| Parkinson’s disease is a second-ranked neurodegenerative disease,compared to Alzheimer’s disease,which incidence is as high as 2 percent in people older than 65.Parkinsonian motor symptoms include bradykinesia,muscular rigidity and resting tremor,while non-motor ones include olfactory dysfunction,cognitive impairment,psychiatric symptoms and autonomic dysfunction.Microscopically,the specific degeneration of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies,which are brain deposits containing a substantial amount of ?-synuclein,have been recognized.It is the main pathological process of Parkinson’s disease that misfolding and aggregation of α-synuclein to form oligomers and fibrils.Due to the rapid and small time scale of its biochemical processes,it is difficult to reveal the pathological process of misfolding and aggregation in experimental studies.Molecular dynamics(MD)simulation can provide detailed structural dynamics information to study protein misfolding and aggregation as well as the pathological mechanism of related diseases.In this paper,we applied molecular dynamics simulation to studying the misfolding and aggregation mechanism of α-synuclein and the inhibitory mechanism of small molecule inhibitors,providing theoretical support for further elucidation of the pathogenesis of Parkinson’s disease and rational new drug design.In the first chapter,we summarized the pathogenesis of Parkinson’s disease,current diagnostic and therapeutic strategies,and the structure and function of α-synuclein and introduced the research progress of molecular dynamics simulation of α-synuclein,as well as the molecular dynamics simulation methods and principles methods.In the following four chapters,we explored the aggregation mechanism of α-synuclein and the inhibition mechanism of corresponding small molecule inhibitors from different structural levels.1)Peptide ?-syn47-56 is the toxic core of ?-synuclein and plays a key role in the process of aggregation and misfolding of a-synuclein.The template induction study of this peptide can reveal the molecular mechanism of a-synuclein misfolding and aggregation.Therefore,to reward the molecular mechanism of the peptide ?-syn47-56 under the guidance of pentamer template of ?-synuclein,we performed a molecular dynamics simulation of 400 ns by placing the peptide ?-syn47-56 on both sides of the ?-synuclein pentamers in Chapter 2.It was found that there are different elongation characteristics on both sides of the pentamer in the peptide ?-syn47-56.The ?-sheet structure was easily formed on the left side of the ?-synuclein pentamer to complete template induction while it is hard to get a ?-sheet secondary structure on the right side of the ?-synuclein pentamer.In addition,we also found that hydrogen bonding,electrostatic interaction and van der Waals force between ?-synuclein pentamer and monomer play important roles in ?-sheet extension.2)SNCA single gene mutation is an important cause of familial Parkinson’s disease.Many experimental studies have shown that mutations E46 K and H50 Q can promote ?-synuclein fibrosis to form amyloid plaques.However,its specific molecular mechanism has not yet been revealed.Therefore,Accelerated Molecular Dynamics(AMD)simulation of 500 ns for structural stability of wild-type and mutant E46 K and H50 Q of ?-synuclein pentamer was conducted.The results showed that mutant E46 K significantly changed the interchain interaction pattern of ?-synuclein pentamer,and solvation could play an important role in maintaining interchain stability.In addition,E46 K mutation can maintain the interchain skeleton hydrogen bond well and thus maintain the ?-sheet secondary structure of the side chain,and the degree of order is increased compared with the wild type.However,for the mutation of H50 Q,the binding free energy was confused,the degree of order was significantly reduced,the skeleton hydrogen bond between the chains almost completely disappeared,and the structural stability was reduced.Therefore,we believe that the pathogenesis of E46 K mutation is different from that of H50 Q mutation.E46 K mutation can change the interaction between chains and the structural tendency of adjacent residues and improve the aggregate stability.However,the pathogenesis of H50 Q mutation may not be related to the misfolding and aggregation process of a-synuclein.In addition,the secondary structural stability of ?-sheet at ?-syn49-55 plays an important role in the overall structural stability of ?-synuclein aggregates,and the discovery of this key folded peptide can provide theoretical support for the research and development of new therapeutic strategies for ?-synuclein.3)The ?-synuclein side chain dissociation process is the reverse of this elongation process.Therefore,in chapter 4,we simulated the Steered Molecular Dynamics(SMD)of the depolymerization process of the side chain of the ?-synuclein pentamer.We studied the dissociation of the side chain of the ?-synuclein pentamer(residue from 44 to 97)and found that hydrophobic interaction plays an important role in the depolymerization of ?-synuclein.Therefore,the corresponding van der Waals interaction is the main driver of ?-synuclein aggregation.In addition,the depolymerization process of ?-synuclein can be divided into four steps: 1.Depolymerization of peptide ?-syn44-55;2.Depolymerization of peptide ?-syn63-66;3.Depolymerization of peptide ?-syn70-79;4.Depolymerization of peptide ?-syn82-97.The peptide ?-syn63-66 is the most difficult one to depolymerize,so it is the key peptide of depolymerization and the corresponding key peptide of ?-synuclein aggregation.4)Inhibition of protein oligomer formation and aggregation by small molecule compounds maybe an effective way to treat Parkinson’s disease.Among these inhibitors,(-)-epigallocatechin-3-gallate(EGCG)is a bioactive compound in green tea that inhibits the fibrosis of a series of amyloid polypeptides,such as ?-synuclein,? amyloid(A?)and international association for preventive pediatrics(IAPP).In order to explore the molecular mechanism of EGCG inhibiting a-synuclein aggregation,in chapter 5,we performed molecular dynamics simulation of the effect of EGCG on ?-synuclein fibers.We took two different sizes of ?-synuclein fibers including ?-synuclein pentamer and ?-synuclein decamerer as our aggregates models.The results showed that EGCG can reduce the structural stability of ?-synuclein fibers and convert the ordered structure into disordered structure.In addition,three possible binding sites of EGCG at the interface of ?-synuclein fibers were identified.After a detailed analysis of the binding mode,it is determined that S1 and S3 are the most likely binding sites with different remodeling mechanisms.In other words,EGCG binds to ?-synuclein fibers and changes the structure by breaking the ?-sheet secondary structure and intramolecular hydrogen bonds to destroy the Greek structure.In addition,EGCG is bound to ?-synuclein fibers by hydrophobic interactions and hydrogen bond interactions.Finally,these residues: ASP 98,LYS 96,GLU 61,LYS 58 and THR 64 play important roles in EGCG binding.The molecular mechanisms revealed by our work will help to understand how EGCG remodels the structure of mature fibers and provide valuable information for the discovery and design of potential inhibitors of ?-synuclein aggregates. |
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