Chapter 9 Understanding Membrane Fusion. Combining Experimental and Simulation Studies

Methods in Cell Biology

Volumn 90, Issue C, 2008, Pages 183-198

  Jena, Bhanu P ^a  

^a WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; LIPOSOME; ORGANOPHOSPHORUS COMPOUND; OXYGEN; PHOSPHORIC ACID DIMETHYL ESTER;

ARTICLE; BIOCHEMISTRY; CHEMISTRY; COMPUTER SIMULATION; LIGHT; MEMBRANE FUSION; METABOLISM; METHODOLOGY; RADIATION SCATTERING; SYNAPSE VESICLE; TIME; X RAY DIFFRACTION;

BIOCHEMISTRY; CALCIUM; COMPUTER SIMULATION; LIGHT; LIPOSOMES; MEMBRANE FUSION; ORGANOPHOSPHORUS COMPOUNDS; OXYGEN; SCATTERING, RADIATION; SYNAPTIC VESICLES; TIME FACTORS; X-RAY DIFFRACTION;

EID: 59049103596     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0091-679X(08)00809-1     Document Type: Review

References (24)

1. Bako I., Hutter J., and Palinkas G. Car-Parrinello molecular dynamics simulation of the hydrated calcium ion. J. Chem. Phys. 117 (2002) 9838-9843
2. Bockmann R.A., and Grubmuller H. Multistep binding of divalent cations to phospholipid bilayers: A molecular dynamics study. Angew. Chem. Int. Ed. 43 (2004) 1021-1024
3. 2 aqueous solutions over a wide range of concentration. Interpretation of diffraction experiments via molecular simulation. J. Chem. Phys. 119 (2003) 8052-8061
4. Cho S.-J., Kelly M., Rognlien K.T., Cho J., Hörber J.K., and Jena B.P. SNAREs in opposing bilayers interact in a circular array to form conducting pores. Biophys. J. 83 (2002) 2522-2527
5. Foloppe N., and MacKerell Jr. A.D. An improved empirical potential energy function for molecular simulations of phospholipids. J. Comput. Chem. 21 (2000) 86-104
6. Guan Y., Wurrey C.J., and Thomas Jr. G.J. Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-. Biophys. J. 66 (1994) 225-235
7. Guan Y., Choy G.S.-C., Glaser Rainer., and Thomas G.J. Vibrational analysis of nucleic acids. 2. Ab initio calculation of the molecular force field and normal modes of dimethyl phosphate. J. Phys. Chem. 99 (1995) 12054-12062
8. Humphrey W., Dalke A., and Schulten K. VMD: Visual molecular dynamics. J. Mol. Grap. 14 (1996) 33-38
9. Jeremic A., Kelly M., Cho J., Cho S.-J., Hörber J.K., and Jena B.P. Calcium drives fusion of SNARE-apposed bilayer. Cell Biol. Int. 28 (2004) 19-31
10. Jeremic A., Cho W.J., and Jena B.P. Membrane fusion: What may transpire at the atomic level. J. Biol. Phys. Chem. 4 (2004) 139-142
11. Katz A., Glusker J.P., Beebe S.A., and Bock C.W. Calcium ion coordination: A comparison with that of beryllium, magnesium, and zinc. J. Am. Chem. Soc. 118 (1996) 5752-5763
12. Laroche G., Dufourc E.J., Dufourcq J., and Pezolet M. Structure and dynamics of dimyristoylphosphatidic acid/calcium complex by 2H NMR, infrared, spectroscopies and small-angle x-ray diffraction. Biochemistry 30 (1991) 3105-3114
13. 2 aqueous solutions. J. Chem. Phys. 64 (1976) 2437-2446
14. Martínez J.M., and Martínez L. Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. J. Comput. Chem. 24 (2003) 819-825
15. McIntosh T.J. Short-range interactions between lipid bilayers measured by X-ray diffraction. Curr. Opin. Struct. Biol. 10 (2000) 481-485
16. Pavlov M., Siegbahn P.E.M., and Sandström M. Hydration of beryllium, magnesium, calcium, and zinc ions using density functional theory. J. Phys. Chem. 102 (1998) 219-228
17. Petrov A.S., Funseth-Smotzer J., and Pack G.R. Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium. Int. J. Quantum Chem. 102 (2005) 645-655
18. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., and Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (2005) 1781-1802
19. 2+, and inhibition by spectrin. Biochemistry 18 (1979) 780-790
20. 2+ mediated local dehydration and membrane fusion in cells. Cell Biol. Int. 32 (2008) 361-366
21. Schneider B., Kabelac M., and Hobza P. Geometry of the phosphate group and its interactions with metal cations in crystals and ab Initio calculations. J. Am. Chem. Soc. 118 (1996) 12207-12217
22. 2+ in water: Comparison of a classical simulation including three-body corrections and Born-Oppenheimer ab initio and density functional theory quantum mechanical/molecular mechanics simulations. J. Chem. Phys. 115 (2001) 10808-10813
23. 2+ in DNA bending: Evidence from an ONIOM-based QM-MM study of a DNA fragment. J. Phys. Chem. 110 (2006) 8826-8831
24. Wilschut J., Duzqunes N., Fraley R., and Papahadjopoulos D. Studies on the mechanism of membrane fusion: Kinetics of calcium ion induced fusion of phosphatidylserine vesicles followed by a new assay for mixing of aqueous vesicle content. Biochemistry 19 (1980) 6011-6021