : (15)

References (36)
  • 1
    • 0001563901 scopus 로고
    • Molecular dynamics simulation of a smectic liquid crystal with atomic detail
    • Egberts, E.; Berendsen, H.J.C. Molecular dynamics simulation of a smectic liquid crystal with atomic detail. J. Chem. Phys. 1988, 89, 3718-3732.
    • (1988) J. Chem. Phys. , vol.89 , pp. 3718-3732
    • Egberts, E.1    Berendsen, H.J.C.2
  • 3
  • 4
    • 0031438285 scopus 로고    scopus 로고
    • A computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems
    • Tieleman, D.P.; Marrink, S.J.; Berendsen, H.J.C. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta 1997, 1331, 235-270.
    • (1997) Biochim. Biophys. Acta , vol.1331 , pp. 235-270
    • Tieleman, D.P.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 5
    • 0000948291 scopus 로고
    • The physical chemistry of lipids from Alkanes to phospholipids
    • Plenum: New York
    • Small, D.M. The Physical Chemistry of Lipids from Alkanes to Phospholipids, Handbook of Lipid Research Series 4; Plenum: New York, 1986.
    • (1986) Handbook of Lipid Research Series , vol.4
    • Small, D.M.1
  • 7
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • Schuler, L.D.; Daura, X.; van Gunsteren, W.F. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 2001, 22, 1205-1218.
    • (2001) J. Comput. Chem. , vol.22 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    Van Gunsteren, W.F.3
  • 8
    • 0038565986 scopus 로고    scopus 로고
    • Sensitivity of molecular dynamics simulations of lipids to the size of the ester carbon
    • Chandrasekhar, I.; van Gunsteren, W.F. Sensitivity of molecular dynamics simulations of lipids to the size of the ester carbon. Curr. Sci. 2001, 81, 1325-1327.
    • (2001) Curr. Sci. , vol.81 , pp. 1325-1327
    • Chandrasekhar, I.1    Van Gunsteren, W.F.2
  • 9
    • 0036585607 scopus 로고    scopus 로고
    • A comparison of the potential energy parameters of aliphatic alkanes: Molecular dynamics simulations of triacylglycerols in the alpha phase
    • Chandrasekhar, I.; van Gunsteren, W.F. A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase. Eur. Biophys. J. 2002, 31, 89-101.
    • (2002) Eur. Biophys. J. , vol.31 , pp. 89-101
    • Chandrasekhar, I.1    Van Gunsteren, W.F.2
  • 11
    • 0000112789 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
    • Tieleman, D.P.; Berendsen, H.J.C. Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys. 1996, 105, 4871-4880.
    • (1996) J. Chem. Phys. , vol.105 , pp. 4871-4880
    • Tieleman, D.P.1    Berendsen, H.J.C.2
  • 12
    • 0011746241 scopus 로고
    • A molecular dynamics study of the decane/water interface
    • van Buuren, A.R.; Marrink, S.J.; Berendsen, H.J.C. A molecular dynamics study of the decane/water interface. J. Phys. Chem. 1993, 97, 9206-9212.
    • (1993) J. Phys. Chem. , vol.97 , pp. 9206-9212
    • Van Buuren, A.R.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 13
    • 0037089015 scopus 로고    scopus 로고
    • Calculation of the free energy of solvation for neutral analogs of amino acid side chains
    • Villa, A.; Mark, A.E. Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J. Comput. Chem. 2002, 23, 548-553.
    • (2002) J. Comput. Chem. , vol.23 , pp. 548-553
    • Villa, A.1    Mark, A.E.2
  • 15
    • 9944232242 scopus 로고
    • Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution
    • Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution. J. Solution Chem. 1981, 10, 563-596.
    • (1981) J. Solution Chem. , vol.10 , pp. 563-596
    • Cabani, S.1    Gianni, P.2    Mollica, V.3    Lepori, L.4
  • 16
    • 0029099308 scopus 로고
    • Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane
    • Chiu, S.W.; Clark, M.; Subramaniam, S.; Scott, H.L.; Jakobsson, E. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys. J. 1995, 69, 1230-1245.
    • (1995) Biophys. J. , vol.69 , pp. 1230-1245
    • Chiu, S.W.1    Clark, M.2    Subramaniam, S.3    Scott, H.L.4    Jakobsson, E.5
  • 17
    • 0000761557 scopus 로고
    • Thermodynamic properties of some mono-, di-, and triesters. Enthalpies of solution in water at 288.15 to 318.15 K and enthalpies of vapourisation and heat capacities at 298.15 K
    • Nilsson, S.-O.; Wadsö, I. Thermodynamic properties of some mono-, di-, and triesters. Enthalpies of solution in water at 288.15 to 318.15 K and enthalpies of vapourisation and heat capacities at 298.15 K. J. Chem. Thermodynam. 1986, 18, 673-681.
    • (1986) J. Chem. Thermodynam. , vol.18 , pp. 673-681
    • Nilsson, S.-O.1    Wadsö, I.2
  • 18
    • 0003228042 scopus 로고
    • Organic solvents: Physical properties and methods of purification
    • Wiley Interscience: New York
    • Riddick, J.A.; Bunger, W.B.; Sakano, T.K. Organic Solvents: Physical properties and methods of purification. In Techniques of Chemistry, 4th Ed.; Wiley Interscience: New York, 1986; Vol. II.
    • (1986) Techniques of Chemistry, 4th Ed. , vol.2
    • Riddick, J.A.1    Bunger, W.B.2    Sakano, T.K.3
  • 19
    • 0001751804 scopus 로고    scopus 로고
    • Parametrization of aliphatic CHn united atoms of GROMOS96 force field
    • Daura, X.; Mark, A.E.; van Gunsteren, W.F. Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comp. Chem. 1998, 19, 535-547.
    • (1998) J. Comp. Chem. , vol.19 , pp. 535-547
    • Daura, X.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 22
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman, B., Ed.; Reidel: Dordrecht
    • Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Hermans, J. Interaction models for water in relation to protein hydration. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 23
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D.L.; DiCapua, F.M. Free energy via molecular simulation: applications to chemical and biomolecular systems. Ann. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
    • (1989) Ann. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 24
    • 0000249851 scopus 로고
    • Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
    • Beutler, T.C.; Mark, A.E.; van Schaik, R.C.; Gerber, P.R.; van Gunsteren, W.F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 1994, 222, 529-539.
    • (1994) Chem. Phys. Lett. , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 25
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu, H.Y.; Mark, A.E.; van Gunsteren, W.F. Estimating the relative free energy of different molecular states with respect to a single reference state. J. Phys. Chem. 1996, 100, 9485-9494.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9485-9494
    • Liu, H.Y.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 26
    • 0024308752 scopus 로고
    • The nomenclature and conformational analysis of lipids and lipid analogues
    • Chandrasekhar, I.; Sasisekharan, V. The nomenclature and conformational analysis of lipids and lipid analogues. Mol. and Cell Biochem. 1989, 91, 173-182.
    • (1989) Mol. and Cell Biochem. , vol.91 , pp. 173-182
    • Chandrasekhar, I.1    Sasisekharan, V.2
  • 27
    • 84934165095 scopus 로고
    • The nomenclature of lipids
    • IUPAC-IUB(CBN). The nomenclature of lipids. Eur. J. Biochem. 1967, 22, 127-131.
    • (1967) Eur. J. Biochem. , vol.22 , pp. 127-131
  • 28
    • 3042749892 scopus 로고
    • The nomenclature of lipids
    • CRC Press: Boca Raton, FL
    • IUPAC-IUB(CBN). The nomenclature of lipids. In CRC Handbook of Chromatography: Lipids; CRC Press: Boca Raton, FL; 1976; 14-32.
    • (1976) CRC Handbook of Chromatography: Lipids , pp. 14-32
  • 32
    • 0036975483 scopus 로고    scopus 로고
    • Membrane water-penetration profiles from spin labels
    • Marsh, D. Membrane water-penetration profiles from spin labels. Eur. Biophys. J. 2002, 31, 559-562.
    • (2002) Eur. Biophys. J. , vol.31 , pp. 559-562
    • Marsh, D.1
  • 34
    • 0031309462 scopus 로고    scopus 로고
    • Length scales of lipid dynamics and molecular dynamics
    • Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E., Eds.; World Scientific: London
    • Feller, S.E.; Pastor, R.W. Length scales of lipid dynamics and molecular dynamics. In Pacific Symposium on Biocomputing '97; Altman, R.B., Dunker, A.K., Hunter, L., Klein, T.E., Eds.; World Scientific: London, 1997; 142-150.
    • (1997) Pacific Symposium on Biocomputing '97 , pp. 142-150
    • Feller, S.E.1    Pastor, R.W.2
  • 36
    • 0038440700 scopus 로고    scopus 로고
    • Molecular dynamics simulations of lipid bilayers: Major artifacts due to truncating electrostatic interactions
    • Patra, M.; Karttunen, M.; Hyvonen, M.T.; Falck, E.; Lindqvist, P.; Vattulainen, I. Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. Biophys. J. 2003, 84, 3636-3645.
    • (2003) Biophys. J. , vol.84 , pp. 3636-3645
    • Patra, M.1    Karttunen, M.2    Hyvonen, M.T.3    Falck, E.4    Lindqvist, P.5    Vattulainen, I.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.