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Volumn 157, Issue 3, 2007, Pages 579-592

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations

Author keywords

Apolipoprotein A I; Assembly; HDL; Molecular dynamics

Indexed keywords

HIGH DENSITY LIPOPROTEIN;

EID: 33847193915     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.08.006     Document Type: Article
Times cited : (113)

References (50)
  • 1
    • 33144485711 scopus 로고    scopus 로고
    • Crystal structure of human apolipoprotein A-I: insights into its protective effect against cardiovascular diseases
    • Ajees A.A., Anantharamaiah G., Mishra V.K., Hussain M.M., and Murthy H.M.K. Crystal structure of human apolipoprotein A-I: insights into its protective effect against cardiovascular diseases. Proc. Natl. Acad. Sci. USA 103 (2006) 2126-2131
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 2126-2131
    • Ajees, A.A.1    Anantharamaiah, G.2    Mishra, V.K.3    Hussain, M.M.4    Murthy, H.M.K.5
  • 2
    • 4444297536 scopus 로고    scopus 로고
    • Homotropic cooperativity of monomeric cytochrome P450 3A4 in a nanoscale native bilayer environment
    • Baas B.J., Denisov I.G., and Sligar S.G. Homotropic cooperativity of monomeric cytochrome P450 3A4 in a nanoscale native bilayer environment. Arch. Biochem. Biophys. 430 (2004) 218-228
    • (2004) Arch. Biochem. Biophys. , vol.430 , pp. 218-228
    • Baas, B.J.1    Denisov, I.G.2    Sligar, S.G.3
  • 3
    • 0030832809 scopus 로고    scopus 로고
    • Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
    • Bahar I., Kaplan M., and Jernigan R.L. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins: Struct. Func. Gen. 29 (1997) 292-308
    • (1997) Proteins: Struct. Func. Gen. , vol.29 , pp. 292-308
    • Bahar, I.1    Kaplan, M.2    Jernigan, R.L.3
  • 4
    • 0142179052 scopus 로고    scopus 로고
    • Self-assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers
    • Bayburt T.H., and Sligar S.G. Self-assembly of single integral membrane proteins into soluble nanoscale phospholipid bilayers. Prot. Sci. 12 (2003) 2476-2481
    • (2003) Prot. Sci. , vol.12 , pp. 2476-2481
    • Bayburt, T.H.1    Sligar, S.G.2
  • 5
    • 0043007514 scopus 로고    scopus 로고
    • Self-assembly of discoidal phospholipid bilayer nanoparticles with membrane scaffold proteins
    • Bayburt T.H., Grinkova Y.V., and Sligar S.G. Self-assembly of discoidal phospholipid bilayer nanoparticles with membrane scaffold proteins. Nano Letters 2 (2002) 853-856
    • (2002) Nano Letters , vol.2 , pp. 853-856
    • Bayburt, T.H.1    Grinkova, Y.V.2    Sligar, S.G.3
  • 6
    • 33744928866 scopus 로고    scopus 로고
    • Assembly of single bacteriorhodopsin trimers in bilayer nanodiscs
    • Bayburt T.H., Grinkova Y.V., and Sligar S.G. Assembly of single bacteriorhodopsin trimers in bilayer nanodiscs. Arch. Biochem. Biophys. 450 (2006) 215-222
    • (2006) Arch. Biochem. Biophys. , vol.450 , pp. 215-222
    • Bayburt, T.H.1    Grinkova, Y.V.2    Sligar, S.G.3
  • 7
    • 0023002101 scopus 로고
    • On computer-assisted analysis of biological sequences: proline punctuation, consensus sequences, and apolipoprotein repeats
    • Boguski M.S., Freeman M., Elshourbagy N.A., Taylor J.M., and Gordon J.I. On computer-assisted analysis of biological sequences: proline punctuation, consensus sequences, and apolipoprotein repeats. J. Lipid Res. 27 (1986) 1011-1034
    • (1986) J. Lipid Res. , vol.27 , pp. 1011-1034
    • Boguski, M.S.1    Freeman, M.2    Elshourbagy, N.A.3    Taylor, J.M.4    Gordon, J.I.5
  • 8
    • 33746856934 scopus 로고    scopus 로고
    • Nanodiscs separate chemoreceptor oligomeric states and reveal their signaling properties
    • Boldog T., Grimme S., Li M., Sligar S.G., and Hazelbauer G.L. Nanodiscs separate chemoreceptor oligomeric states and reveal their signaling properties. Proc. Natl. Acad. Sci. USA 103 (2006) 11509-11514
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11509-11514
    • Boldog, T.1    Grimme, S.2    Li, M.3    Sligar, S.G.4    Hazelbauer, G.L.5
  • 9
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • Bond P.J., and Sansom M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128 (2006) 2697-2704
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 10
    • 10344247720 scopus 로고    scopus 로고
    • MD simulations of spontaneous membrane protein/detergent micelle formation
    • Bond P.J., Cuthbertson J.M., Deol S.S., and Sansom M.S.P. MD simulations of spontaneous membrane protein/detergent micelle formation. J. Am. Chem. Soc. 126 (2004) 15948-15949
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 15948-15949
    • Bond, P.J.1    Cuthbertson, J.M.2    Deol, S.S.3    Sansom, M.S.P.4
  • 11
    • 27844534774 scopus 로고    scopus 로고
    • Simulation studies of the interactions between membrane proteins and detergents
    • Bond P., Cuthbertson J., and Sansom M.S.P. Simulation studies of the interactions between membrane proteins and detergents. Biochem. Soc. Trans. 33 (2005) 910-912
    • (2005) Biochem. Soc. Trans. , vol.33 , pp. 910-912
    • Bond, P.1    Cuthbertson, J.2    Sansom, M.S.P.3
  • 12
    • 0030732162 scopus 로고    scopus 로고
    • Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation
    • Borhani D.W., Rogers D.P., Engler J.A., and Brouillette C.G. Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation. Proc. Natl. Acad. Sci. USA 94 (1997) 12291-12296
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 12291-12296
    • Borhani, D.W.1    Rogers, D.P.2    Engler, J.A.3    Brouillette, C.G.4
  • 13
    • 4143150532 scopus 로고    scopus 로고
    • Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices
    • Braun R., Engelman D.M., and Schulten K. Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices. Biophys. J. 87 (2004) 754-763
    • (2004) Biophys. J. , vol.87 , pp. 754-763
    • Braun, R.1    Engelman, D.M.2    Schulten, K.3
  • 16
    • 0004224163 scopus 로고
    • Ceve G. (Ed), Marcel Dekker, New York
    • In: Ceve G. (Ed). Phospholipids Handbook (1993), Marcel Dekker, New York
    • (1993) Phospholipids Handbook
  • 17
    • 0042691480 scopus 로고    scopus 로고
    • Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers
    • 562-563
    • Civjan N.R., Bayburt T.H., Schuler M.A., and Sligar S.G. Direct solubilization of heterologously expressed membrane proteins by incorporation into nanoscale lipid bilayers. Biotechniques 35 (2003) 556-560 562-563
    • (2003) Biotechniques , vol.35 , pp. 556-560
    • Civjan, N.R.1    Bayburt, T.H.2    Schuler, M.A.3    Sligar, S.G.4
  • 18
    • 0038373278 scopus 로고    scopus 로고
    • The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles: a mass specrometry study
    • Davidson W.S., and Hilliard G.M. The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles: a mass specrometry study. J. Biol. Chem. 278 (2003) 27199-27207
    • (2003) J. Biol. Chem. , vol.278 , pp. 27199-27207
    • Davidson, W.S.1    Hilliard, G.M.2
  • 19
    • 27144459868 scopus 로고    scopus 로고
    • Kinetics of dithionite-dependent reduction of cytochrome P450 3A4: heterogeneity of the enzyme caused by its oligomerization
    • Davydov D.R., Fernando H., Baas B.J., Sligar S.G., and Halpert J.R. Kinetics of dithionite-dependent reduction of cytochrome P450 3A4: heterogeneity of the enzyme caused by its oligomerization. Biochemistry 44 (2005) 13902-13913
    • (2005) Biochemistry , vol.44 , pp. 13902-13913
    • Davydov, D.R.1    Fernando, H.2    Baas, B.J.3    Sligar, S.G.4    Halpert, J.R.5
  • 20
    • 1642382983 scopus 로고    scopus 로고
    • Directed self-assembly of monodisperse phospholipid bilayer nanodiscs with controlled size
    • Denisov I., Grinkova Y., Lazarides A., and Sligar S. Directed self-assembly of monodisperse phospholipid bilayer nanodiscs with controlled size. J. Am. Chem. Soc. 126 (2004) 3477-3487
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 3477-3487
    • Denisov, I.1    Grinkova, Y.2    Lazarides, A.3    Sligar, S.4
  • 21
    • 24344483500 scopus 로고    scopus 로고
    • Thermotropic phase transition in soluble nanoscale lipid bilayers
    • Denisov I., McLean M., Shaw A., Grinkova Y., and Sligar S. Thermotropic phase transition in soluble nanoscale lipid bilayers. J. Phys. Chem. B 109 (2005) 15580-15588
    • (2005) J. Phys. Chem. B , vol.109 , pp. 15580-15588
    • Denisov, I.1    McLean, M.2    Shaw, A.3    Grinkova, Y.4    Sligar, S.5
  • 22
    • 1642463798 scopus 로고    scopus 로고
    • Co-incorporation of heterologously expressed Arabidopsis cytochrome P450 and P450 reductase into soluble nanoscale lipid bilayers
    • Duan H., Civjan N.R., Sligar S.G., and Schuler M.A. Co-incorporation of heterologously expressed Arabidopsis cytochrome P450 and P450 reductase into soluble nanoscale lipid bilayers. Arch. Biochem. Biophys. 424 (2004) 141-153
    • (2004) Arch. Biochem. Biophys. , vol.424 , pp. 141-153
    • Duan, H.1    Civjan, N.R.2    Sligar, S.G.3    Schuler, M.A.4
  • 24
    • 0024523877 scopus 로고
    • Defined apolipoprotein A-I conformations in reconstituted high density lipoprotein discs
    • Jonas A., Kézdy K.E., and Wald J.H. Defined apolipoprotein A-I conformations in reconstituted high density lipoprotein discs. J. Biol. Chem. 264 (1989) 4818-4824
    • (1989) J. Biol. Chem. , vol.264 , pp. 4818-4824
    • Jonas, A.1    Kézdy, K.E.2    Wald, J.H.3
  • 25
    • 0025648850 scopus 로고
    • Apolipoprotein A-I structure and lipid properties in homogeneous reconstituted spherical and discoidal high density lipoproteins
    • Jonas A., Wald J.H., Toohill K.L.H., Krul E.S., and Kézdy K.E. Apolipoprotein A-I structure and lipid properties in homogeneous reconstituted spherical and discoidal high density lipoproteins. J. Biol. Chem. 265 (1990) 22123-22129
    • (1990) J. Biol. Chem. , vol.265 , pp. 22123-22129
    • Jonas, A.1    Wald, J.H.2    Toohill, K.L.H.3    Krul, E.S.4    Kézdy, K.E.5
  • 26
    • 0033591430 scopus 로고    scopus 로고
    • The structure of human lipoprotein A-I. Evidence for the "belt" model
    • Koppaka V., Silvestro L., Engler J., Brouillette C., and Axelsen P. The structure of human lipoprotein A-I. Evidence for the "belt" model. J. Biol. Chem. 274 (1999) 14541-14544
    • (1999) J. Biol. Chem. , vol.274 , pp. 14541-14544
    • Koppaka, V.1    Silvestro, L.2    Engler, J.3    Brouillette, C.4    Axelsen, P.5
  • 27
    • 33745511381 scopus 로고    scopus 로고
    • Functional reconstitution of Beta2-adrenergic receptors utilizing self-assembling nanodisc technology
    • Leitz A., Bayburt T., Barnakov A., Springer B., and Sligar S. Functional reconstitution of Beta2-adrenergic receptors utilizing self-assembling nanodisc technology. Biotechniques 40 (2006) 601-612
    • (2006) Biotechniques , vol.40 , pp. 601-612
    • Leitz, A.1    Bayburt, T.2    Barnakov, A.3    Springer, B.4    Sligar, S.5
  • 30
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink S.J., de Vries A.H., and Mark A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 108 (2004) 750-760
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    de Vries, A.H.2    Mark, A.E.3
  • 31
    • 0026736891 scopus 로고
    • Conformational analysis of apolipoprotein A-I and E-3 based on primary sequence and circular dichroism
    • Nolte R., and Atkinson D. Conformational analysis of apolipoprotein A-I and E-3 based on primary sequence and circular dichroism. Biophys. J. 63 (1992) 1221-1239
    • (1992) Biophys. J. , vol.63 , pp. 1221-1239
    • Nolte, R.1    Atkinson, D.2
  • 32
    • 0035900724 scopus 로고    scopus 로고
    • Apolipoprotein A-I adopts a belt-like orientation in reconstituted high density lipoproteins
    • Panagotopulos S., Horace E., Maiorano J., and Davidson W. Apolipoprotein A-I adopts a belt-like orientation in reconstituted high density lipoproteins. J. Biol. Chem. 276 (2001) 42965-42970
    • (2001) J. Biol. Chem. , vol.276 , pp. 42965-42970
    • Panagotopulos, S.1    Horace, E.2    Maiorano, J.3    Davidson, W.4
  • 33
    • 0030786781 scopus 로고    scopus 로고
    • Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks
    • Phillips J.C., Wriggers W., Li Z., Jonas A., and Schulten K. Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks. Biophys. J. 73 (1997) 2337-2346
    • (1997) Biophys. J. , vol.73 , pp. 2337-2346
    • Phillips, J.C.1    Wriggers, W.2    Li, Z.3    Jonas, A.4    Schulten, K.5
  • 35
    • 33746657174 scopus 로고    scopus 로고
    • MD simulations of mistic: conformational stability in detergent micelles and water
    • Psachoulia E., Bond P.J., and Sansom M.S.P. MD simulations of mistic: conformational stability in detergent micelles and water. Biochemistry 45 (2006) 9053-9058
    • (2006) Biochemistry , vol.45 , pp. 9053-9058
    • Psachoulia, E.1    Bond, P.J.2    Sansom, M.S.P.3
  • 36
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • Reith D., Pütz M., and Müller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J. Comp. Chem. 24 (2003) 1624-1636
    • (2003) J. Comp. Chem. , vol.24 , pp. 1624-1636
    • Reith, D.1    Pütz, M.2    Müller-Plathe, F.3
  • 37
    • 0017446960 scopus 로고
    • Amphipathic helixes and plasma lipoproteins: thermodynamic and geometric considerations
    • Segrest J. Amphipathic helixes and plasma lipoproteins: thermodynamic and geometric considerations. Chem. Phys. Lipids 18 (1977) 7-22
    • (1977) Chem. Phys. Lipids , vol.18 , pp. 7-22
    • Segrest, J.1
  • 38
    • 0028216402 scopus 로고
    • The amphipathic alpha helix: a multifunctional structural motif in plasma apolipoproteins
    • Segrest J., Garber D., Brouillette C., Harvey S., and Anantharamaiah G. The amphipathic alpha helix: a multifunctional structural motif in plasma apolipoproteins. Adv. Protein Chem. 45 (1994) 303-369
    • (1994) Adv. Protein Chem. , vol.45 , pp. 303-369
    • Segrest, J.1    Garber, D.2    Brouillette, C.3    Harvey, S.4    Anantharamaiah, G.5
  • 41
    • 11244346546 scopus 로고    scopus 로고
    • Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins
    • Shih A.Y., Denisov I.G., Phillips J.C., Sligar S.G., and Schulten K. Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. Biophys. J. 88 (2005) 548-556
    • (2005) Biophys. J. , vol.88 , pp. 548-556
    • Shih, A.Y.1    Denisov, I.G.2    Phillips, J.C.3    Sligar, S.G.4    Schulten, K.5
  • 42
    • 33644893631 scopus 로고    scopus 로고
    • A coarse grained protein-lipid model with application to lipoprotein particles
    • Shih A.Y., Arkhipov A., Freddolino P.L., and Schulten K. A coarse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B 110 (2006) 3674-3684
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4
  • 43
    • 20544444749 scopus 로고    scopus 로고
    • A mass spectrometric determination of the conformation of dimeric apolipoprotein A-I in discoidal high density lipoproteins
    • Silva R.A.G.D., Hilliard G.M., Li L., Segrest J.P., and Davidson W.S. A mass spectrometric determination of the conformation of dimeric apolipoprotein A-I in discoidal high density lipoproteins. Biochemistry 44 (2005) 8600-8607
    • (2005) Biochemistry , vol.44 , pp. 8600-8607
    • Silva, R.A.G.D.1    Hilliard, G.M.2    Li, L.3    Segrest, J.P.4    Davidson, W.S.5
  • 44
    • 0028885767 scopus 로고
    • Effects of the neutral lipid content of high density lipoprotein on apolipoprotein A-I structure and particle stability
    • Sparks D., Davidson W., Lund-Katz S., and Phillips M. Effects of the neutral lipid content of high density lipoprotein on apolipoprotein A-I structure and particle stability. J. Biol. Chem. 270 (1995) 26910-26917
    • (1995) J. Biol. Chem. , vol.270 , pp. 26910-26917
    • Sparks, D.1    Davidson, W.2    Lund-Katz, S.3    Phillips, M.4
  • 45
    • 11044233935 scopus 로고    scopus 로고
    • Coarse-grained simulations of lipid bilayers
    • Stevens M.J. Coarse-grained simulations of lipid bilayers. J. Chem. Phys. 121 (2004) 11942-11948
    • (2004) J. Chem. Phys. , vol.121 , pp. 11942-11948
    • Stevens, M.J.1
  • 46
    • 27844448643 scopus 로고    scopus 로고
    • Systematic coarse-graining of atomistic models for simulation of polymeric systems
    • Sun Q., and Faller R. Systematic coarse-graining of atomistic models for simulation of polymeric systems. Comp. Chem. Engr. 29 (2005) 2380-2385
    • (2005) Comp. Chem. Engr. , vol.29 , pp. 2380-2385
    • Sun, Q.1    Faller, R.2
  • 47
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 protease
    • Tozzini V., and McCammon A. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem. Phys. Lett. 413 (2005) 123-128
    • (2005) Chem. Phys. Lett. , vol.413 , pp. 123-128
    • Tozzini, V.1    McCammon, A.2
  • 48
    • 0025221262 scopus 로고
    • Investigation of the lipid domains and apolipoprotein orientation in reconstituted high density lipoproteins by fluorescence and IR methods
    • Wald J., Coormaghtigh E., Meutter J.D., Ruysschaert J., and Jonas A. Investigation of the lipid domains and apolipoprotein orientation in reconstituted high density lipoproteins by fluorescence and IR methods. J. Biol. Chem. 265 (1990) 20044-20050
    • (1990) J. Biol. Chem. , vol.265 , pp. 20044-20050
    • Wald, J.1    Coormaghtigh, E.2    Meutter, J.D.3    Ruysschaert, J.4    Jonas, A.5
  • 49
    • 0742321817 scopus 로고    scopus 로고
    • HDL: the metabolism, function, and therapeutic importance
    • Wang M., and Briggs M.R. HDL: the metabolism, function, and therapeutic importance. Chem. Rev. 104 (2004) 119-137
    • (2004) Chem. Rev. , vol.104 , pp. 119-137
    • Wang, M.1    Briggs, M.R.2
  • 50
    • 0031916717 scopus 로고    scopus 로고
    • How do potentials derived from structural databases relate to "true" potentials?
    • Zhang L., and Skolnick J. How do potentials derived from structural databases relate to "true" potentials?. Prot. Sci. 7 (1998) 112-122
    • (1998) Prot. Sci. , vol.7 , pp. 112-122
    • Zhang, L.1    Skolnick, J.2


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