Persistent voids: A new structural metric for membrane fusion

Bioinformatics

Volumn 23, Issue 14, 2007, Pages 1753-1759

  Kasson, Peter M ^a   Zomorodian, Afra ^b   Park, Sanghyun ^a   Singhal, Nina ^c   Guibas, Leonidas J ^c   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

^b Dartmouth Department of Computer Science_Dartmouth College   (United States)

^c Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID;

ARTICLE; CHANNEL GATING; ENTROPY; GEOMETRY; MEMBRANE FUSION; MEMBRANE VESICLE; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS; STRUCTURAL HOMOLOGY; STRUCTURAL PROTEOMICS;

EID: 34547888694     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm250     Document Type: Article

References (30)

1. Chernomordik,L. et al. (1995) The hemifusion intermediate and its conversion to complete fusion - Regulation by membrane-composition. Biophys. J., 69, 922-929.
2. Chernomordik,L.V. and Kozlov,M.M. (2005) Membrane hemifusion: Crossing a chasm in two leaps. Cell, 123, 375-382.
3. Cohen,I.S. and Melikyan,G.B. (2004) The energetics of membrane fusion from binding, through hemifusion, pore formation, and pore enlargement. J. Membr. Biol., 199, 1-14.
4. Cormen,T,H. et al. (2001) Introduction to Algorithms. MIT Press, Cambridge, MA.
5. Edelsbrunner,H. and Mucke,E.P. (1994) 3-Dimensional alpha-shapes. Acm Trans. Graph., 13, 43-72.
6. Evans,K.O. and Lentz,B.R. (2002) Kinetics of lipid rearrangements during poly(ethylene glycol)-mediated fusion of highly curved unilamellar vesicles. Biochemistry, 41, 1241-1249.
7. Giraudo,C.G. et al. (2005) SNAREs can promote complete fusion and hemifusion as alternative outcomes. J. Cell Biol., 170, 249-260.
8. Kasson,P.M. et al. (2006) Ensemble molecular dynamics yields sub-millisecond kinetics and intermediates of membrane fusion. Proc. Natl Acad. Sci. USA, 103, 11916-11921.
9. Katsov,K. et al. (2004) Field theoretic study of bilayer membrane fusion. I. Hemifusion mechanism. Biophys. J., 87, 3277-3290.
10. Kemble,G.W. et al. (1994) Lipid-anchored influenza hemagglutinin promotes hemifusion, not complete fusion. Cell, 76, 383-391.
11. Kozlovsky,Y. and Kozlov,M.M. (2002) Stalk model of membrane fusion: solution of energy crisis. Biophys. J., 82, 882-895.
12. Liang,J. et al. (1998a) Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins, 33, 1-17.
13. Liang,J. et al. (1998b) Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins, 33, 18-29.
14. Llinas,R. et al. (1981) Relationship between presynaptic calcium current and postsynaptic potential in squid giant synapse. Biophys. J., 33, 323-351.
15. Markin,V.S. et al. (1984) On the theory of membrane fusion. The stalk mechanism. Gen. Physiol. Biophys., 3, 361-377.
16. Marrink,S.J. et al. (2004) Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B, 108, 750-760.
17. Marrink,S.J. and Mark,A.E. (2003a) The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J. Am. Chem. Soc., 125, 11144-11145.
18. Marrink,S.J. and Mark,A.E. (2003b) Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J. Am. Chem. Soc., 125, 15233-15242.
19. Muller,M. et al. (2003) A new mechanism of model membrane fusion determined from Monte Carlo simulation. Biophys. J., 85, 1611-1623.
20. Shirts,M. and Pande,V.S. (2000) Computing - screen savers of the world unite! Science, 290, 1903-1904.
21. Siegel,D.P. (1993) Energetics of intermediates in membrane-fusion - comparison of stalk and inverted micellar intermediate mechanisms. Biophys. J., 65, 2124-2140.
22. Singhal,N. et al. (2004) Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J. Chem. Phys., 121, 415-425.
23. Snow,C.D. et al. (2005) How well can simulation predict protein folding kinetics and thermodynamics? Annu. Rev. Biophys. Biomol. Struct., 34, 43-69.
24. Stevens,M.J. et al. (2003) Insights into the molecular mechanism of membrane fusion from simulation: Evidence for the association of splayed tails. Phys. Rev. Lett., 91(18): 188102.
25. Swope,W.C. et al. (2004a) Describing protein folding kinetics by molecular dynamics simulations. 1. Theory. J. Phys. Chem. B, 108, 6571-6581.
26. Swope,W.C. et al. (2004b) Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and beta-hairpin peptide. J. Phys. Chem. B, 108, 6582-6594.
27. Van der Spoel,D. et al. (2005) GROMACS: Fast, flexible, and free. J. Comput. Chem., 26, 1701-1718.
28. Xu,Y. et al. (2005) Hemifusion in SNARE-mediated membrane fusion. Nat. Struct. Mol. Biol., 12, 417-422.
29. Zomorodian,A.J. (2005) Topology for Computing. Cambridge University Press, Cambridge, UK, New York.
30. Zomorodian,A. and Carlsson,G. (2005) Computing persistent homology. Discrete Computat. Geom., 33, 249-274.