Numerical simulations of glutamate diffusion in a synaptic cleft. Dependence on the geometry and its possible interactions
Wojciech Goch (Institute of Biochemistry and Biophysics PAS), Wojciech Bal (Institute of Biochemistry and Biophysics PAS)
The second issue we are interested in is a possible participation of zinc in Aβ peptide aggregation - one of the hallmarks of Alzheimer Disease. As the dysfunction of zinc homeostasis is considered, we aim to investigate the interactions of 〖Zn〗^(2+) ions with glutamate in the confined volume of the synapse.
In order to achieve these goals we developed dedicated software within the Wolfram Mathematica environment. Our simulations illustrate the Brownian motion of glutamate molecules and zinc ions in a small volume, constrained by 2D surfaces (modeling the pre- and postsynaptic membrane) with an arbitrary chosen shape. The interactions between glutamate and 〖Zn〗^(2+) and receptors/transporters are defined by collision induced reactions. The electrostatic interactions between molecules and the membrane surface are also considered. The proposed model shows a dependence between the geometry of the synaptic cleft and the time-course of glutamate, thus providing an insight into the role of zinc in Alzheimer Disease.