Interpretation of small angle X-ray measurements guided by molecular dynamics simulations of lipid bilayers

Chemistry and Physics of Lipids

Volumn 126, Issue 2, 2003, Pages 211-223

  Sachs, Jonathan N ^a   Petrache, Horia I ^b   Woolf, Thomas B ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

Author keywords

Bilayer thickness; Electron density profile; Form factors; Fourier reconstruction; Lipid headgroup; Lipid volume

Indexed keywords

DIPALMITOYLPHOSPHATIDYLCHOLINE; HYDROCARBON; PALMITIC ACID DERIVATIVE;

ARTICLE; COMPARATIVE STUDY; ELECTRON; FOURIER ANALYSIS; LIGHT SCATTERING; LIPID BILAYER; MEMBRANE STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; VOLUMETRY; X RAY ANALYSIS;

EID: 0242498757     PISSN: 00093084     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphyslip.2003.08.001     Document Type: Article

References (62)

1. Armen R.S., Uitto O.D., Feller S.E., Phospholipid component volumes: determination and application to bilayer structure calculations. Biophys. J. 75:1998;734-744.
2. Balgavý P., Dubničková M., Kučerka N., Kiselev M.A., Yaradaikin S.P., Uhríková D., Bilayer thickness and lipid interface area in unilamellar extruded 1,2-diacylphosphatidylcholine liposomes: a small-angle neutron scattering study. Biochim. Biophys. Acta. 1512:2001;40-52.
3. Berger O., Edholm O., Jähnig F., Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:1997;2002-2013.
4. Blaurock A.E., Structure of the nerve myelin membrane: proof of the low-resolution profile. J. Mol. Biol. 56:1971;35-52.
5. Bloom M., Evans E., Mouritsen O.G., Physical-properties of the fluid lipid-bilayer component of cell-membranes - a perspective. Q. Rev. Biophys. 24:1991;293-397.
6. Bloom, M., Linseisen, F., Lloyd-Smith, J., Crawford, M., 1999. Magnetic resonance and brain function: approaches from physics. In: Maraviglia, B. (Ed.), Proceedings of the June 23-July 3 1998 Enrico Fermi International School of Physics, Course CXXXIX, Varenna, Italy. IOS Press, Amsterdam, 1999, pp. 527-553.
7. Botelho A.V., Gibson N.J., Thurmond R.L., Wang Y., Brown M.F., Conformational energetics of rhodopsin modulated by non-lamellar-forming lipids. Biochemistry. 41:2002;6354-6368.
8. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D., Swaminathan S., Karplus M.J., CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
9. Brown M.F., Modulation of rhodopsin function by properties of the membrane bilayer. Chem. Phys. Lipids. 73:1994;159-180.
10. Chiu S.-W., Clark M., Balaji V., Subramanian S., Scott H.L., Jakobsson E., Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane. Biophys. J. 69:1995;1230-1245.
11. Elliott J.R., Needham D., Dilger J.P., Haydon D.A., The effects of bilayer thickness and tension on gramicidin single-channel lifetime. Biochim. Biophys. Acta. 735:1983;95-103.
12. Franks N.P., Arunachalam T., Caspi E., A direct method for determination of membrane electron density profile on an absolute scale. Nature. 276:1978;530-532.
13. Feller S.E., Pastor R.W., Constant surface tension simulations of lipid bilayers: the sensitivity of surface areas and compressibilities. J. Chem. Phys. 111:1999;1281-1287.
14. Feller S.E., Venable R.M., Pastor R.W., Computer simulation of a DPPC phospholipid bilayer: structural changes as a function of molecular surface area. Langmuir. 13:1997;6555-6561.
15. Greathouse D.V., Hinton J.F., Kim K.S., Koeppe R.E. II, Gramicidin-A short-chain phospholipid dispersions-chain-length dependence of gramicidin conformation and lipid organization. Biochemistry. 33:1994;4292-4299.
16. Gruner S.M., Stability of lyotropic phases with curved interfaces. J. Phys. Chem. 22:1989;7562-7570.
17. Hardy B.J., Pastor R.W., Conformational sampling of hydrocarbon and lipid chains in an orienting potential. J. Comput. Chem. 15:1994;208-226.
18. Harroun T.A., Heller W.T., Weiss T.M., Yang L., Huang H.W., Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers. Biophys. J. 76:1999;845-937.
19. Hofsäß C., Lindahl E., Edholm O., Molecular dynamics simulations of phopholipid bilayers with cholesterol. Biophys. J. 84:2003;2192-2206.
20. Huang H.W., Deformation free-energy of bilayer-membrane and its effect on gramicidin channel lifetime. Biophys. J. 50:1986;1061-1070.
21. Huber, T., 1999. Ph.D. Thesis. Ludwig Maximilians University, Munich.
22. Huber T., Beyer K., Multiscale properties of the aqueous boundary of biological membranes from simulation. Biophys. J. 78:2000;1069.
23. 2 H NMR and molecular dynamics simulations J. Am. Chem. Soc. 124:2002;298-309.
24. Israelachvili, J.N., 1992. Intermolecular and Surface Forces. Academic Press, London.
25. β′ phases of oriented dipalmitoylphosphatidylcholine multibilayers J. Phys. Chem. 99:1995;4141-4147.
26. Killian J.A., Heijne G.V., How proteins adapt to a membrane-water interface. Trends Biochem. Sci. 25:2000;429-434.
27. Leikin S., Parsegian V.A., Rau D.C., Rand R.P., Hydration forces. Annu. Rev. Phys. Chem. 44:1993;369-395.
28. Lesslauer W., Cain J.E., Blasie J.K., X-ray diffraction studies of lecithin biomolecular leaflets with incorporated fluorescent probes. Proc. Natl. Acad. Sci. 69:1972;1499-1503.
29. Lyatskaya Y., Liu Y.F., Tristram-Nagle S., Katsaras J., Nagle J.F., Method for obtaining structure and interactions from oriented lipid bilayers. Phys. Rev. E. 63:2001;011907.
30. Marsh D., Water adsorption isotherms and hydration forces for lysolipids and diacyl phospholipids. Biophys. J. 55:1989;1093-1100.
31. Mashl R.J., Scott H.L., Subramaniam S., Jakobsson E., Molecular simulation of dioleoylphophatidylcholine lipid bilayers at differing levels of hydration. Biophys. J. 81:2001;3005-3015.
32. McIntosh T.J., Simon S.A., Hydration force and bilayer deformation - a reevaluation. Biochemistry. 25:1986a;4058-4066.
33. McIntosh T.J., Simon S.A., Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine. Biochemistry. 25:1986b;4948-4952.
34. McIntosh T.J., Simon S.A., Contributions of hydration and steric (entropic) pressures to the interactions between phophatidylcholine bilayers: experiments with the subgel phase. Biochemistry. 32:1993;8374-8384.
35. Nagle J.F., Wiener M.C., Relations for lipid bilayers - connection of electron-density profiles to other structural quantities. Biophys. J. 55:1989;309-313.
36. Nagle J.F., Tristram-Nagle S., Structure of lipid bilayers. Biochim. Biophys. Acta. 1469:2000;159-195.
37. α phase dipalmitoylphosphatidylcholine bilayers Biophys. J. 70:1996;1419-1431.
38. Pabst G., Rappolt M., Amenitsch H., Laggner P., Structural information from multilamellar liposomes at full hydration: full. q -range fitting with high quality X-ray data Phys. Rev. E. 62:2000;4000-4009.
39. Petrache H.I., Feller S.E., Nagle J.F., Determination of component volumes of lipid bilayers from simulations. Biophys. J. 72:1997;2237-2242.
40. Petrache H.I., Gouliev N., Tristram-Nagle S., Suter R.M., Nagle J.F., Interbilayer interactions from high-resolution X-ray scattering. Phys. Rev. E. 57:1998a;7014-7024.
41. Petrache H.I., Tristram-Nagle S., Nagle J.F., Fluid phase structure of EPC and DMPC bilayers. Chem. Phys. Lipids. 95:1998b;83-94.
42. Petrache H.I., Grossfield A., MacKenzie K.R., Engelman D.M., Woolf T.B., Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J. Mol. Biol. 302:2000;727-746.
43. Petrache H.I., Zuckerman D.M., Sachs J.N., Killian J.A., Koeppe R.E., Woolf T.B., Hydrophobic matching mechanism investigated by molecular dynamics simulations. Langmuir. 18:2002;1340-1351.
44. Press, W.H., Flannery, B.P., Teukolsky, S.A., Vetterling, W.T., 1988. Numerical Recipies. The Art of Scientific Computing. Cambridge University Press, New York.
45. Rand R.P., Parsegian V.A., Hydration forces between phospholipid- bilayers. Biochim. Biophys. Acta. 988:1989;351-376.
46. Rawicz W., Olbrich K.C., McIntosh T.J., Needham D., Evans E., Effect of chain length and unsaturation on elasticity of lipid bilayers. Biophys. J. 79:2000;328-339.
47. Schalke M., Losche M., Structural models of lipid surface monolayers from X-ray and neutron reflectivity measurements. Adv. Coll. Int. Sci. 88:2000;243-274.
48. Small, D.M., 1996. The Physical Chemistry of Lipids, Handbook of Lipid Research, vol. 4. Plenum Press, New York.
49. Smondyrev A.M., Berkowitz M.L., Molecular dynamics study of Sn-1 and Sn-2 chain conformations in DPPC membranes. J. Chem. Phys. 110:1999;3981-3985.
50. Sun W.J., Suter R.M., Knewtson M.A., Worthington C.R., Tristram-Nagle S., Zhang R., Nagle J.F., Order and disorder in fully hydrated unoriented bilayers of gel phase DPPC. Phys. Rev. E. 49:1994;4665-4676.
51. Sun W.J., Tristram-Nagle S., Suter R.M., Nagle J.F., Structure of gel phase saturated lecithin bilayers: temperature and chain length dependence. Biophys. J. 71:1996a;885-891.
52. Sun W.J., Tristram-Nagle S., Suter R.M., Nagle J.F., Structure of the ripple phase in lecithin bilayers. Proc. Natl. Acad. Sci. 93:1996b;7008-7012.
53. Tieleman D.P., Marrink S.J., Berendsen H.J.C., A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta. 1331:1997;235-270.
54. Tobias D.J., Tu K.C., Klein M.L., Atomic-scale molecular dynamics simulations of lipid membranes. Current Opin. Colloid Interf. Sci. 2:1997;15-26.
55. Tristram-Nagle S., Suter R.M., Sun W.-J., Nagle J.F., Kinetics of subgel formation in DPPC - X-ray-diffraction proves nucleation-growth hypothesis. Biochim. Biophys. Acta. 1991:1994;14-20.
56. Tristram-Nagle S., Petrache H.I., Nagle J.F., Structure and interactions of fully hydrated dioleoylphosphatidylcholine bilayers. Biophys. J. 75:1998;917-925.
57. Tristram-Nagle S., Liu Y.F., Legleiter J., Nagle J.F., Structure of gel phase DMPC determined by X-ray diffraction. Biophys. J. 83:2002;3324-3335.
58. Wack D.C., Webb W.W., Synchrotron X-ray study of the modulated lamellar phase in the lecithin-water system. Phys. Rev. A. 40:1989;2712-2730.
59. Wiener M.C., White S.H., Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of X-ray and neutron-diffraction data. 3. Complete structure. Biophys. J. 61:1992;434-447.
60. Wiener M.C., Suter R.M., Nagle J.F., Structure of the fully hydrated gel phase of DPPC. Biophys. J. 55:1989;315-325.
61. Worthington C.R., Interpretation of low-angle X-ray data from planar and concentric multilayered structures - use of one-dimensional electron density strip models. Biophys. J. 9:1969;222-234.
62. Zimmerberg J., Chernomordik L.V., Membrane fusion. Adv. Drug Deliv. Rev. 38:1999;197-205.