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Introduction of the thesis
The global structure of proteins is sensitively dependent on the constituent peptides, their ordering, any substituted groups, the ambient chemistry as well as temperature and pH and other physical conditions. As a result, proteins often exhibit anomalous behaviours in vivo. Since a protein’s structure is intricately linked to its function, misfolding may cause pathological functioning of the protein. Indeed, the pathology of many diseases has been ascribed to the misfolding of certain proteins.
Misfolded proteins, or parts thereof, are known to aggregate, i.e. associate with each other to form large, regular, insoluble structures which are thermodynamically stable. These structures are termed amyloid fibrils. In fact, aggregation and formation of amyloid fibrils is a feature that seems to be inherent to the nature of polypeptide chains. The structure and aggregation process of amyloid fibrils is interesting to study for several reasons.
First, out of diseases related to protein misfolding, many are correlated with the formation of amyloid fibrils. One example that stands out is the CAG triplet disorders, in which proteins are found to have enlarged sections of consecutive glutamines (Q) in their primary structure. The severity of the diseases correlates positively with the length of the repeats. It is also found that the polyQs aggregate and form macroscopic cell inclusions, and it is believed that the aggregates, especially in their early stages, may be pathological. This has prompted both theoretical and experimental studies on the process of polyQ aggregation. As is especially apparent in the case of Alzheimer’s disease, these disorders no longer rare, and so the need to understand the process of aggregation is well-motivated.
Secondly, it has been suggested that amyloid fibrils may not always be pathological; on the contrary, they may play various functional roles. Finally, the study of aggregation kinetics is theoretically well-motivated. Simple physical models often capture the essential features seen in aggregation, and many phenomenological models now exist to describe the various mechanisms by which polypeptides nucleate and aggregate.
Kinetic studies of aggregation rely on knowing the number of growing ends per unit weight of the fibril. While measuring this directly has proved challenging, a group at the University of Pittsburgh demonstrated a viable method. This technique involves growing the fibril using biotinylated polyglutamine monomers, and then tagging by fluorescent Eu-streptavidin, a protein that binds strongly and specifically to biotin. What is yet unclear is why this procedure yields counts proportional to the number of growing ends, and not proportional to the total weight of the fibrils. In other words, why is the assay selective at all?
In this master’s thesis, we address this question using Molecular Dynamics (MD) simulation of a biotinylated glutamine residue attached to a polyQ fibril. First, we present the background in more detail and motivate the project. Then, we discuss the methods adopted, following which we state the research problem. Finally, we present the data gathered and some analysis, and end with a discussion of future directions that are open and interesting.
Citation
Bapat, A., “A Molecular Dynamics Study of the Site-dependent Interaction of a Polyglutamine Fibril with an Attached Biotinylated Residue”, Masters’ thesis, Freie Universität Berlin.
@phdthesis{bapat2017molecular,
title={A Molecular Dynamics Study of the Site-dependent Interaction of a Polyglutamine Fibril with an Attached Biotinylated Residue},
author={Bapat, Aniruddha A},
year={2017},
school={Freie Universität Berlin}
}