Using Molecular Dynamics Simulations And To Simplify The 83-89 Fragment Of The Protein Model For Human Microglobulin Oligomers Self-assembly Process

More than 20 neurodegenerative diseases are connected with the aggregation of amyloid-forming proteins,including Alzheimer's,Parkinson's diseases,BSE and dialysis amyloidosis.The aggregation of humanβ2-microglobulin(β2m) discussed in this thesis are related to the dialysis disease.In the past 20 years,scientists have known little about the mechanisms and details about the early steps of the protein aggregation,although great efforts have been made,both in experiments and theories. Evidence shows that soluble oligomers of the aggregates might be more cytotoxic than mature fibrils.Research on the early steps of protein aggregation may supply the details about formation of oligomers on the atomic level.The sequence depending influence on the dynamics and structures of aggregation may also be investigated.Although it has been shown that many proteins can aggregate to form amyloid fibrils, the formations and structures of the intermediate states are still unknown.Because the aggregation process of peptides is complex and entropy plays an important role,most of the experimental methods fail to detect the aggregation details in scales of nm and ns.Under this circumstance,computer simulations become an efficient method to investigate the aggregation process.The amyloid fribrils display common properties,including their morphologies, tendency to bind Congo Red and cross-βX-ray diffraction patterns.Attentions of nowadays researchers are paid to several essential aspects:the detailed structures of cross-βcharacteristics,the structures of building blocks,nucleation process of aggregation and amino acids sequence dependence.In this thesis,amyloid-forming segment 83-89 from humanβ2m is studied by molecular dynamics simulations,using coarse-grained model 'Optimized Potential for Efficient peptide structure Prediction' (OPEP).The free energy surfaces of tetramer and heptamer are studied.Early aggregation process of 16mer is also recorded.We focus on the structures of building blocks and nucleation process of the system.The main results are given in the following chapters:1.The tetramer ofβ2-microglobulin(β2m) 83-89 segment is first studied.We select fourβ2m(83-89) peptide chains because only dimer of theβ2m(83-89) has been investigated by computer simulations.Both molecular dynamics and Mont Carlo simulations are performed to monitor the aggregation process.We found that the ordered structures which may lead to the protofibrils have low populations, suggesting that the nucleation may need larger systems.In our simulations,curved monolayer and ring like conformations are found,which are believed to be the intermediate states to larger and more stable structures according to previous experimental and theoretical results.2.In our simulations onβ2m(83-89) heptamer,it is found that larger the system is, more important the hydrophobic interaction becomes.During the heptamer simulations,monolayerβ-sheets are not observed while bilayerβ-sheets become highly populated.A stable hydrophobic core is formed between the two layers ofβ-sheets.β-barrel structure is an interesting discovery during the simulations. Strong hydrophobic interactions exist in the center of the barrel,formed among the non-polar side chain atoms.There might be two pathways to form theβ-barrel structures.One is to add monomers to the curved monolayerβ-sheet.The other is to convert directly from perpendicular bilayerβ-sheet.We propose that theβ-barrel may exist as an intermediate state.3.Considering the high efficiency of MD-OPEP method,we go on with the 16mer of 83-89 segment simulations.In the six 100-ns MD runs,the system can not form well-orderedβ-sheet structures.However,the diversity of the conformations explains the time consuming problem of the aggregation process.4.In sum,by comparing the threeβ2m(83-89) systems containing different numbers of fragments,we investigate the various orderedβ-sheet structures,the primary interactions maintaining these conformations,the building blocks of protofibrils, the interesting intermediate states and the nucleation process.