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Volumn 94, Issue 6, 2008, Pages 2306-2319

Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN A1; CHOLESTEROL; HIGH DENSITY LIPOPROTEIN; PHOSPHATIDYLCHOLINE; SOLVENT;

EID: 44049107643     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115857     Document Type: Article
Times cited : (83)

References (73)
  • 1
    • 14944381287 scopus 로고    scopus 로고
    • HDL as a target in the treatment of atherosclerotic cardiovascular disease
    • Linsel-Nitschke, P., and A. R. Tall. 2005. HDL as a target in the treatment of atherosclerotic cardiovascular disease. Nat. Rev. Drug Discov. 4:193-205.
    • (2005) Nat. Rev. Drug Discov , vol.4 , pp. 193-205
    • Linsel-Nitschke, P.1    Tall, A.R.2
  • 2
    • 1542283778 scopus 로고    scopus 로고
    • Formation and metabolism of prebeta-migrating, lipid-poor apolipoprotein A-I
    • Rye, K. A., and P. J. Barter. 2004. Formation and metabolism of prebeta-migrating, lipid-poor apolipoprotein A-I. Arterioscler. Thromb. Vasc. Biol. 24:421-428.
    • (2004) Arterioscler. Thromb. Vasc. Biol , vol.24 , pp. 421-428
    • Rye, K.A.1    Barter, P.J.2
  • 3
    • 0037108095 scopus 로고    scopus 로고
    • Evidence that phospholipids play a key role in pre-β apoA-I formation and high-density lipoprotein remodeling
    • Rye, K. A., M. Duong, M. K. Psaltis, L. K. Curtiss, D. J. Bonnet, R. Stocker, and P. J. Barter. 2002. Evidence that phospholipids play a key role in pre-β apoA-I formation and high-density lipoprotein remodeling. Biochemistry. 41:12538-12545.
    • (2002) Biochemistry , vol.41 , pp. 12538-12545
    • Rye, K.A.1    Duong, M.2    Psaltis, M.K.3    Curtiss, L.K.4    Bonnet, D.J.5    Stocker, R.6    Barter, P.J.7
  • 4
    • 25444463073 scopus 로고    scopus 로고
    • ATP-binding cassette transporter A1: A cell cholesterol exporter that protects agains cardiovascular disease
    • Oram, J. F., and J. W. Heinecke. 2005. ATP-binding cassette transporter A1: a cell cholesterol exporter that protects agains cardiovascular disease. Physiol. Rev. 85:1343-1372.
    • (2005) Physiol. Rev , vol.85 , pp. 1343-1372
    • Oram, J.F.1    Heinecke, J.W.2
  • 5
    • 0034672281 scopus 로고    scopus 로고
    • Lecithin cholesterol acyltransferase
    • Jonas, A. 2000. Lecithin cholesterol acyltransferase. Biochim. Biophys. Acta. 1529:245-256.
    • (2000) Biochim. Biophys. Acta , vol.1529 , pp. 245-256
    • Jonas, A.1
  • 7
    • 0141988913 scopus 로고    scopus 로고
    • Influence of the HDL receptor SR-BI on lipoprotein metabolism and atherosclerosis
    • Trigatti, B. L., M. Krieger, and A. Rigotti. 2003. Influence of the HDL receptor SR-BI on lipoprotein metabolism and atherosclerosis. Arte rioscler. Thromb. Vasc. Biol. 23:1732-1738.
    • (2003) Arte rioscler. Thromb. Vasc. Biol , vol.23 , pp. 1732-1738
    • Trigatti, B.L.1    Krieger, M.2    Rigotti, A.3
  • 8
    • 0031054798 scopus 로고    scopus 로고
    • Evidence that cholesteryl ester transfer protein-mediated reductions in reconstituted high density lipoprotein size involve particle fusion
    • Rye, K. A., N. J. Hime, and P. J. Barter. 1997. Evidence that cholesteryl ester transfer protein-mediated reductions in reconstituted high density lipoprotein size involve particle fusion. J. Biol. Chem. 272:3953-3960.
    • (1997) J. Biol. Chem , vol.272 , pp. 3953-3960
    • Rye, K.A.1    Hime, N.J.2    Barter, P.J.3
  • 9
    • 0031892993 scopus 로고    scopus 로고
    • Triglyceride-enrichment of high density lipoproteins enhances their remodelling by phospholipid transfer protein
    • Rye, K. A., M. Jauhiainen, P. J. Barter, and C. Ehnholm. 1998. Triglyceride-enrichment of high density lipoproteins enhances their remodelling by phospholipid transfer protein. J. Lipid Res. 39:613-622.
    • (1998) J. Lipid Res , vol.39 , pp. 613-622
    • Rye, K.A.1    Jauhiainen, M.2    Barter, P.J.3    Ehnholm, C.4
  • 10
    • 0035089679 scopus 로고    scopus 로고
    • The impact of phospholipid transfer protein (PLTP) on HDL metabolism
    • Huuskonen, J., V. M. Olkkonen, M. Jauhiainen, and C. Ehnholm. 2001. The impact of phospholipid transfer protein (PLTP) on HDL metabolism. Atherosclerosis. 155:269-281.
    • (2001) Atherosclerosis , vol.155 , pp. 269-281
    • Huuskonen, J.1    Olkkonen, V.M.2    Jauhiainen, M.3    Ehnholm, C.4
  • 11
    • 0023829776 scopus 로고
    • Early incorporation of cell- derived cholesterol into prebeta-migrating high density lipoprotein
    • Castro, G. R., and J. C. Fielding. 1988. Early incorporation of cell- derived cholesterol into prebeta-migrating high density lipoprotein. Biochemistry. 27:25-29.
    • (1988) Biochemistry , vol.27 , pp. 25-29
    • Castro, G.R.1    Fielding, J.C.2
  • 12
    • 0030933460 scopus 로고    scopus 로고
    • The molecular pathology of lecithin: Cholesterol acyltransferase (LCAT) deficiency syndromes
    • Kuivenhoven, J. A., H. Pritchard, J. Hill, J. Frohlich, G. Assmann, and J. Kastelein. 1997. The molecular pathology of lecithin: cholesterol acyltransferase (LCAT) deficiency syndromes. J. Lipid Res. 38:191-205.
    • (1997) J. Lipid Res , vol.38 , pp. 191-205
    • Kuivenhoven, J.A.1    Pritchard, H.2    Hill, J.3    Frohlich, J.4    Assmann, G.5    Kastelein, J.6
  • 13
    • 0021180802 scopus 로고
    • Characterization of lipoprotein particles isolated by immunoaffinity chromatography: Particles containing A-I and A-II and particles containing A-I but no A-II
    • Cheung, M. C., and J. J. Albers. 1984. Characterization of lipoprotein particles isolated by immunoaffinity chromatography: particles containing A-I and A-II and particles containing A-I but no A-II. J. Biol. Chem. 259:12201-12209.
    • (1984) J. Biol. Chem , vol.259 , pp. 12201-12209
    • Cheung, M.C.1    Albers, J.J.2
  • 14
    • 0032812981 scopus 로고    scopus 로고
    • Remodelling of high density lipoproteins by plasma factors
    • Rye, K. A., M. A. Clay, and P. J. Barter. 1999. Remodelling of high density lipoproteins by plasma factors. Atherosclerosis. 145:227-238.
    • (1999) Atherosclerosis , vol.145 , pp. 227-238
    • Rye, K.A.1    Clay, M.A.2    Barter, P.J.3
  • 15
    • 0033770856 scopus 로고    scopus 로고
    • Influence of phospholipid depletion on the size, structure, and remodeling of reconstituted high density lipoproteins
    • Rye, K. A., and M. Duong. 2000. Influence of phospholipid depletion on the size, structure, and remodeling of reconstituted high density lipoproteins. J. Lipid Res. 41:1640-1650.
    • (2000) J. Lipid Res , vol.41 , pp. 1640-1650
    • Rye, K.A.1    Duong, M.2
  • 16
    • 0027076642 scopus 로고
    • The charge and structural stability of apolipoprotein A-I in discoidal and spherical recombinant high density lipoprotein particles
    • Sparks, D. L., S. Lund-Katz, and M. C. Phillips. 1992. The charge and structural stability of apolipoprotein A-I in discoidal and spherical recombinant high density lipoprotein particles. J. Biol. Chem. 267:25839-25847.
    • (1992) J. Biol. Chem , vol.267 , pp. 25839-25847
    • Sparks, D.L.1    Lund-Katz, S.2    Phillips, M.C.3
  • 17
    • 20544456888 scopus 로고    scopus 로고
    • Apolipoprotein structure and dynamics
    • Gursky, O. 2005. Apolipoprotein structure and dynamics. Curr. Opin. Lipidol. 16:287-294.
    • (2005) Curr. Opin. Lipidol , vol.16 , pp. 287-294
    • Gursky, O.1
  • 18
    • 14344258702 scopus 로고    scopus 로고
    • A three-dimensional molecular model of lipid-free apolipoprotein A-I determined by cross-linking/mass spectrometry and sequence threading
    • Silva, R. A. G. D., G. M. Hilliard, J. Fang, S. Macha, and W. S. Davidson. 2005. A three-dimensional molecular model of lipid-free apolipoprotein A-I determined by cross-linking/mass spectrometry and sequence threading. Biochemistry. 44:2759-2769.
    • (2005) Biochemistry , vol.44 , pp. 2759-2769
    • Silva, R.A.G.D.1    Hilliard, G.M.2    Fang, J.3    Macha, S.4    Davidson, W.S.5
  • 19
    • 20544470749 scopus 로고    scopus 로고
    • Apolipoprotein structural organization in high density lipoproteins: Belts, bundles, hinges and hairpins
    • Davidson, W. S., and R. A. G. D. Silva. 2005. Apolipoprotein structural organization in high density lipoproteins: belts, bundles, hinges and hairpins. Curr. Opin. Lipidol. 16:295-300.
    • (2005) Curr. Opin. Lipidol , vol.16 , pp. 295-300
    • Davidson, W.S.1    Silva, R.A.G.D.2
  • 21
    • 0018402243 scopus 로고
    • Apolipoproteins and the structural organization of plasma lipoproteins: Human plasma high density lipoprotein-3
    • Edelstein, C., F. J. Kezdy, A. M. Scanu, and B. W. Shen. 1979. Apolipoproteins and the structural organization of plasma lipoproteins: human plasma high density lipoprotein-3. J. Lipid Res. 20:143-153.
    • (1979) J. Lipid Res , vol.20 , pp. 143-153
    • Edelstein, C.1    Kezdy, F.J.2    Scanu, A.M.3    Shen, B.W.4
  • 22
    • 0028360934 scopus 로고
    • Interactions of synthetic peptide analogs of the class A amphipathic helix with lipids. Evidence for the snorkel hypothesis
    • Mishra, V. K., M. N. Palgunachari, J. P. Segrest, and G. M. Anantharamaiah. 1994. Interactions of synthetic peptide analogs of the class A amphipathic helix with lipids. Evidence for the snorkel hypothesis. J. Biol. Chem. 269:7185-7191.
    • (1994) J. Biol. Chem , vol.269 , pp. 7185-7191
    • Mishra, V.K.1    Palgunachari, M.N.2    Segrest, J.P.3    Anantharamaiah, G.M.4
  • 23
    • 0034669402 scopus 로고    scopus 로고
    • Structure of low density lipoprotein (LDL) particles: Basis for understanding molecular changes in modified LDL
    • Hevonoja, T., M. O. Pentikäinen, M. T. Hyvonen, P. T. Kovanen, and M. Ala-Korpela. 2000. Structure of low density lipoprotein (LDL) particles: Basis for understanding molecular changes in modified LDL. Biochim. Biophys. Acta. 1488:189-210.
    • (2000) Biochim. Biophys. Acta , vol.1488 , pp. 189-210
    • Hevonoja, T.1    Pentikäinen, M.O.2    Hyvonen, M.T.3    Kovanen, P.T.4    Ala-Korpela, M.5
  • 25
    • 0034673999 scopus 로고    scopus 로고
    • The conformation of apolipoprotein A-I in high density lipoproteins is influenced by core lipid composition and particle size: A surface plasmon resonance study
    • Curtiss, L. K., D. J. Bonnet, and K. A. Rye. 2000. The conformation of apolipoprotein A-I in high density lipoproteins is influenced by core lipid composition and particle size: a surface plasmon resonance study. Biochemistry. 39:5712-5721.
    • (2000) Biochemistry , vol.39 , pp. 5712-5721
    • Curtiss, L.K.1    Bonnet, D.J.2    Rye, K.A.3
  • 26
    • 0030732162 scopus 로고    scopus 로고
    • Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation
    • Borhani, D. W., D. P. Rogers, J. A. Engler, and C. G. Brouillette. 1997. Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation. Proc. Natl. Acad. Sci. USA. 94:12291-12296.
    • (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
  • 28
    • 0037131260 scopus 로고    scopus 로고
    • ApoA-I structure on discs and spheres. Variable helix registry and conformational states
    • Li, H. H., D. S. Lyles, W. Pan, E. Alexander, M. J. Thomas, and M. G. Sorci-Thomas. 2002. ApoA-I structure on discs and spheres. Variable helix registry and conformational states. J. Biol. Chem. 277:39093-39101.
    • (2002) J. Biol. Chem , vol.277 , pp. 39093-39101
    • Li, H.H.1    Lyles, D.S.2    Pan, W.3    Alexander, E.4    Thomas, M.J.5    Sorci-Thomas, M.G.6
  • 30
    • 0030786781 scopus 로고    scopus 로고
    • Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks
    • Phillips, J. C., W. Wriggers, Z. Li, A. Jonas, and K. Schulten. 1997. Predicting the structure of apolipoprotein A-I in reconstituted high density lipoprotein disks. Biophys. J. 73:2337-2346.
    • (1997) Biophys. J , vol.73 , pp. 2337-2346
    • Phillips, J.C.1    Wriggers, W.2    Li, Z.3    Jonas, A.4    Schulten, K.5
  • 31
    • 0033029275 scopus 로고    scopus 로고
    • Molecular dynamics on a model for nascent high-density lipoprotein: Role of salt bridges
    • Sheldahl, C., and S. C. Harvey. 1999. Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges. Biophys. J. 76:1190-1198.
    • (1999) Biophys. J , vol.76 , pp. 1190-1198
    • Sheldahl, C.1    Harvey, S.C.2
  • 32
    • 0036926084 scopus 로고    scopus 로고
    • Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apoA-I belt model
    • Klon, A. E., J. P. Segrest, and S. C. Harvey. 2002. Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apoA-I belt model. J. Mol. Biol. 324:703-721.
    • (2002) J. Mol. Biol , vol.324 , pp. 703-721
    • Klon, A.E.1    Segrest, J.P.2    Harvey, S.C.3
  • 33
    • 11244346546 scopus 로고    scopus 로고
    • Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins
    • Shih, A. Y., I. G. Denisov, J. C. Phillips, S. G. Sligar, and K. Schulten. 2005. Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. Biophys. J. 88:548-556.
    • (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
  • 35
    • 0038373278 scopus 로고    scopus 로고
    • The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles. A mass spectrometry study
    • Davidson, W. S., and G. M. Hilliard. 2003. The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles. A mass spectrometry study. J. Biol. Chem. 278:27199-27207.
    • (2003) J. Biol. Chem , vol.278 , pp. 27199-27207
    • Davidson, W.S.1    Hilliard, G.M.2
  • 36
    • 25444491569 scopus 로고    scopus 로고
    • IntermolecularcontactbetweenglobularN-terminal fold and C-terminal domain of apoA-I stabilizes its lipid bound conformation. Studies employing chemical cross-linking and mass spectrometry
    • Bhat, S., M. G. Sorci-Thomas, E. T. Alexander, M. P. Samuel, and M. J. Thomas. 2005. IntermolecularcontactbetweenglobularN-terminal fold and C-terminal domain of apoA-I stabilizes its lipid bound conformation. Studies employing chemical cross-linking and mass spectrometry. J. Biol. Chem. 280:33015-33025.
    • (2005) J. Biol. Chem , vol.280 , pp. 33015-33025
    • Bhat, S.1    Sorci-Thomas, M.G.2    Alexander, E.T.3    Samuel, M.P.4    Thomas, M.J.5
  • 38
    • 33744830288 scopus 로고    scopus 로고
    • atte, A., J. C. Patterson, M. K. Jones, W. G. Jerome, D. Bashtovyy, Z. Su, F. Gu, J. Chen, M. P. Aliste, S. C. Harvey, L. Li, G. Weinstein, and . P. Segrest. 2006. Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study. Biophys. J. 90:4345-4360.
    • atte, A., J. C. Patterson, M. K. Jones, W. G. Jerome, D. Bashtovyy, Z. Su, F. Gu, J. Chen, M. P. Aliste, S. C. Harvey, L. Li, G. Weinstein, and . P. Segrest. 2006. Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study. Biophys. J. 90:4345-4360.
  • 39
    • 33644893631 scopus 로고    scopus 로고
    • Carse grained protein-lipid model with application to lipoprotein particles
    • Shih, A. Y., A. Arkhipov, P. L. Freddolino, and K. Schulten. 2006. Carse grained protein-lipid model with application to lipoprotein particles. J. Phys. Chem. B. 110:3674-3684.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkhipov, A.2    Freddolino, P.L.3    Schulten, K.4
  • 40
    • 33847193915 scopus 로고    scopus 로고
    • Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
    • Shih, A. Y., P. L. Freddolino, A. Arkhipov, and K. Schulten. 2007. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. J. Struct. Biol. 157:579-592.
    • (2007) J. Struct. Biol , vol.157 , pp. 579-592
    • Shih, A.Y.1    Freddolino, P.L.2    Arkhipov, A.3    Schulten, K.4
  • 41
    • 33646178936 scopus 로고    scopus 로고
    • Atomistic simulation studies of cholesteryl oleates: Model for the core of lipoprotein particles
    • Heikelä, M., I. Vattulainen, and M. T. Hyvonen. 2006. Atomistic simulation studies of cholesteryl oleates: model for the core of lipoprotein particles. Biophys. J. 90:2247-2257.
    • (2006) Biophys. J , vol.90 , pp. 2247-2257
    • Heikelä, M.1    Vattulainen, I.2    Hyvonen, M.T.3
  • 44
    • 16844365398 scopus 로고    scopus 로고
    • Role of cholesterol and polyunsaturated chains in lipid-protein interactions: Molecular dynamics simulation of rhodopsin in a realistic membrane environment
    • Pitman, M. C., A. Grossfield, F. Suits, and S. E. Feller. 2005. Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment. J. Am. Chem. Soc. 127:4576-4577.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 4576-4577
    • Pitman, M.C.1    Grossfield, A.2    Suits, F.3    Feller, S.E.4
  • 45
    • 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. Yin, R. W. Pastor, and A. D. MacKerell. 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.2    Pastor, R.W.3    MacKerell, A.D.4
  • 46
    • 0022804387 scopus 로고
    • Conformation of the oleate chains in crystals of cholesteryl oleate at 123 K
    • Gao, Q., and B. M. Craven. 1986. Conformation of the oleate chains in crystals of cholesteryl oleate at 123 K. J. Lipid Res. 27:1214-1221.
    • (1986) J. Lipid Res , vol.27 , pp. 1214-1221
    • Gao, Q.1    Craven, B.M.2
  • 48
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., J. Chandrasekhar, and J. D. Madura. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 50
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S. J., A. H. de Vries, and A. E. Mark. 2004. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B. 108:750-760.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    de Vries, A.H.2    Mark, A.E.3
  • 51
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and assembly of membrane proteins via simulation
    • Bond, P. J., and M. S. P. Sansom. 2006. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128:2697-2704.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 53
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr., D. Bashford, M. Bellot, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102: 3586-3616.
    • MacKerell, A. D., Jr., D. Bashford, M. Bellot, R. L. Dunbrack Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102: 3586-3616.
  • 56
    • 1842738520 scopus 로고    scopus 로고
    • Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration and structural properties
    • Patra, M., and M. Karttunen. 2004. Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration and structural properties. J. Comput. Chem. 25:678-689.
    • (2004) J. Comput. Chem , vol.25 , pp. 678-689
    • Patra, M.1    Karttunen, M.2
  • 58
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: An N-log(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
  • 59
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
    • (2001) J. Mol. Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 60
    • 85031368399 scopus 로고    scopus 로고
    • Alignment to principal axes in VMD from the VMD Script Library
    • Alignment to principal axes in VMD from the VMD Script Library. 2002. http://www.ks.uiuc.edu/Research/vmd/script-library/scripts/orient/.
    • (2002)
  • 61
    • 0037382083 scopus 로고    scopus 로고
    • Simulation of MscL gating in a bilayer under stress
    • Colombo, G., S. J. Marrink, and A. E. Mark. 2003. Simulation of MscL gating in a bilayer under stress. Biophys. J. 84:2331-2337.
    • (2003) Biophys. J , vol.84 , pp. 2331-2337
    • Colombo, G.1    Marrink, S.J.2    Mark, A.E.3
  • 64
    • 0034466399 scopus 로고    scopus 로고
    • Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications
    • Segrest, J. P., S. C. Harvey, and V. Zannis. 2000. Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications. Trends Cardiovasc. Med. 10:246-252.
    • (2000) Trends Cardiovasc. Med , vol.10 , pp. 246-252
    • Segrest, J.P.1    Harvey, S.C.2    Zannis, V.3
  • 65
    • 0035812426 scopus 로고    scopus 로고
    • Simulation of the spontaneous aggregation of phospholipids into bilayers
    • Marrink, S. J., E. Lindahl, O. Edholm, and A. E. Mark. 2001. Simulation of the spontaneous aggregation of phospholipids into bilayers. J. Am. Chem. Soc. 123:8638-8639.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 8638-8639
    • Marrink, S.J.1    Lindahl, E.2    Edholm, O.3    Mark, A.E.4
  • 66
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by molecular dynamics
    • Brunger, A. T., J. Kuriyan, and M. Karplus. 1987. Crystallographic R factor refinement by molecular dynamics. Science. 235:458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brunger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 68
    • 0038054912 scopus 로고    scopus 로고
    • Feig, M., A. D. MacKerell Jr., and C. L. Brooks III. 2003. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2831-2836.
    • Feig, M., A. D. MacKerell Jr., and C. L. Brooks III. 2003. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B. 107:2831-2836.
  • 69
    • 5444228752 scopus 로고    scopus 로고
    • Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle
    • Van Wynsberghe, A., G. Li, and Q. Cui. 2004. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 43:13083-13096.
    • (2004) Biochemistry , vol.43 , pp. 13083-13096
    • Van Wynsberghe, A.1    Li, G.2    Cui, Q.3
  • 70
    • 0038724257 scopus 로고    scopus 로고
    • Membrane protein dynamics versus environment simulations of OmpA in a micelle and in a bilayer
    • Bond, P. J., and M. S. P. Sansom. 2003. Membrane protein dynamics versus environment simulations of OmpA in a micelle and in a bilayer. J. Mol. Biol. 329:1035-1053.
    • (2003) J. Mol. Biol , vol.329 , pp. 1035-1053
    • Bond, P.J.1    Sansom, M.S.P.2
  • 71
    • 0027444701 scopus 로고
    • Effect of cholesterol on the charge and structure of apolipoprotein A-I in recombinant high density lipoprotein particles
    • Sparks, D. L., W. S. Davidson, S. Lund-Katz, and M. C. Phillips. 1993. Effect of cholesterol on the charge and structure of apolipoprotein A-I in recombinant high density lipoprotein particles. J. Biol. Chem. 268:23250-23257.
    • (1993) J. Biol. Chem , vol.268 , pp. 23250-23257
    • Sparks, D.L.1    Davidson, W.S.2    Lund-Katz, S.3    Phillips, M.C.4
  • 72
    • 0036712111 scopus 로고    scopus 로고
    • Comparative models for human apolipoprotein A-I bound to lipid in discoidal high-density lipoprotein particles
    • Klon, A. E., J. P. Segrest, and S. C. Harvey. 2002. Comparative models for human apolipoprotein A-I bound to lipid in discoidal high-density lipoprotein particles. Biochemistry. 41:10895-10905.
    • (2002) Biochemistry , vol.41 , pp. 10895-10905
    • Klon, A.E.1    Segrest, J.P.2    Harvey, S.C.3
  • 73
    • 0027210507 scopus 로고
    • Preparation and characterization of spheroidal, reconstituted high-density lipoproteins with apolipoprotein A-I only or with apolipoprotein A-I and A-II
    • Rye, K. A., K. H. Garrety, and P. J. Barter. 1993. Preparation and characterization of spheroidal, reconstituted high-density lipoproteins with apolipoprotein A-I only or with apolipoprotein A-I and A-II. Biochim. Biophys. Acta. 1167:316-325.
    • (1993) Biochim. Biophys. Acta , vol.1167 , pp. 316-325
    • Rye, K.A.1    Garrety, K.H.2    Barter, P.J.3


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