Document Type


Date of Award


Degree Name

Doctor of Philosophy in Applied Physics - (Ph.D.)



First Advisor

Cristiano L. Dias

Second Advisor

Wenda Cao

Third Advisor

Ken Keunhyuk Ahn

Fourth Advisor

Junjie Yang

Fifth Advisor

Yuanwei Zhang

Sixth Advisor

Treena Livingston Arinzeh

Seventh Advisor

Bradley L. Nilsson


Proteins play a critical role in living systems by performing most of the functions inside cells. The latter is determined by the protein's three-dimensional structure when it is folded in its native state. However, under pathological conditions, proteins can misfold and aggregate, accounting for the formation of highly ordered insoluble assemblies known as amyloid fibrils. These assemblies are associated with diseases like Parkinson's and Alzheimer's. Strong evidence suggests that three mechanisms are critical for forming amyloid fibrils. These mechanisms are the nucleation of amyloid fibrils in solution (primary nucleation) as well as on the surface of existing fibrils (secondary nucleation) and the elongation of fibrils. This dissertation aims to provide insights into the complex mechanisms underlying the formation of amyloid-like fibrils at the atomic level, which remains poorly understood. This knowledge will enable the rational design of drugs to treat diseases.

This dissertation is divided into three parts. First, extensive molecular dynamics simulations are performed to show that all-atom models can account for the aggregation of peptides into amyloid-like fibrils. These simulations are conducted using different amino acid sequences at different temperatures. They highlight the importance of hydrophobic interactions in aggregation. This is supported by an increase in the rate of fibril formation with increasing temperature, which is a characteristic behavior of hydrophobic interactions. Moreover, the effect of NaCl on the aggregation of sequences made with non-polar residues that exhibit a low degree of hydrophobicity is investigated. Results provide evidence that screening electrostatic interactions with salts promotes aggregation. Furthermore, the results of this study demonstrate that peptides made from the same amino acids located at different positions in the sequence form fibrils with different propensity. An analysis of these systems indicates that the propensity to form fibrils in-vitro correlates positively with the propensity to form fibrils in-silico when long simulations (2-3 µs) are conducted.

Second, all-atom simulations are performed to provide new insights into the kinetics of fibril growth and the role played by the fibril surface in this phenomena. Results of this study show that peptides can land on the fibril tip via two pathways: bulk-docking and surface-docking. In bulk-docking, the peptide binds from the bulk solution directly to the tip to elongate the fibril. In the surface-docking, the peptide lands and diffuses on the fibril surface to reach the tip. Peptides are usually assumed to populate the fibril tip via bulk-docking. However, simulation results show that surface-docking can contribute significantly to this phenomena. In particular, changing the temperature and aspect ratio of the fibril affects the relative contribution of these two docking pathways. A continuum model is proposed by collaborators to quantify the effect of fibril surface, length, and temperature in bulk-and surface-docking.

Third, all-atom simulations are performed to provide insights into primary nucleation. An intermediate state is observed to form spontaneously on the pathway to fibril formation, which is made of two laminated β-sheets with peptides oriented perpendicularly to each other. This state remains stable for ~ 0.5 µs after which β-sheets rotate to account for the spine of amyloid fibrils where peptides are aligned with each other. This study also emphasizes the importance of side chain interactions in aligning docked peptides with the fibril template. Docked peptides get trapped in local minima when conformational changes are not driven by side chain interactions at high temperatures. The role played by non-polar patches on the fibril surface in secondary nucleation is also discussed.



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