Inter-ring rotation of apolipoprotein A-I protein monomers for the double-belt model using biased molecular dynamics

Journal of Molecular Graphics and Modelling

Volumn 29, Issue 8, 2011, Pages 1006-1014

  Caulfield, Thomas R ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Apolipoprotein A I; Discoidal high density lipoprotein; Double belt model; HDL; Milano mutant; Paris mutant; Simulation

Indexed keywords

APOLIPOPROTEIN A-I; DOUBLE BELT MODEL; HDL; HIGH DENSITY LIPOPROTEIN; MILANO MUTANT; PARIS MUTANT; SIMULATION;

AMINO ACIDS; COMPUTER SIMULATION; MOLECULAR DYNAMICS; MONOMERS; PROTEINS;

ROTATION;

APOLIPOPROTEIN A1; ARGININE; ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; GLUTAMINE; HIGH DENSITY LIPOPROTEIN; LYSINE; MONOMER; MUTANT PROTEIN;

ARTICLE; CHOLESTEROL TRANSPORT; DOUBLE BELT MODEL; LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR MODEL; MUTATIONAL ANALYSIS; PRIORITY JOURNAL; PROTEIN FUNCTION; ROTATION;

AMINO ACID SUBSTITUTION; APOLIPOPROTEIN A-I; BIOLOGICAL TRANSPORT; CHOLESTEROL; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 79957879319     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.04.005     Document Type: Article

References (48)

1. J.P. Segrest, R.L. Jackson, J.D. Morrisett, A.M. Gotto Jr., A molecular theory of lipid-protein interactions in the plasma lipoproteins, FEBS Lett. 38 (1974) 247-253.
2. D. Atkinson, M.A. Davis, R.B. Leslie, The structure of a high density lipoprotein (HDL3) from porcine plasma, Proc. Natl. Acad. Sci. U.S.A. 186 (1974) 165-180.
3. C.G. Brouillette, G.M. Anantharamaiah, Structural models of human apolipoprotein A-I, Biochim. Biophys. Acta 1256 (1995) 103-129.
4. E. Aakerloef, H. Joernvall, H. Slotte, A. Pousette, Identification of apolipoprotein-A1 and immunoglobulin as components of a serum complex that mediates activation of human sperm motility, Biochemistry 30 (1991) 8986-8990.
5. W. Zhou, M.M. Ross, A. Tessitore, D. Ornstein, A. Vanmeter, L.A. Liotta, et al., An initial characterization of the serum phosphoproteome, Proteome Res. 8 (2009) 5523-5531.
6. W.P.R. Castelli, P.W.F. Garrison, R.D. Wilson, S.K. Abbott, W.B. Kannel, Incidence of coronary heart disease and lipoprotein cholesterol levels, J. Am.Med. Assoc. 256 (1986) 2835-2838.
7. G.J. Miller, N.E. Miller, Plasma-high-density-lipoprotein concentration and development of ischaemic heart disease, Lancet i (1975).
8. N.E. Miller, D.S. Thelle, O.H. Fördé, O.D. Mjös, The Tromso Heart Study: high-density lipoprotein and coronary heart disease: a prospective case-control study, Lancet i (1977).
9. A. Wlodawer, J.P. Segrest, B.H. Chung, R. Chiovetti Jr, J.N. Weinstein, High-density lipoprotein recombinants: evidence for a bicycle tire micelle structure obtained by neutron scattering and electron microscopy, FEBS Lett. 104 (1979) 231-235.
10. D. Atkinson, D.M. Small, G.G. Shipley, X-ray and neutron scattering studies of plasma lipoproteins, Ann. N.Y. Acad. Sci. 348 (1980) 284-298.
11. A. Jonas, J.H. Wald, K.L. Toohill, E.S. Krul, K.E. Kezdy, Apolipoprotein A-I structure and lipid properties in homogeneous, reconstituted spherical and discoidal high density lipoproteins, J. Biol. Chem. 265 (1990) 22123-22129. (Pubitemid 120014276)
12. D.M. Monti, F. Guglielmi, M. Monti, F. Cozzolino, S. Torrassa, A. Relini, et al., Effects of a lipid environment on the fibrillogenic pathway of the N-terminal polypeptide of human apolipoprotein A-I, responsible for in vivo amyloid fibril formation, Eur. Biophys. J. 39 (2009) 1289-1299.
13. D.W. Borhani, D.P. Rogers, J.A. Engler, C.G. Brouillette, Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation, Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 12285-12290.
14. J.P. Segrest, M.K. Jones, A.E. Klon, C.J. Sheldahl, M. Hellinger, H. De Loof, et al., A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein, J. Biol. Chem. 274 (1999) 31755-31758.
15. A.E. Klon, M.K. Jones, J.P. Segrest, S.C. HArvey, Molecular belt models for the apolipoprotein A-I Paris and Milano mutations, Biophys. J. 79 (2000) 1679-1685.
16. C.J. Sheldahl, S.C. Harvey, Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges, Biophys. J. 76 (1999) 1190-1198. (Pubitemid 29262602)
17. H. Heller, M. Schaefer, K. Schulten, Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases, J. Chem. Phys. 97 (1993) 8843-9360.
18. M.N. Palgunachari, V.K. Mishra, S. Lund-Katz, M.C. Phillips, S.O. Adeyeye, S. Alluri, et al., Only the two end helixes of eight tandem amphipathic helical domains of human Apo A-I have significant lipid affinity: implications for hdl assembly, Arterioscl. Thromb. Vascul. Biol. 16 (1996) 328-338. (Pubitemid 26056254)
19. V.K. Mishra, M.N. Palgunachari, Interaction of model class A1, class A2, and class Y amphipathic helical peptides with membranes, Biochemistry 35 (1996) 11210-11220.
20. M.K. Jones, G.M. Anantharamaiah, J.P. Segrest, Computer programs to identify and classify amphipathic alpha helical domains, J. Lipid Res. (1992) 287-296.
21. J.P. Segrest, H. De Loof, J.G. Dohlman, C.G. Brouillette, G.M. Anantharamaiah, Amphipathic helix motif: classes and properties, Proteins 8 (1990) 103-117. (Pubitemid 20262536)
22. K.H. Weisgraber, J.S.C. Rall, T.P. Bersot, R.W.Mahley, G. Franceschini, C.R. Sirtori, Apolipoprotein A-I (Milano), J. Biol. Chem. 258 (1983) 2508-2513.
23. E.A. Bruckert, E.H. Funke, I. Beucler, H. Wiebusch, G. Turpin, G. Assmann, The replacement of arginine by cysteine at residue 151 in apolipoprotein A-I Milano produces a phenotype similar to that of apolipoprotein A-I, Arterioscl. Thromb. Vascul. Biol. 128 (1997) 121-128. (Pubitemid 27065268)
24. A.G. Rocco, L. Mollica, E. Gianazza, L. Calabresi, G. Franceschini, C.R. Sirtori, et al., Model structure for the heterodimer apoA-IMilano-apoA-II supports its peculiar susceptibility to proteolysis, Biophys. J. 91 (2006) 3043-3049. (Pubitemid 44526494)
25. L.G. Calabresi, A. Franceschi, A. Burkybile, A. Jonas, Activation of lecithin cholesterol acyltransferase by a disulfide-linked apolipoprotein A-I dimer, Biochem. Biophys. Res. Commun. 232 (1997) 345-349. (Pubitemid 27216216)
26. G. Franceschini, L.G. Calabresi, G. Chiesa, C. Parolini, C.R. Sirtori, M. Canavesi, et al., Increased cholesterol efflux potential of sera from ApoA-I(Milano) carriers and transgenic mice, J. Clin. Investig. 66 (1999) 892-900.
27. U. Daum, C. Lanager, N. Duverger, F. Emmanuel, P. Benoit, P. Denefle, et al., Apolipoprotein A-I(R151C)Paris is defective in activation of lecithin: cholesterol acyltransferase but not in initial lipid binding, formation of reconstituted lipoproteins, or promotion of cholesterol efflux, J. Mol. Med. (1999) 77.
28. M. Pérusse, A. Pascot, J.P. Després, C. Couillard, B. Lamarche, A new method for HDL particle sizing by polyacrylamide gradient gel electrophoresis using whole plasma, J. Lipid Res. 42 (2001) 1331-1334. (Pubitemid 32744258)
29. A.E. Klon, J.P. Segrest, S.C. Harvey, Comparative models for human apolipoprotein a-I bound to lipid in discoidal high-density lipoprotein particles, Biochemistry 41 (2002) 10895-10905. (Pubitemid 35001201)
30. Accelrys, I. Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, USA. amaiti@accelrys.com. INSIGHT-II. 2000.
31. W. Humphrey, A. Dalke, K. Schulten, VMD: visual molecular dynamics, J. Mol. Graph. 14 (33-8) (1996) 27-28.
32. J.P. Krawetz, A. Shinozaki, K. Varadarajan, K. Schulten, NAMD2: greater scalability for parallel molecular dynamics, J. Comput. Phys. 151 (1999) 283-312.
33. M. Nelson, W. Humphrey, A. Gursoy, A. Dalke, L. Kalé, R.D. Skeel, et al., NAMD - a parallel object-oriented molecular dynamics program, J. Supercomput. Appl. 10 (1996) 251-268.
34. M.K. Jones, A. Catte, L. Li, J.P. Segrest, Dynamics of lecithin:cholesterol acyltransferase activation by apolipoprotein A-I, Biochemistry 48 (2009) 11196.
35. A.E. Klon, M.K. Jones, J.P. Segrest, S.C. Harvey, Molecular belt models for the apolipoprotein A-I Paris and Milano mutations, Biophys. J. 79 (2000) 1679-1685.
36. M.K. Jones, A. Catte, J.C. Patterson, F. Gu, J. Chen, L. Li, et al., Thermal stability of apolipoprotein A-I in high-density lipoproteins by molecular dynamics 96 (2) (2009) 354-371.
37. A. Catte, J.C. Patterson, M.K. Jones, W.G. Jerome, D. Bashtovyy, Z. Su, et al., Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study, Biophys. J. 90 (2006) 4345-4360. (Pubitemid 43830883)
38. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983) 926-935.
39. B.R. Brooks, R.E.B. Olafson, D.J. States, S. Swaminathan, M. Karplus, CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4 (1983) 187-217.
40. J. Ryckaert, G. Ciccotti, H. Berendsen, SHAKE: numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977) 327-341.
41. T. Darden, D. York, L. Pedersen, Paticle Mesh Ewald-an N. Log(N) method for Ewald sums in large systems, J. Chem. Phys. 98 (1993) 10089-10092.
42. E. Nosé, A unified formulation of the constant temperature molecular dynamics method, J. Chem. Phys. 81 (1984) 511-519.
43. W.G. Hooover, Canonical dynamics: equilibrium phase-space distributions, Phys. Rev. A 31 (1985) 1695-1697.
44. H.J.C. Berendsen, J. Postma, W. Van Gunsteren, A. Dinola, J. Haak, Molecular-dynamics with coupling to an external bath, J. Chem. Phys. 81 (1984) 3684-3690.
45. T. Caulfield, B. Devkota, G. Rollins, Examinations of tRNA range of motion using simulations of cryo-EM microscopy and X-ray data, J. Biophys. 2011 (2011), doi:10.1155/2011/219515.
46. S.C. Harvey, H.A. Gabb, Conformational transitions using molecular dynamics with minimum biasing, Biopolymers 33 (1993) 1167-1172. (Pubitemid 23208836)
47. F. Gu, M.K. Jones, J. Chen, J.C. Patterson, A. Catte, W.G. Jerome, et al., Structures of discoidal high density lipoproteins: a combined computational-experimental approach, J. Biol. Chem. 285 (2010) 4652-4665.
48. A. Catte, J.C. Patterson, D. Bashtovyy, M.K. Jones, F. Gu, L. Li, et al., Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulation, Biophys. J. 94 (2008) 2306.