| dc.description.abstracteng | Robust signal transmission between cells is vital for our daily lives. It relies on fine
orchestration of many processes, particularly taking place at chemical synapses. Here,
chemical reactions occur in precise order, guiding synaptic vesicles (SV) to release their
neurotransmitters upon incoming stimulation. The involved processes host a multitude of
different proteins each performing crucial, specific functions. Despite signal transmission
being one of the best studied cellular pathways, the mobility of involved proteins only
recently has gained increased attention albeit it is expected to have a large impact.
In this thesis, I employed computational simulations to validate, refine and identify over-
arching, physical principals governing protein mobility. To achieve this, I compared sim-
ulations to experimental data, gathered in synapses in neuronal cultures or reconstituted
systems.
Overall, I set up two distinct sets of simulations. In the first one, I investigated protein
mobility at the scale of the entire presynaptic bouton. Here, we used a kinetic Monte
Carlo algorithm, the next subvolume method, to examine the influence of the synaptic
geometry and binding to synaptic vesicles on protein mobility. We fitted fluorescence
recovery after photobleaching experiments with these simulations to identify diffusion
coefficients, SV-binding and SV-unbinding rates of 40 different synaptic proteins. Our
approach revealed a length scale governing protein concentrating recovery. It is set by the
interplay of the proteins mobility parameters and the geometry of the synaptic bouton
itself.
In the second project, I explored the temporal spatial organisation of the synaptic vesicle
cluster (SVC). Using patchy particles we examined the role of short interactions of intrin-
sically disordered regions of proteins and their interplay between different constituents of
the SVC. We first modified to the existing model from the literature enabling simulations
equilibrating an order of magnitude faster, which makes larger system sizes accessible.
Subsequently, we used these modifications to successively implement different features of
molecular design of key constituents of the SVC, such as interaction strength or size dif-
ferences. Using this approach, we dissected the individual contributions of these features
and of different types of proteins seen in experiments. We identified, how dimerization can
effectively increase diffusion, by allowing higher temperatures of droplet formation and
how α-Synuclein changes the density of the SVC by reducing connectivity and increasing
solubility of Synapsin 1. Additionally, SVs can increase the stability of bonds with their
vicinity creating a nucleation point for condensation. | de |