Alzheimer's amyloid-beta and the disordered structural ensemble characterized using molecular dynamics and NMR spectroscopy

We used simulations and NMR experiments to investigate the diverse structure of amyloid-beta (Abeta) peptide in the soluble non-aggregated form in order to better understand this peptide's role in Alzheimer's disease. Because amyloid-beta is intrinsically disordered in its monomeric state, the combination of molecular dynamics simulation and NMR spectroscopy was crucial to determining the individual conformations that make up the amyloid-beta structural ensemble. Initially we focused on amyloid-beta 1-42 (Abeta42), which is the most toxic form of amyloid-beta. We collected homonuclear Nuclear Overhauser Effect (NOE) data on the peptide, and used extensive molecular dynamics simulations to characterize its conformational ensemble. We found that the conformational ensemble of Abeta42 is extremely heterogeneous. However, it also contains many structured populations with long-range NOE contacts. This is in contrast to Abeta21-30, an amyloid-beta fragment. Abeta21-30 is mostly extended and unstructured, with no long- range NOEs measured. Next we characterized Abeta40, another common form of amyloid-beta, which is less toxic and aggregation prone than Abeta42. Again we saw many long-range NOEs and structured conformations in the Abeta40 ensemble, but the most populated conformations for Abeta40 and Abeta42 were quite different. From our simulations we had seen that Abeta42 adopts a beta-turn and beta-strand, which together form the most common long-range interaction of the peptide, and that this turn is consistent with the same bend and beta-strand segment seen in the aggregated form of the peptide. Abeta40 also adopts many different long-range beta-strand conformations, however, none of them are similar to the fibril-like turn and beta-strand seen in the Abeta42 ensemble. This is one possible explanation for the greater aggregation rate and toxicity of Abeta42.;Amyloid-beta presents a difficult case for characterizing an intrinsically disordered disease protein because it contains many structured conformations within its ensemble. We therefore decided to examine the effectiveness of different computational methods for determining the conformational ensemble of this intrinsically disordered protein. We compared the knowledge- based approach to our de novo molecular dynamics approach. The knowledge-based approach randomly generates an ensemble and refines it to fit the NMR data. The de novo molecular dynamics approach, on the other hand, uses no experimental information to form the amyloid-beta ensemble. In both methods, we compare the simulated ensemble to the experimental data after it is created. We found that the knowledge-based approach is highly dependent on the starting pool of structures that it refines, and that a randomly generated pool does not contain structured conformations which are able to fit the NMR data. We also found that certain types of NMR data, like J-coupling constants and NOEs, do a much better job of distinguishing between vastly different ensembles than other types of NMR data like chemical shifts, which are calculated to be the same for both unstructured and heterogeneous structured ensembles.;After fully characterizing the amyloid-beta monomer ensemble, we were interested in studying an oligomer of amyloid-beta, which is believed to be the toxic agent in Alzheimer's disease. In collaboration with the Schaffer group, we assessed the toxicity of an Abeta42 oligomer, known as the globulomer, on cultures of human cortical neurons. This oligomer, which can be prepared consistently and does not aggregate to form fibrils, was found to induce neuronal cell death, indicating that it could be a toxic complex of amyloid-beta. This led us to an investigation of the Abeta42 globulomer structure, known to consist of beta-sheets. One proposed model of the globulomer is based on NMR data from a small globulomer precursor. Another model of the globulomer derives from coarse grain simulations of amyloid-beta prefibrils. We used molecular dynamics simulations to begin a comparison of these two models. Based on our preliminary simulations, the prefibrillar model seems to maintain a more stable beta-sheet structure than the NMR-based model. However, so far the NMR-based model has only been simulated as a dimer unit, and may be more stable when more chains are added. (Abstract shortened by UMI.).