Probing beta amyloid aggregation using fluorescence anisotropy : experiments and simulation

The aggregation of beta amyloid (Ab) protein is associated with the development of Alzheimer's disease. In this work we monitor Ab aggregation using fluorescence anisotropy, a technique that provides information on the rotational diffusion of the fluorescing tyrosine (Tyr) side chains. We also perform Monte Carlo (MC) and fully atomistic Molecular Dynamics (MD) simulations to interpret the experiments. The experimental results show that there are two different rotational timescales contributing to the anisotropy. Our MC simulation captures this behaviour in a coarse-scale manner, and, more importantly, shows that the Tyr side chains must have their movements restricted in order to reproduce the anisotropy. The MD simulations provide a molecular scale view, and indeed show that aggregation restricts the Try side chains to yield anisotropy in line with the experimental results. This combination of experiment and simulation therefore provides a unique insight into the aggregation process, and we suggest how this approach might be used to gain further information on aggregating protein systems

A multi-disciplinary study of the early stages of beta amyloid aggregation

Amyloid fibrils have been linked to many diseases, with different proteins being associated with different health issues. The aggregation of Beta Amyloid (Aß) peptides can lead to Alzheimer's disease. These peptides are found in the body naturally, although Aß function is still not clear. The aggregation process is still a matter of research, however it is widely accepted that a lag period is followed by rapid aggregate growth and then a saturation phase where growth halts. Understanding how and why this happens is imperative for disease prevention. It has been found that toxicity occurs during the formation of oligomer. Collaborative work involving simulation and experimental methods has become commonplace, improving the understanding of this process. Consequently, the work presented here is a multidisciplinary study of the early stages of amyloid aggregation in Aß1-40 and Aß1-42. These are the two most common species and are 40 and 42 amino acid groups long respectively. They have been studied through the use of Molecular Dynamics (MD) and Monte Carlo (MC) simulations, which have been complemented by probing Aß1-40 with the experimental methods: fluorescence spectroscopy, fluorescence anisotropy and dynamic light scattering.Experimentation proved challenging, due to the noise encountered in Aß samples and alternative solvent compositions were studied in an attempt to overcome this. These experiments had limited success but when combined with simulation models, revealed potential insight into the aggregation through the movements of the tyrosine (Tyr) side-chain, an amino acid group found in the Aß proteins. MD simulations and MC simulations were used in order to probe the underlying mechanisms surrounding Tyr movements and their environments during the aggregation process and how it affects fluorescence anisotropy. The MD simulations also revealed conformational changes in the protein due to the presence of ions and discovered two new Tyr orientations which occur in protofibrils.Amyloid fibrils have been linked to many diseases, with different proteins being associated with different health issues. The aggregation of Beta Amyloid (Aß) peptides can lead to Alzheimer's disease. These peptides are found in the body naturally, although Aß function is still not clear. The aggregation process is still a matter of research, however it is widely accepted that a lag period is followed by rapid aggregate growth and then a saturation phase where growth halts. Understanding how and why this happens is imperative for disease prevention. It has been found that toxicity occurs during the formation of oligomer. Collaborative work involving simulation and experimental methods has become commonplace, improving the understanding of this process. Consequently, the work presented here is a multidisciplinary study of the early stages of amyloid aggregation in Aß1-40 and Aß1-42. These are the two most common species and are 40 and 42 amino acid groups long respectively. They have been studied through the use of Molecular Dynamics (MD) and Monte Carlo (MC) simulations, which have been complemented by probing Aß1-40 with the experimental methods: fluorescence spectroscopy, fluorescence anisotropy and dynamic light scattering.Experimentation proved challenging, due to the noise encountered in Aß samples and alternative solvent compositions were studied in an attempt to overcome this. These experiments had limited success but when combined with simulation models, revealed potential insight into the aggregation through the movements of the tyrosine (Tyr) side-chain, an amino acid group found in the Aß proteins. MD simulations and MC simulations were used in order to probe the underlying mechanisms surrounding Tyr movements and their environments during the aggregation process and how it affects fluorescence anisotropy. The MD simulations also revealed conformational changes in the protein due to the presence of ions and discovered two new Tyr orientations which occur in protofibrils

Tyrosine Rotamer States in Beta Amyloid: Signatures of Aggregation and Fibrillation

During the early stages of β amyloid (Ab) peptide aggregation, toxic oligomers form which have been recognized as a likely cause of Alzheimer's disease. In this work, we use fully atomistic molecular dynamics simulation to study the amorphous aggregation of the peptide as well as model β-sheet protofibril structures. In particular, we study the rotamer states of the single fluorescent tyrosine (Tyr) residue present in each Ab. We find that the occupation of the four previously identified rotamers is different for monomeric and amorphous aggregates because of the differing environments of the Tyr side-chains. Surprisingly, we also identify two new rotamers that uniquely appear for the β-sheet structures, so that together the rotamers provide distinct signatures for the different stages of aggregation and fibrillation. We propose that these rotamers could be identified in fluorescence spectroscopy, with each rotamer having a distinct fluorescence lifetime because of its different exposures to the solvent. The identification of the two new rotamers therefore provides a new means to probe amyloid formation kinetics and to monitor the effect of additives including prospective drugs