Geometric and many-particle aspects of transmitter binding

Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis

Serial ligation is the repeated reversible binding of a ligand to one receptor after another. It is a widespread phenomenon throughout biochemical systems, occurring anytime receptors are clustered together and ligand binding is reversible. Computer simulations are used in this work to investigate a representative example, which is the serial ligation of an extracellular aspartate molecule to the membrane-bound chemotaxis receptors of an Escherichia coli bacterium. It is found that the initial binding site of a ligand to a cluster of receptors is more likely to be near the edge of the cluster than near the middle, although there is no overall bias when all rebindings are considered. Serial ligation does not lead directly to signal amplification or attenuation but instead causes binding events to be correlated in both space and time: a ligand is likely to bind many times in rapid succession in a small region of the receptor cluster, but there can also be long intervals between bindings. This leads to an increased level of noise in the received signal but may allow a single ligand to be sensed above a uniform level of background noise. The focus of this paper is on the interpretation of simulation results so they can be generalized to a wide variety of other systems and to allow the identification of systems in which serial ligation is likely to be important. In the process, several characteristic times are identified, as are scaling laws for the spatial and temporal dynamics.

A theoretical description of microdialysis with mass transport coupled to chemical events

A random-walk simulation of microdialysis is used to examine how a reaction that consumes analyte in the medium external to the probe affects the extraction and recovery processes. The simulations suggest that such a reaction can promote the extraction process while simultaneously inhibiting the recovery process, which appears to be consistent with recent experimental evidence of asymmetry in the extraction and recovery of the neurotransmitter, dopamine, during brain microdialysis. This suggests that quantitative microdialysis strategies that rely on the extraction fraction as a measure of the probe recovery value, such as the no-net-flux method, will produce an underestimate of the analyte concentration in the external medium when that analyte is consumed by a reaction in the external medium. Furthermore, if experimental conditions arise under which the kinetics of the reaction are changed, then changes in the extraction and recovery processes are likely to occur as well. The implications of these theoretical findings for the quantitative interpretation of in vivo microdialysis results obtained for the neurotransmitter dopamine are examined.

Collective binding properties of receptor arrays

Binding kinetics of receptor arrays can differ dramatically from that of the isolated receptor. We simulate synaptic transmission using a microscopically accurate Brownian dynamics routine. We study the factors governing the rise and decay of the activation probability as a function of the number of transmitter molecules released. Using a realistic receptor array geometry, the simulation reproduces the time course of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor-mediated excitatory postsynaptic currents. A consistent interpretation of experimentally observed synaptic currents in terms of rebinding and spatial correlations is discussed.