Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 32, 2006, Pages 11916-11921

  Kasson, Peter M ^a   Kelley, Nicholas W ^a   Singhal, Nina ^b   Vrljic, Marija ^a   Brunger, Axel T ^a,c   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Computer simulation; Lipid membrane; Markovian state models; Reaction mechanism; Vesicle

Indexed keywords

ARTICLE; CELL KINETICS; LIPID MEMBRANE; MATHEMATICAL COMPUTING; MEMBRANE FUSION; METHODOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROBABILITY; SIMULATION;

ALGORITHMS; BIOCHEMISTRY; COMPUTER SIMULATION; KINETICS; LIPIDS; MARKOV CHAINS; MEMBRANE FUSION; MEMBRANE LIPIDS; MOLECULAR CONFORMATION; PROTEIN FOLDING; SOFTWARE; THERMODYNAMICS; TIME FACTORS;

EID: 33747064957     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0601597103     Document Type: Article

References (35)

1. Jahn, R., Lang, T. & Sudhof, T. C. (2003) Cell 112, 519-533.
2. Skehel, J. J. & Wiley, D. C. (2000) Annu. Rev. Biochem. 69, 531-569.
3. Chen, Y. A. & Scheller, R. H. (2001) Nat. Rev. Mol. Cell Biol. 2, 98-106.
4. Bentz, J. (2000) Biophys. J. 78, 227-245.
5. Marrink, S. J. & Mark, A. E. (2003) J. Am. Chem. Soc. 125, 11144-11145.
6. Llinas, R., Steinbeig, I. Z. & Walton, K. (1981) Biophys. J. 33, 323-351.
7. Singhal, N., Snow, C. D. & Pande, V. S. (2004) J. Chem. Phys. 121, 415-425.
8. Swope, W. C., Pitera, J. W. & Suits, F. (2004) J. Phys. Chem. B 108, 6571-6581.
9. Shirts, M. & Pande, V. S. (2000) Science 290, 1903-1904.
10. Marrink, S. J. & Mark, A. E. (2003) J. Am. Chem. Soc. 125, 15233-15242.
11. Marrink, S. J., de Vries, A. H. & Mark, A. E. (2004) J. Phys. Chem. B 108, 750-760.
12. Muller, M., Katsov, K. & Schick, M. (2003) J. Polym. Sci. 41, 1441-1450.
13. Shillcock, J. C. & Lipowsky, R. (2005) Nat. Mat. 4, 225-228.
14. Brouillette, C. G., Segrest, J. P., Ng, T. C. & Jones, J. L. (1982) Biochemistry 21, 4569-4575.
15. Dennison, S. M., Bowen, M. E., Brunger, A. T. & Lentz, B. (2006) Biophys J. 90, 1661-1675.
16. Li, Y., Han, X., Lai, A. L., Bushweller, J. H, Cafiso, D. S. & Tamm, L. K. (2005) J. Virol. 79, 12065-12076.
17. Siegel, D. P. & Epand, R. M. (1997) Biophys. J. 73, 3089-3111.
18. Haque, M. E., McIntosh, T. J. & Lentz, B. R. (2001) Biochemistry 40, 4340-4348.
19. Siegel, D. P. (1993) Biophys. J. 65, 2124-2140.
20. Yang, L. & Huang, H. W. (2002) Science 297, 1877-1879.
21. Markin, V. S., Kozlov, M. M. & Borovjagin, V. L. (1984) Gen. Physiol. Biophys. 3, 361-377.
22. Chernomordik, L., Chanturiya, A., Green, J. & Zimmerberg, J. (1995) Biophys. J. 69, 922-929.
23. Ellens, H., Bentz, J. & Szoka, F. C. (1985) Biochemistry 24, 3099-3106.
24. Kemble, G. W., Danieli, T. & White, J. M. (1994) Cell 76, 383-391.
25. Xu, Y., Zhang, F., Su, Z., McNew, J. A. & Shin, Y. K. (2005) Nat. Struct. Mol. Biol. 12, 417-422.
26. Giraudo, C. G., Hu, C., You, D., Slovic, A. M., Mosharov, E. V., Sulzer, D., Melia, T. J. & Rothman, J. E. (2005) J. Cell Biol. 170, 249-260.
27. Cohen, F. S. & Melikyan, G. B. (2004) J. Membr. Biol. 199, 1-14.
28. Blumenthal, R., Balipuri, A., Walter, A., Covell, D. & Eidelman, O. (1987) J. Biol. Chem. 262, 13614-13619.
29. Struck, D. K., Hoekstra, D. & Pagano, R. E. (1981) Biochemistry 20, 4093-4099.
30. Lee, J. & Lentz, B. R. (1997) Biochemistry 36, 6251-6259.
31. von Gersdorff, H., Sakaba, T., Berglund, K. & Tachibana, M. (1998) Neuron 21, 1177-1188.
32. Katz, B. & Miledi, R. (1965) Proc. R. Soc. London Ser. B 161, 483-495.
33. Berendsen, H. J. C., Vanderspoel, D. & Vandrunen, R. (1995) Comput. Phys. Commun. 91, 43-56.
34. Lindahl, E., Hess, B. & van der Spoel, D. (2001) J. Mol. Model. 7, 306-317.
35. Sutton, R. B., Fasshauer, D., Jahn, R. & Brunger, A. T. (1998) Nature 395, 347-353.