Molecular Simulation Study On The Misfolding And Aggregation Of α-synuclein Under The Effects Of External Factors And Small Molecules

α-synuclein(α-Syn)is an internally disordered protein expressed at presynaptic and perinuclear sites in the central nervous system.The misfolding and aggregation ofα-Syn is closely related to the occurrence of some neuro-degenerative diseases,such as Parkinson’s diseases,multiple system atrophy and dementia with Lewy bodies.Therefore,it is of great value to explore the aggregation mechanism of α-Syn in different conditions and the inhibition mechanism of inhibitors for understanding the pathogenesis of the disease and the development of therapeutic drugs.However,it is difficult to reveal the detailed process and molecular mechanism of the conformational transition of protein by traditional experimental methods.By contrast,molecular dynamics simulation methods have obvious advantages in studying these problems.In this thesis,we investigated the effects of external factors and small molecules on the misfolding and aggregation of α-Syn by conventional molecular dynamics simulation and enhance sampling molecular dynamics simulation.Moreover,a variety of trajectory analysis methods were also applied.This thesis mainly includes the following three parts:In the first part,we investigated the effects of α-Syn fibrils polymorphism on the dissociation mechanism of the boundary chains and the misfolding mechanism of monomers.α-Syn fibrils are polymorphic,exhibiting different misfolded structures under different environments.To explore how different misfolding structures form,here,we compared the dissociation processes of the boundary chains in three different α-Syn fibrils by steered molecular dynamics simulation,which included α-Syn fibrils isolated from diseased human brain(human brain system),generated by in vitro cofactor-tau induction(cofactor-tau system)and obtained by in vitro cofactor-free induction(cofactor-free system).The results showed that the dissociation paths of boundary chains in the three systems were different.According to the reverse process of dissociation,we concluded that in diseased human brain system,the binding of monomer and template started from C-terminal,and gradually misfolded toward the Nterminal.In cofactor-tau system,the monomer binding started from residues 58-66,followed by the C-terminal coil(residues 67-79).Then the N-terminal coil(residues36-41)and residues 50-57 bound to the template,and finally residues 42-49.In the cofactor-free system,two misfolding paths were found.One was that the monomer bound to N/C-terminal and then bound to the remaining residues.The other one was that the monomer bound sequentially from the C-terminal to N-terminal.Furthermore,in the diseased human brain and cofactor-tau systems,electrostatic interactions(especially residues 58-66)were the main driving force during misfolding processes,whereas in the cofactor-free system,the contributions of electrostatic and van der Waals interactions were comparable.In the second part,we explored the mechanism of misfolding of Tau monomer induced by α-Syn aggregates.The first part in this thesis have showed that Tau protein could affect the aggregation of α-Syn.Furthermore,some studies find that α-Syn can also affect the aggregation of Tau,and there are cross-seeding between the two proteins.Therefore,in order to study the misfolding mechanism under cross-induction,we indicated the misfolding mechanism of Tau monomer induced by α-Syn aggregates through a 2μs conventional molecular dynamics simulation combined with Markov state model.The results showed that α-Syn aggregates could induce R2 and R3 to form structures which are more conducive to aggregation.Besides,the degree was that R3 was stronger than R2.And R3 mainly formed β-sheet structures.Moreover,the main residues during the interaction between α-Syn and R3 were A56-V66 of α-Syn and the C-terminal residues of R3: N327,H329,and K331.The misfolding mechanism of R3 was firstly elongation and then the formation of β-sheet structures.The third part is the study of the molecular mechanism of depolymerization of α-Syn aggregates by natural polyphenols.Polyphenols have been demonstrated to inhibit aggregation of α-Syn at the experimental level.In order to further explain the inhibition mechanism of these molecules,a 500 ns conventional molecular dynamics simulation was performed to compare the inhibition mechanisms of multiple natural polyphenols(Baicalein,EGCG,Dihydromyricetin and Scutellarin)on aggregation of α-Syn.The results suggested that Baicalein and EGCG had common depolymerization mechanisms.Both of them affected C-terminal of α-Syn aggregates and formed hydrogen bond interactions with D98.However,Dihydromyricetin and Scutellarin mainly affected the region where residues 54-58 are located in α-Syn aggregates.Moreover,there were also differences in the locations where the hydroxyl groups(-OH)of the four small molecules exert the hydrogen bond interactions.In summary,all four small molecules could reduce the β-sheet content of α-Syn aggregates to achieve depolymerization,but the depolymerization mechanisms were not the same.In summary,the thesis has elucidated the effects of external factors and small molecules on the misfolding and aggregation of α-Syn at the atomic level,which is helpful to understand the pathogenesis of the neurodegenerative diseases and provide theoretical guidance for the rational design of new small molecular compounds that inhibit protein aggregation.