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Volumn 38, Issue 5, 2012, Pages 414-418

An application of improved force field to fully hydrated DPPC and POPC bilayers in a tensionless NPT ensemble: A test of CHARMM 27-based new force field by Högberg et al.

Author keywords

all atom potential model; DPPC; molecular dynamics calculation; phospholipid bilayer; POPC

Indexed keywords

DPPC; MOLECULAR DYNAMICS CALCULATION; PHOSPHOLIPID BILAYER; POPC; POTENTIAL MODEL;

EID: 84859191271     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2010.548385     Document Type: Conference Paper
Times cited : (4)

References (28)
  • 3
    • 0034250744 scopus 로고    scopus 로고
    • An improved empirical potential energy function for molecular simulations of phospholipids
    • S.E. Feller, and A.D. MacKerell, Jr, An improved empirical potential energy function for molecular simulations of phospholipids, J. Phys. Chem. B 104 (2000), pp. 7510-7515.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7510-7515
    • Feller, S.E.1    MacKerell Jr., A.D.2
  • 4
    • 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
    • J.B. Klauda, B.R. Brooks, A.D. MacKerell, Jr., R.M. Venable, and R.W. Pastor, 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 (2005), pp. 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
  • 6
    • 0030999097 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature
    • O. Berger, O. Edholm, and F. Jähnig, Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature, Biophys. J. 72 (1997), pp. 2002-2013.
    • (1997) Biophys. J. , vol.72 , pp. 2002-2013
    • Berger, O.1    Edholm, O.2    Jähnig, F.3
  • 7
    • 0035425883 scopus 로고    scopus 로고
    • An improved gromos96 force field for aliphatic hydrocarbons in the condensed phase
    • L.D. Schuler, X. Daura, and W.F. van Gunsteren, An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase, J. Comput. Chem. 22 (2001), pp. 1205-1218.
    • (2001) J. Comput. Chem. , vol.22 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    Van Gunsteren, W.F.3
  • 8
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The gromos force-field parameter sets 53a5 and 53a6
    • C. Oostenbrink, A. Villa, A.E. Mark, and W.F. van Gunsteren, A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6, J. Comput. Chem. 25 (2004), pp. 1656-1676.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 9
    • 34250372191 scopus 로고    scopus 로고
    • Reparameterization of all-Atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension
    • J. Sonne, M.O. Jensen, F.Y. Hansen, L. Hemmingsen, and G.H. Peters, Reparameterization of all-Atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension, Biophys. J. 92 (2007), pp. 4157-4167.
    • (2007) Biophys. J. , vol.92 , pp. 4157-4167
    • Sonne, J.1    Jensen, M.O.2    Hansen, F.Y.3    Hemmingsen, L.4    Peters, G.H.5
  • 10
    • 52649147983 scopus 로고    scopus 로고
    • Modification of the charmm force field for dmpc lipid bilayer
    • G.J. Högberg, A.M. Nikitin, and A.P. Lyubartsev, Modification of the CHARMM force field for DMPC lipid bilayer, J. Comp. Chem. 29 (2008), pp. 2359-2369.
    • (2008) J. Comp. Chem. , vol.29 , pp. 2359-2369
    • Högberg, G.J.1    Nikitin, A.M.2    Lyubartsev, A.P.3
  • 11
    • 60649103257 scopus 로고    scopus 로고
    • Validation of all-Atom phosphatidylcholine lipid force fields in the tensionless npt ensemble
    • J. Taylor, N.E. Whiteford, G. Bradley, and G.W. Watson, Validation of all-Atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble, Biochim. Biophys. Acta 1788 (2009), pp. 638-649.
    • (2009) Biochim. Biophys. Acta , vol.1788 , pp. 638-649
    • Taylor, J.1    Whiteford, N.E.2    Bradley, G.3    Watson, G.W.4
  • 12
    • 33744920795 scopus 로고    scopus 로고
    • Closer look at structure of fully hydrated fluid phase dppc bilayers
    • N. Kučerka, S.T. Nagle, and J.F. Nagle, Closer look at structure of fully hydrated fluid phase DPPC bilayers, Biophys. J.: Biophys. Lett. 90 (2006), p. L83.
    • (2006) Biophys. J.: Biophys. Lett. , vol.90
    • Kučerka, N.1    Nagle, S.T.2    Nagle, J.F.3
  • 14
    • 0030033065 scopus 로고    scopus 로고
    • X-ray structure determination of fully hydrated la phase dipalmitoylphosphatidylcholine bilayers
    • J.F. Nagle, R. Zhang, S. Tristram-Nagle, W. Sun, H.I. Petrache, and R.M. Suter, X-ray structure determination of fully hydrated La phase dipalmitoylphosphatidylcholine bilayers, Biophys. J. 70 (1996), pp. 1419-1431.
    • (1996) Biophys. J. , vol.70 , pp. 1419-1431
    • Nagle, J.F.1    Zhang, R.2    Tristram-Nagle, S.3    Sun, W.4    Petrache, H.I.5    Suter, R.M.6
  • 15
    • 33646446451 scopus 로고    scopus 로고
    • Structure of fully hydrated phase lipid bilayers with monounsaturated chains
    • N. Kučerka, S. Tristram-Nagle, and J.F. Nagle, Structure of fully hydrated phase lipid bilayers with monounsaturated chains, J. Membrane Biol. 208 (2005), pp. 193-202.
    • (2005) J. Membrane Biol. , vol.208 , pp. 193-202
    • Kučerka, N.1    Tristram-Nagle, S.2    Nagle, J.F.3
  • 16
    • 33751157933 scopus 로고
    • Solvent induced forces between two hydrophilic groups
    • S.R. Durell, B.R. Brooks, and A. Ben-Naim, Solvent induced forces between two hydrophilic groups, J. Phys. Chem. 98 (1994), pp. 2198-2202.
    • (1994) J. Phys. Chem. , vol.98 , pp. 2198-2202
    • Durell, S.R.1    Brooks, B.R.2    Ben-Naim, A.3
  • 17
    • 33846823909 scopus 로고
    • Particle mesh ewald: An nlog(n) method for ewald sums in large systems
    • T. Darden, D. York, and L. Pederesn, Particle mesh Ewald: An Nlog(n) method for Ewald sums in large systems, J. Chem. Phys. 98 (1993), pp. 10089-10093.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10093
    • Darden, T.1    York, D.2    Pederesn, L.3
  • 18
    • 26144434487 scopus 로고
    • Crystal structure and pair potentials: A molecular dynamics study
    • M. Parrinello and A. Rahman, Crystal structure and pair potentials: A molecular dynamics study, Phys. Rev. Lett. 45 (1980), pp. 1196-1199.
    • (1980) Phys. Rev. Lett. , vol.45 , pp. 1196-1199
    • Parrinello, M.1    Rahman, A.2
  • 19
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S. Nosé, A unified formulation of the constant temperature molecular dynamics methods, J. Chem. Phys. 81 (1984), pp. 511-520.
    • (1984) J. Chem. Phys. , vol.81 , pp. 511-520
    • Nosé, S.1
  • 20
    • 36449000062 scopus 로고
    • Nosé -hoover chains: The canonical ensemble via continuous dynamics
    • G.J. Martyna, M.E. Tuckerman, and M.L. Klein, Nosé -Hoover chains: The canonical ensemble via continuous dynamics, J. Chem. Phys. 97 (1992), pp. 2635-2644.
    • (1992) J. Chem. Phys. , vol.97 , pp. 2635-2644
    • Martyna, G.J.1    Tuckerman, M.E.2    Klein, M.L.3
  • 21
    • 0000026966 scopus 로고    scopus 로고
    • Explicit reversible integrators for extended systems dynamics
    • G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein, Explicit reversible integrators for extended systems dynamics, Mol. Phys. 87 (1996), pp. 1117-1157.
    • (1996) Mol. Phys. , vol.87 , pp. 1117-1157
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 23
    • 0035857205 scopus 로고    scopus 로고
    • Effect of unsaturated lipid chains on dimensions, molecular order and hydration of membranes, j
    • H. Binder and K. Gawrisch, Effect of unsaturated lipid chains on dimensions, molecular order and hydration of membranes, J. Phys. Chem. B 105 (2001), pp. 12378-12390.
    • (2001) Phys. Chem. B , vol.105 , pp. 12378-12390
    • Binder, H.1    Gawrisch, K.2
  • 24
    • 84882884096 scopus 로고    scopus 로고
    • High pressure effects in molecular bioscience
    • M.R. Manna, ed. Elsevier Amsterdam
    • R. Winter, High pressure effects in molecular bioscience, in Chemistry at Extreme Conditions, M.R. Manna, ed., Elsevier, Amsterdam, 2004, pp. 29-82.
    • (2004) Chemistry at Extreme Conditions , pp. 29-82
    • Winter, R.1
  • 26
    • 0016283654 scopus 로고
    • Phospholipid bilayer measured by deuterium magnetic resonance
    • A. Seelig and J. Seelig, Phospholipid bilayer measured by deuterium magnetic resonance, Biochemistry 13 (1974), pp. 4839-4845.
    • (1974) Biochemistry , vol.13 , pp. 4839-4845
    • Seelig, A.1    Seelig, J.2
  • 27
    • 0028929692 scopus 로고
    • Restatement of order parameters in biomembranes: Calculation of czc bond order parameters from c-d quadrupolar splittings
    • J.P. Douliez, A. Léonard, and E.J. Dufourc, Restatement of order parameters in biomembranes: Calculation of CZC bond order parameters from C-D quadrupolar splittings, Biophys. J. 68 (1995), pp. 1727-1739.
    • (1995) Biophys. J. , vol.68 , pp. 1727-1739
    • Douliez, J.P.1    Léonard, A.2    Dufourc, E.J.3
  • 28
    • 0017808625 scopus 로고
    • Molecular order in cis and trans unsaturated phospholipid bilayers
    • J. Seelig and N. Waespe-Sǎrčevic, Molecular order in cis and trans unsaturated phospholipid bilayers, Biochemistry 17 (1978), pp. 3310-3315.
    • (1978) Biochemistry , vol.17 , pp. 3310-3315
    • Seelig, J.1    Waespe-Sǎrčevic, N.2


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