Hydration layer dynamics and association mechanisms of food and antifreeze proteins

Brotzakis, Phaedon (cover) web

Thesis Brotzakis, P.

University of Amsterdam

The aim of this thesis is threefold. First to better understand the role of water at the hydration shell of single proteins in terms of structure and dynamics, secondly to understand the association and first steps of self-assembly mechanisms of food and anti-freeze proteins, and thirdly to understand the role of water during the association mechanism. By performing Molecular Dynamics, we are able to investigate the H-bond structure and dynamics of water around hydrophilic and hydrophobic protein groups, as well as the effect of unfolding on water dynamics.
We are able to correlate water reorientation dynamics with the H-bond structure at the hydration shell of anti-freeze proteins. Moreover, by employing Transition Path Sampling and Molecular Dynamics we study how anti-freeze peptides self-assemble into nanotubes, as well as their stability as a function of size. We further study the dimerization mechanism of globular proteins, the important interactions playing a role during the transition as well as the role of water. In order to do so, since the dimerization transition is rare, and the transition barrier asymmetric, we develop and employ a novel Transition Path Sampling shooting scheme that efficiently samples rare transitions with asymmetric barriers which simultaneously gives access to the transition state region.