Full-atom Molecular Dynamics Simulations Of Protein Aggregation Molecular Mechanism Of Amino Acid Fragment Of Human Microglobulin

The human neurodegenerative diseases and amyloidosis have aroused public attention in the past few years,and it is supposed that these kinds of disease connect with protein misfolding and aggregation.However,their mechanism and process are not so clear revealed by scientific reports so far.The so-called "amyliodosis" are the series of diseases,including Alzheimer's disease, Parkinson's disease,Huntington's disease,prion disease,Down Syndrom,multiple Myeloma and Chronic Renal Failure etc.The tissue samples of these diseases share the same features under the observation of microscopy,and we can see amyloid fibrils withβ-sheet zipper spine.Usually,the native states of these proteins are soluble in physiological condition,however,the misfolded proteins aggregate to the insoluble amyloid fibrils and cannot be decomposed by enzymes.The humanβ2-microglobulin was verified as a key role of dialysis related amyloidosis.The amyioid fibrils aggregated by insoluble denatured protein damage human tissues and then cause the renal failure and bone/joint complications.Amyloidosis of humanβ2-microglobulin is a severe complication always found in patients who receive long time hemo-dialysis.In recent years,many reports show that two fragments 20-41 and 83-99 in humanβ2-microglobulin play important roles in protein aggregation and amyloid formation.Eisenberg et al.find that the fragments 72-99,83-89 and 91-96 can form amyloid fibrils by themselves in solutions.Moreover,they predict that the fragment 83-99 form a typicalβ-hairpin structure to stack and construct of the spine region of amyloid fibril.Goto et al.find that the K3 peptide can form amyloid fibrils by itself in several different solvent conditions,and use solid state NMR to reveal the 3D structure of K3 fibrils.They propose that the fibril state K3 peptide is with trans Pro32 and the region 20-28 flips over by comparing with native state,the hydrophobic side-chain of Phe22 and Tyr26 are buried inside the double layerβ-sheet.However,the aggregation mechanism and atomic level structures of amyloid fibril are still poorly understood.In this thesis,we perform several series molecular dynamics simulations to study the structures and aggregation mechanism of these two peptides in solution,and try to get more information about amyloid formation process at an atomic level of detail.First,we find that the monomer of fragment 83-99 has strong propensity to adoptβ-strand conformation and formβ-hairpin like topologies,andβ-strand was considered as the element of the amyloid fibril spine.In the dimer simulation of fragment 83-99,we start from random coil conformation and finally get the "intertwinedβ-hairpin" structure.We not only illustrate the key role of the hydrophobic residue side-chain in the C-terminal of peptide,but also reveal the aggregation process of intertwinedβ-hairpin dimer.Based on the result of dimer simulation,we propose a protofibrii model of full-length protein and verify its stability by molecular dynamics simulation.Second,due to the importance of tans or cis-Pro32 in fragment 20-41(K3 peptide) and effect of folding/aggregation both in peptide and full-length protein,we perform replica exchange molecular dynamics simulation on these two isomers,and try to understand the distribution of their conformational space and free energy landscape.We find that most of the structures are random coil both in trans and cis-K3,however,the intermediate state with low percentage of β-strand or PPⅡwould play a crucial role in aggregation process.