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This article is part of the supplement: NIPS workshop on New Problems and Methods in Computational Biology

Open Access Review

The Secrets of a Functional Synapse – From a Computational and Experimental Viewpoint

Michal Linial

Author Affiliations

Dept of Biological Chemistry, The Hebrew University of Jerusalem, 91904, Israel

BMC Bioinformatics 2006, 7(Suppl 1):S6  doi:10.1186/1471-2105-7-S1-S6

Published: 20 March 2006



Neuronal communication is tightly regulated in time and in space. The neuronal transmission takes place in the nerve terminal, at a specialized structure called the synapse. Following neuronal activation, an electrical signal triggers neurotransmitter (NT) release at the active zone. The process starts by the signal reaching the synapse followed by a fusion of the synaptic vesicle and diffusion of the released NT in the synaptic cleft; the NT then binds to the appropriate receptor, and as a result, a potential change at the target cell membrane is induced. The entire process lasts for only a fraction of a millisecond. An essential property of the synapse is its capacity to undergo biochemical and morphological changes, a phenomenon that is referred to as synaptic plasticity.


In this survey, we consider the mammalian brain synapse as our model. We take a cell biological and a molecular perspective to present fundamental properties of the synapse:(i) the accurate and efficient delivery of organelles and material to and from the synapse; (ii) the coordination of gene expression that underlies a particular NT phenotype; (iii) the induction of local protein expression in a subset of stimulated synapses. We describe the computational facet and the formulation of the problem for each of these topics.


Predicting the behavior of a synapse under changing conditions must incorporate genomics and proteomics information with new approaches in computational biology.