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Bioinformatics Advance Access originally published online on May 8, 2007
Bioinformatics 2007 23(14):1753-1759; doi:10.1093/bioinformatics/btm250
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Persistent voids: a new structural metric for membrane fusion

Peter M. Kasson 1,2,*, Afra Zomorodian 3, Sanghyun Park 2, Nina Singhal 4, Leonidas J. Guibas 4 and Vijay S. Pande 2,*

1Medical Scientist Training Program, 2Department of Chemistry, Stanford University, Stanford CA 94305, 3Department of Computer Science, Dartmouth College, Hanover NH 03755 and 4Department of Computer Science, Stanford University, Stanford CA 94305, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Membrane fusion constitutes a key stage in cellular processes such as synaptic neurotransmission and infection by enveloped viruses. Current experimental assays for fusion have thus far been unable to resolve early fusion events in fine structural detail. We have previously used molecular dynamics simulations to develop mechanistic models of fusion by small lipid vesicles. Here, we introduce a novel structural measurement of vesicle topology and fusion geometry: persistent voids.

Results: Persistent voids calculations enable systematic measurement of structural changes in vesicle fusion by assessing fusion stalk widths. They also constitute a generally applicable technique for assessing lipid topological change. We use persistent voids to compute dynamic relationships between hemifusion neck widening and formation of a full fusion pore in our simulation data. We predict that a tightly coordinated process of hemifusion neck expansion and pore formation is responsible for the rapid vesicle fusion mechanism, while isolated enlargement of the hemifusion diaphragm leads to the formation of a metastable hemifused intermediate. These findings suggest that rapid fusion between small vesicles proceeds via a small hemifusion diaphragm rather than a fully expanded one.

Availability: Software available upon request pending public release.

Contact: kasson{at}cmgm.stanford-edu or pande{at}stanford.edu

Supplementary information: Supplementary data are available on Bioinformatics online.

Associate Editor: Anna Tramontano

Received on February 10, 2007; revised on April 13, 2007; accepted on May 2, 2007

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