Folding Free-Energy Landscape Of Alpha-Synuclein (35-97) Via Replica Exchange Molecular Dynamics

JOURNAL OF CHEMICAL INFORMATION AND MODELING(2021)

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Abstract
The misfolding and aggregation of alpha-synuclein (alpha-syn) in Lewy bodies are implicated in the pathogenesis of various neurodegenerative disorders, such as Parkinson's disease and dementia. The formation of alpha-syn fibrils is a complex process, involving various intermediates and oligomeric forms. These intermediates establish at an early stage of aggregation and subsequently lead to fibrillation. Determining which conformations are accessible to monomeric alpha-syn and especially, as shown in a recent work, to the central amino acids from residue 35 to residue 97 (63 residues) is thus crucial to understand the formation of these oligomers. Here, we carry out extensive replica exchange molecular dynamics (total time-18 mu s) with an all-atom model and explicit solvent to characterize the free-energy landscape of human alpha-syn (residue 35 to residue 97). The simulation results lead us to identify two free-energy basins. Clustering analysis for the deepest free-energy minimum reveals a compact structure, with a secondary structure predominantly alpha-helix, while the shallower minimum corresponds to an elongated conformation, also predominantly alpha-helix. Furthermore, at physiological temperature, we find that conformational rearrangements happen via helix breaks due to the presence of glycine. We also show that the most likely conformations are characterized by the a-helix structure rather than the beta-hairpin structure (for residue 38 to residue 53), in contrast with prior simulation studies using coarse-grained models or an implicit solvent. For higher temperatures, we observe a shift in secondary structure with a decrease in the population of alpha-helix in favor of random coils, beta-bend, and beta-turns.
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free-energy
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