Protein Mobility in the Complex Physical Environment of the Synapse
by Simon Dannenberg
Date of Examination:2025-04-23
Date of issue:2025-05-22
Advisor:Prof. Dr. Stefan Klumpp
Referee:Prof. Dr. Stefan Klumpp
Referee:Prof. Dr. Marcus Müller
Persistent Address:
http://dx.doi.org/10.53846/goediss-11278
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Abstract
English
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.
Keywords: Biophysics; Physic of Complex Systems; Protein Mobility; Synapse
