- Hydration layer dynamics and association mechanisms of food and antifreeze proteins
- A Molecular Dynamics and Transition Path Sampling study
- Award date
- 7 March 2017
- Number of pages
- Document type
- PhD thesis
- Faculty of Science (FNWI)
- Van 't Hoff Institute for Molecular Sciences (HIMS)
By the time the reader reads this line, billions of protein association events just occurred in our body, such as the ones regulating cell communication, signaling pathways, or in initiating a self-assembly processes, such as tissue fabrication, etc.
The timescale of such transitions is slow, compared to atom vibrations and such events are termed rare, the reason being that protein or/and solvent interactions have to be disrupted and reformed in order for the transition to occur. In other words there is a barrier for the transition to occur.
Having an atomistic insight into rare transitions and their respective important interactions is pivotal for understanding and experimentally controlling such processes. Water is an important agent on its own in facilitating protein folding, recognizing ice crystal planes (anti-freeze proteins) and in mediating protein association. By using molecular simulations we better understand the role of water at the hydration shell of single proteins in terms of structure and dynamics, we resolve the mechanisms of association and first steps of self-assembly food and anti-freeze proteins, and elucidate the role of water during protein association. Finally, in order to improve the efficiency of rare event sampling we develop a new algorithm which efficiently samples complex rare transitions as well as gives insight into the barrier region of the transition.
Thesis (complete) (Embargo up to and including 07 March 2019)
4. Correlation between water structure and dynamics in the hydration layer of a type III ocean pout anti-freeze protein (Embargo up to and including 07 March 2018)
5. Stability and growth mechanism of self-assembling anti-freeze cyclic peptides (Embargo up to and including 07 March 2018)
7. Elucidating the mechanism and role of solvent for β-lactoglobulin dimerization using Transition Path Sampling (Embargo up to and including 07 March 2019)
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