A comprehensive kinetic model of the exocytotic process: Evaluation of the reaction mechanism

Aviv Mezer*, Eran Bosis, Uri Ashery, Esther Nachliel, Menachem Gutman

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

This study presents a comprehensive, quantitative description of the exocytotic process that has both analytic and predictive powers. The model utilizes strict chemical formalism and is based on a set of equilibria between the various SNARE proteins, their complexes and the reaction which free Ca 2+ ions. All these reactions are linked by first and second order rate constants. With the proper set of rate constants, which were selected by a systematic search in a multi dimensional parameter space, the model reconstructs the fusion dynamics as recorded under divergent experimental protocols: the effect of repeated depolarization, recovery after depletion of the vesicular pools of the cell, and over-expression or knockout of specific proteins.The model provides a detailed scenario of the maturation process, where the vesicles progress from the early steps of the SNARE complex formation up to the last event of the vesicles' fusion with the cells' plasma membrane. The dynamics of each intermediate enable us to describe the experimental result in terms of overall flow, where upstream intermediates are mobilized during the progression of the reaction.

Original languageAmerican English
Title of host publicationSystems Biology and Regulatory Genomics - Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, Revised Selected Papers
Pages249-257
Number of pages9
StatePublished - 2007
Externally publishedYes
EventJoint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics - San Diego, CA, United States
Duration: 2 Dec 20054 Dec 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4023 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceJoint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics
Country/TerritoryUnited States
CitySan Diego, CA
Period2/12/054/12/05

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