메뉴 건너뛰기




Volumn 28, Issue 6, 1999, Pages 478-488

Constructing the suitable initial configuration of the membrane-protein system in molecular dynamics simulations

Author keywords

Dimyristoylphosphatidylcholine; Gramicidin a; Ion channel; Lipid bilayer; Membrane protein interaction

Indexed keywords

DIMYRISTOYLPHOSPHATIDYLCHOLINE; GRAMICIDIN A;

EID: 0032850757     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002490050230     Document Type: Article
Times cited : (10)

References (55)
  • 1
    • 0021288949 scopus 로고
    • Gramicidin channels
    • Andersen OS (1984) Gramicidin channels. Annu Rev Physiol 46: 531-548
    • (1984) Annu Rev Physiol , vol.46 , pp. 531-548
    • Andersen, O.S.1
  • 2
    • 0021892874 scopus 로고
    • 1H-NMR study of gramicidin-A transmembrane ion channel. Head-to-head right-handed, single stranded helices
    • Arseniev AS, Bystrov VF, Ivanov TV, Ovchinnikov YA (1985) 1H-NMR study of gramicidin-A transmembrane ion channel. Head-to-head right-handed, single stranded helices. FEBS Lett 186: 168-174
    • (1985) FEBS Lett , vol.186 , pp. 168-174
    • Arseniev, A.S.1    Bystrov, V.F.2    Ivanov, T.V.3    Ovchinnikov, Y.A.4
  • 3
    • 33751385411 scopus 로고
    • Solute diffusion in lipid bilayer membrane: An atomic level study by molecular dynamics
    • Bassolino D, Alper HE, Stouch TR (1993) Solute diffusion in lipid bilayer membrane: an atomic level study by molecular dynamics. Biochemistry 32: 12624-12637
    • (1993) Biochemistry , vol.32 , pp. 12624-12637
    • Bassolino, D.1    Alper, H.E.2    Stouch, T.R.3
  • 7
    • 0029099308 scopus 로고
    • Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane
    • Chiu SW, Clark M, Balaji V, Subramanian S, Scott HL, Jakobsson E (1995) Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys J 69: 1230-1245
    • (1995) Biophys J , vol.69 , pp. 1230-1245
    • Chiu, S.W.1    Clark, M.2    Balaji, V.3    Subramanian, S.4    Scott, H.L.5    Jakobsson, E.6
  • 8
    • 0028025665 scopus 로고
    • Solid-state NMR structural studies of peptides and proteins in membranes
    • Cross TA, Opella SJ (1994) Solid-state NMR structural studies of peptides and proteins in membranes. Curr Opin Struct Biol 4: 547-581
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 547-581
    • Cross, T.A.1    Opella, S.J.2
  • 9
    • 0028316186 scopus 로고
    • A comparison between DMPC and DLPE based lipid bilayers
    • Damodaran KV, Merz KM Jr (1994) A comparison between DMPC and DLPE based lipid bilayers. Biophys J 66: 1076-1087
    • (1994) Biophys J , vol.66 , pp. 1076-1087
    • Damodaran, K.V.1    Merz K.M., Jr.2
  • 10
    • 0029100115 scopus 로고
    • Interaction of small pepetides with lipid bilayers
    • Damodaran KV, Merz KM Jr, Gaber BP (1995) Interaction of small pepetides with lipid bilayers. Biophys J 69: 1299-1308
    • (1995) Biophys J , vol.69 , pp. 1299-1308
    • Damodaran, K.V.1    Merz K.M., Jr.2    Gaber, B.P.3
  • 11
    • 0029026347 scopus 로고
    • Structure and fluctuations of bacteriorhodpsin in the purple membrane: A molecular dynamics study
    • Edholm O, Berger O, Jahnig F (1995) Structure and fluctuations of bacteriorhodpsin in the purple membrane: a molecular dynamics study. J Mol Biol 250: 94-111
    • (1995) J Mol Biol , vol.250 , pp. 94-111
    • Edholm, O.1    Berger, O.2    Jahnig, F.3
  • 12
    • 0001563901 scopus 로고
    • Molecular dynamics simulation of a smectic liquid crystal with atomic detail
    • Egberts E, Berendsen HJC (1988) Molecular dynamics simulation of a smectic liquid crystal with atomic detail. J Chem Phys 89: 3718-3732
    • (1988) J Chem Phys , vol.89 , pp. 3718-3732
    • Egberts, E.1    Berendsen, H.J.C.2
  • 13
    • 0028258175 scopus 로고
    • Molecular dynamics simulation of a phospholipid membrane
    • Egberts E, Marrink SJ, Berendsen HJC (1994) Molecular dynamics simulation of a phospholipid membrane. Eur Biophys J 22: 423-436
    • (1994) Eur Biophys J , vol.22 , pp. 423-436
    • Egberts, E.1    Marrink, S.J.2    Berendsen, H.J.C.3
  • 14
    • 0021104058 scopus 로고
    • Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles
    • Engelman DM, Lewis BA (1983) Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J Mol Biol 166: 211-217
    • (1983) J Mol Biol , vol.166 , pp. 211-217
    • Engelman, D.M.1    Lewis, B.A.2
  • 15
    • 0029767694 scopus 로고    scopus 로고
    • On simulation lipid bilayer with an applied surface tension: Periodic boundary conditions and undulations
    • Feller SE, Pastor RW (1996) On simulation lipid bilayer 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
  • 17
    • 0027459169 scopus 로고
    • X-ray scattering with momentum transfer in the plane of membrane. Application to gramicidin organization
    • He K, Ludtke SJ, Wu Y, Huang HW (1993) X-ray scattering with momentum transfer in the plane of membrane. Application to gramicidin organization. Biophys J 64: 157-162
    • (1993) Biophys J , vol.64 , pp. 157-162
    • He, K.1    Ludtke, S.J.2    Wu, Y.3    Huang, H.W.4
  • 18
    • 0001008704 scopus 로고
    • Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases
    • Heller H, Schaefer M, Schulten K (1993) Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases. J Phys Chem 97: 8343-8360
    • (1993) J Phys Chem , vol.97 , pp. 8343-8360
    • Heller, H.1    Schaefer, M.2    Schulten, K.3
  • 19
    • 0019068826 scopus 로고
    • Relation of Raman order parameters to spin labeling parameters
    • Horvath LI, Cirak J, Vigh L (1980) Relation of Raman order parameters to spin labeling parameters. Chem Phys Lipids 27: 237-250
    • (1980) Chem Phys Lipids , vol.27 , pp. 237-250
    • Horvath, L.I.1    Cirak, J.2    Vigh, L.3
  • 20
    • 0028882402 scopus 로고
    • Tryptophan dynamics and structure refinement in a lipid bilayer environment: Solid state NMR of the gramicidin channel
    • Hu W, Lazo D, Cross TA (1995) Tryptophan dynamics and structure refinement in a lipid bilayer environment: solid state NMR of the gramicidin channel. Biochemistry 34: 14138-14146
    • (1995) Biochemistry , vol.34 , pp. 14138-14146
    • Hu, W.1    Lazo, D.2    Cross, T.A.3
  • 21
    • 0842330182 scopus 로고    scopus 로고
    • Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural, and dielectric properties of liquid water
    • Hunenberger PH, Van Gunsteren WF (1998) Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: influence on the simulated energetic, structural, and dielectric properties of liquid water. J Chem Phys 108: 6117-6134
    • (1998) J Chem Phys , vol.108 , pp. 6117-6134
    • Hunenberger, P.H.1    Van Gunsteren, W.F.2
  • 22
    • 0030953326 scopus 로고    scopus 로고
    • Computer simulation studies of biological membranes: Progress, promise and pitfalls
    • Jakobsson E (1997) Computer simulation studies of biological membranes: progress, promise and pitfalls. Trends Biochem Sci 22: 339-344
    • (1997) Trends Biochem Sci , vol.22 , pp. 339-344
    • Jakobsson, E.1
  • 24
    • 0025048105 scopus 로고
    • Molecular dynamics simulation in biology
    • Karplus M, Petsko GA (1990) Molecular dynamics simulation in biology. Nature 347: 631-639
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 25
    • 0027360175 scopus 로고
    • High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR
    • Ketchem RR, Hu W, Cross TA (1993) High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science 261: 1457-1460
    • (1993) Science , vol.261 , pp. 1457-1460
    • Ketchem, R.R.1    Hu, W.2    Cross, T.A.3
  • 27
    • 0026073608 scopus 로고
    • Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane
    • Loof HD, Harvey SC, Segrest JP, Pastor RW (1991) Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane. Biochemistry 30: 2099-2113
    • (1991) Biochemistry , vol.30 , pp. 2099-2113
    • Loof, H.D.1    Harvey, S.C.2    Segrest, J.P.3    Pastor, R.W.4
  • 29
    • 33751158845 scopus 로고
    • Simulation of water transport through a lipid membrane
    • Marrink SJ, Berendsen HJC (1994) Simulation of water transport through a lipid membrane. J Phys Chem 98: 4155-4168
    • (1994) J Phys Chem , vol.98 , pp. 4155-4168
    • Marrink, S.J.1    Berendsen, H.J.C.2
  • 31
    • 0141911433 scopus 로고
    • Multipulse dynamics nuclear magnetic resonance of phospholipid membranes
    • Meier P, Ohmes E, Kothe G (1986) Multipulse dynamics nuclear magnetic resonance of phospholipid membranes. J Chem Phys 85: 3598-3614
    • (1986) J Chem Phys , vol.85 , pp. 3598-3614
    • Meier, P.1    Ohmes, E.2    Kothe, G.3
  • 32
    • 0343118775 scopus 로고    scopus 로고
    • Molecular dynamics simulation of lipid bilayer
    • Merz KM Jr (1997) Molecular dynamics simulation of lipid bilayer. Curr Opin Struct Biol 7: 511-517
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 511-517
    • Merz K.M., Jr.1
  • 33
    • 0027251833 scopus 로고
    • Area/lipid of bilayer from NMR
    • Nagle JF (1993) Area/lipid of bilayer from NMR. Biophys J 64: 1476-1481
    • (1993) Biophys J , vol.64 , pp. 1476-1481
    • Nagle, J.F.1
  • 34
    • 0030033065 scopus 로고    scopus 로고
    • X-ray structure determination of fully hydrated L-α phase dipalmitoylphosphatidylcholine bilayers
    • Nagle JF, Zhang R, Tristram-Nagle S, Sun W, Petrache HI, Suter RM (1996) X-ray structure determination of fully hydrated L-α phase dipalmitoylphosphatidylcholine bilayers. Biophys J 70: 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
  • 35
    • 0028124519 scopus 로고
    • Molecular dynamics and Monte Carlo simulation of lipid bilayer
    • Pastor RW (1994) Molecular dynamics and Monte Carlo simulation of lipid bilayer. Curr Opin Struct Biol 4: 486-492
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 486-492
    • Pastor, R.W.1
  • 37
    • 0028321565 scopus 로고
    • Molecular dynamics simulation of the gramicidin channel
    • Roux B, Karplus M (1994) Molecular dynamics simulation of the gramicidin channel. Annu Rev Biophys Biomol Struct 23: 731-761
    • (1994) Annu Rev Biophys Biomol Struct , vol.23 , pp. 731-761
    • Roux, B.1    Karplus, M.2
  • 38
    • 49549141675 scopus 로고
    • Molecular dynamics of liquid n-butane near boiling point
    • Ryckaert JP, Bellemans A (1975) Molecular dynamics of liquid n-butane near boiling point. Chem Phys Lett 30: 123-125
    • (1975) Chem Phys Lett , vol.30 , pp. 123-125
    • Ryckaert, J.P.1    Bellemans, A.2
  • 39
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327-341
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 40
    • 0016283654 scopus 로고
    • The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance
    • Seelig A, Seelig J (1974) The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry 13: 4839-4845
    • (1974) Biochemistry , vol.13 , pp. 4839-4845
    • Seelig, A.1    Seelig, J.2
  • 41
    • 0018982584 scopus 로고
    • Lipid conformation in model membranes and biological membranes
    • Seelig J, Seelig A (1980) Lipid conformation in model membranes and biological membranes. Q Rev Biophys 13: 19-61
    • (1980) Q Rev Biophys , vol.13 , pp. 19-61
    • Seelig, J.1    Seelig, A.2
  • 42
    • 0030966534 scopus 로고    scopus 로고
    • Transmembrane helix structure, dynamics, and interaction: Multi-nanosecond molecular dynamics simulation
    • Shen L, Bassolino D, Stouch T (1997) Transmembrane helix structure, dynamics, and interaction: multi-nanosecond molecular dynamics simulation. Biophys J 73: 3-20
    • (1997) Biophys J , vol.73 , pp. 3-20
    • Shen, L.1    Bassolino, D.2    Stouch, T.3
  • 43
    • 0000112789 scopus 로고    scopus 로고
    • Molecular dynamics simulation of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters
    • Tieleman DP, Berendsen HJC (1996) Molecular dynamics simulation of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J Chem Phys 105: 4871-3880
    • (1996) J Chem Phys , vol.105 , pp. 4871-13880
    • Tieleman, D.P.1    Berendsen, H.J.C.2
  • 44
    • 0024513676 scopus 로고
    • Interfacial properties of gramicidin and gramicidin-lipid mixtures measured with static and dynamics monolayer techniques
    • Tournois H, Gieles P, Demel R, Gier J De, Krujiff B De (1989) Interfacial properties of gramicidin and gramicidin-lipid mixtures measured with static and dynamics monolayer techniques. Biophys J 55: 557-569
    • (1989) Biophys J , vol.55 , pp. 557-569
    • Tournois, H.1    Gieles, P.2    Demel, R.3    De Gier, J.4    De Kruiff, B.5
  • 45
    • 0030031374 scopus 로고    scopus 로고
    • Molecular dynamics investigation of the structure of a fully hydrated gel phase DPPC bilayer
    • Tu K, Tobia DJ, Blaise JK, Klein ML (1996) Molecular dynamics investigation of the structure of a fully hydrated gel phase DPPC bilayer. Biophys J 70: 595-680
    • (1996) Biophys J , vol.70 , pp. 595-680
    • Tu, K.1    Tobia, D.J.2    Blaise, J.K.3    Klein, M.L.4
  • 46
    • 0015027073 scopus 로고
    • The gramicidin A transmembrane channel: A proposed pi(l,d) helix
    • Urry DW (1971) The gramicidin A transmembrane channel: a proposed pi(l,d) helix. Proc Natl Acad Sci USA 68: 672-676
    • (1971) Proc Natl Acad Sci USA , vol.68 , pp. 672-676
    • Urry, D.W.1
  • 47
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • Van Gunsteren WF, Berendsen HJC (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 34: 1311-1327
    • (1977) Mol Phys , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 48
    • 0023993998 scopus 로고
    • The role of computer simulation techniques in protein engineering
    • Van Gunsteren WF (1988) The role of computer simulation techniques in protein engineering. Protein Eng 2: 5-13
    • (1988) Protein Eng , vol.2 , pp. 5-13
    • Van Gunsteren, W.F.1
  • 50
    • 0027515072 scopus 로고
    • Molecular dynamics simulation of a lipid bilayer and hexadecane: An investigation of membrane fluidity
    • Venable RM, Zhang Y, Hardy BJ, Pastor RW (1993) Molecular dynamics simulation of a lipid bilayer and hexadecane: an investigation of membrane fluidity. Science 262: 223-226
    • (1993) Science , vol.262 , pp. 223-226
    • Venable, R.M.1    Zhang, Y.2    Hardy, B.J.3    Pastor, R.W.4
  • 51
    • 0025310051 scopus 로고
    • Gramicidin channels and pores
    • Wallace BA (1990) Gramicidin channels and pores. Annu Rev Biophys Chem 19: 127-157
    • (1990) Annu Rev Biophys Chem , vol.19 , pp. 127-157
    • Wallace, B.A.1
  • 52
    • 0025298802 scopus 로고
    • Hydrophobic mismatch in gramicidin A/lecithin systems
    • Watnick PI, Chan SI, Dea P (1990) Hydrophobic mismatch in gramicidin A/lecithin systems. Biochemistry 29: 6215-6221
    • (1990) Biochemistry , vol.29 , pp. 6215-6221
    • Watnick, P.I.1    Chan, S.I.2    Dea, P.3
  • 53
    • 0028020035 scopus 로고
    • Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
    • Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc Natl Acad Sci USA 91: 11631-11635
    • (1994) Proc Natl Acad Sci Usa , vol.91 , pp. 11631-11635
    • Woolf, T.B.1    Roux, B.2
  • 54
    • 0030038849 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of lipid-protein interaction: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer
    • Woolf TB, Roux B (1996) Structure, energetics, and dynamics of lipid-protein interaction: a molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins Struct Funct Genet 24: 92-114
    • (1996) Proteins Struct Funct Genet , vol.24 , pp. 92-114
    • Woolf, T.B.1    Roux, B.2
  • 55
    • 0026548002 scopus 로고
    • Monte Carlo studies of a model for lipid-gramicidin A bilayer
    • Xing J, Scott HL (1992) Monte Carlo studies of a model for lipid-gramicidin A bilayer. Biochem Biophys Acta 1106: 227-232
    • (1992) Biochem Biophys Acta , vol.1106 , pp. 227-232
    • Xing, J.1    Scott, H.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.