Computational examination of biomolecular systems related to Alzheimer’s and Parkinson’s diseases

The aggregation of proteins has long been implicated in the pathogenesis of neurodegenerative disorders, such as Alzheimer’s and Parkinson’s diseases, through their deposition in amyloid plaques and Lewy bodies. The interaction of metal ions with these proteins has attracted signif- icant attention due to their potential role in accelerating protein aggregation and neurotoxicity. In this thesis, Amyloid-β (Aβ) and α-Synuclein (αS) were studied using molecular dynamics (MD), to investigate the effect of metal ions on their structure and folding. Given the wide array of force fields available, the first part of this thesis focused on the evaluation of force fields and solvent models in simulating the average structure of Aβ16 in complexation with Zn(II), derived from an NMR study. The parameterisation of the metal ion and coordinating atoms was performed using quantum mechanic (QM) calculations on the metal-binding site (His6, His13, His14, Glu11), and incorporated into the force field to allow for the description of the metal ion and coordinating residues. The conformational landscape explored during the MD was expanded using accelerated MD (aMD), through the introduction of an energy bias to permit the crossing of energy barriers. The simulations revealed the ff14SB force field with the GBSA implicit solvent model to be the most accurate in reproducing the experimental structure. The parameterisation described above was thus applied to a more disordered system, look- ing at the coordination of Cu(II) to αS. The simulations revealed that the force field was less ideal in reproducing the experimental characteristics of the protein, with better representation instead coming from ff03ws with the OBC continuum model. The aMD simulations revealed that the Cu(II) coordination to αS increased the stability of β-hairpins, while decreasing the N-terminal helical content, which has the potential to increase the rate of secondary nucleation. The Cu(I) coordination to αS was also investigated, due to the copper ions’ interconversion during the catalytic release of reactive oxygen species. The system’s average structure was suggestive of an intermediary state between the Cu(II) and apo forms. Following that, a differ- ent way of simulating the metal ion was implemented, through the use of cationic dummy atom models, eliminating the need for pre-defined bonded interactions with the coordinating atoms. This allowed the calculation of relative binding affinities to the metal ion. The model was also applied to study the αS-dimer in the presence and absence of Cu(II). The simulations on these systems, suggests the metal ion is a stabilising factor in the aggregation of αS, facilitating the formation of β-strand interlinkages between the chains. The last part of this thesis, looked at two of the modifications often described in PD patients, in particular the phosphorylation at S129 (pS129) and the A53T mutation. The former systems suggested a protective effect to the aggregation of the protein, while the A53T mutation, espe- cially in the case of the Cu(II)-bound system, presented longer-lasting β-characteristics, which could be indicative of a more stable aggregation with other peptides. Taken together, the results provide an understanding of the structural changes elicited by the association of these metal ions with the proteins, along with their influence on the aggregation process

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times

Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein

We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein