Persistent voids: a new structural metric for membrane fusion.

Persistent voids: a new structural metric for membrane fusion. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Persistent voids: a new structural metric for membrane fusion. Abstract Text:

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

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. SUPPLEMENTARY INFORMATION: Supplementary data are available on Bioinformatics online.

Persistent voids: a new structural metric for membrane fusion. Publishing Authors By Initials

PM Kasson,A Zomorodian,S Park,N Singhal,LJ Guibas,VS Pande,

For similar viruses research abstracts see: viruses research

PUBMED ID PMID:

MEDLINE DATE:

Persistent voids: a new structural metric for membrane fusion. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: 1753-9

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 8

MONTH: 05

YEAR: 2007

Persistent voids: a new structural metric for membrane fusion. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9808944

Persistent voids: a new structural metric for membrane fusion. Keywords Mesh Terms:

KEYWORDS: Viruses

MESH TERMS: metabolism

Chemical & Substance for Abstract: Persistent voids: a new structural metric for membrane fusion. Information

Substance Name: 1-palmitoyl-2-oleoylphosphatidylethanola

Registry Number: 10015-88-0

Grant and Affiliation Information for Persistent voids: a new structural metric for membrane fusion.

AFFILIATION: Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA. kasson@cmgm.stanford-edu

Country: England

AGENCY: United States NIGMS

GRANT: GM072970

ACRONYM: GM

MEDLINETA: Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Persistent voids: a new structural metric for membrane fusion Related Publications

• Accurate and efficient corrections for missing dispersion interactions in molecular simulations.
• Bilateral optic disc oedema associated with latanoprost.
• Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics.
• Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics.
• Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.
• Crash data analysis: Collective vs. individual crash level approach.
• Differential regulation of the lateral mobility of plasma membrane phospholipids by the extracellular matrix and cholesterol.
• Effect of collision-activated dissociation gas and collision energy on the fragmentation of dipyridamole and its rapid and sensitive liquid chromatography/electrospray ionization tandem mass spectrometric determination in human plasma.
• Effects of long-range electrostatic forces on simulated protein folding kinetics.
• Folding and misfolding of the collagen triple helix: markov analysis of molecular dynamics simulations.
• Health financing options for Fiji's health system.
• Health financing: the Fijian experience.
• Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece.
• Interaction in the cerebral metabolism of the biogenic amines: effect of intravenous infusion of L-tryptophan on the metabolism of dopamine and 5-hydroxyindoles in brain and cerebrospinal fluid.
• Lens epithelial cell regression on the posterior capsule with different intraocular lens materials.
• Nanotube confinement denatures protein helices.
• Persistent voids: a new structural metric for membrane fusion.
• Postoperative conjunctival chemosis in cataract surgery caused by subconjunctival gentamicin injection.
• Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.
• Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide.
• Protein folding under confinement: a role for solvent.
• Rattling the cage: computational models of chaperonin-mediated protein folding.
• Registration and reporting of clinical trials.
• Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles.
• Solvent viscosity dependence of the protein folding dynamics.
• Statistical characterization of protein ensembles.
• The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations.
• The challenge of grandmultiparity in obstetric practice.
• Theory for an order-driven disruption of the liquid state in water.
• Tophaceous pseudogout--an unusual cause of nodulosis in rheumatoid arthritis.