Molecular Modeling Study Of Conformational Transition Mechanism Of Prion Protein And Peptide Inhibitor Design

Prion diseases,also known as infectious spongiform encephalopathies,are a series of neurodegenerative diseases in general,including mad cow disease and scrapie in animals,and Creutzfeldt-Jakob disease,fatal familial insomnia,Gerstmann syndrome and Kuru in humans.Due to the unclear pathogenic mechanism,there is still no effective treatment for this disease.It has been widely reported that the conformational transition from cellular form prion protein?PrP^C?to pathogenic"scrapie"form prion protein(PrP^Sc)is considered to be a key matter to prion disease.Therefore,it is greatly important to study the conformational transformation mechanism of PrP^C into PrP^Scc in order to deeply understand the pathogenesis of prion disease and find effective treatments for prion disease.Compared to experimental methods,computational molecular dynamics?MD?simulations can show the dynamic conformational transition process of prion protein and its detailed information on changes in structure and energy.In this paper,on the basis of summarizing the research of prion disease pathogenesis,we first explored the effects of acidic conditions and H187R mutation on the prion protein?PrP?misfolding process based on metadynamics simulation and dynamical network analysis.Based on this,we further designed a series of peptide molecules that inhibit the PrP aggregation by molecular simulations.The specific content includes:In the first work,we studied the misfolding mechanism of the prion using metadynamics simulations under acidic and H187R mutation conditions.The?2C-terminus is widely considered to be an important site for the conformational transition of PrP,so it can be used to investigate the potential misfolding mechanism of PrP.In addition,a series of experimental studies have shown that acidic conditions as well as H187R mutation can accelerate the PrP misfolding.Introduction of these two conditions can be used to efficiently study the conformational transition mechanism of PrP.Therefore,in order to gain the possible implications for PrP misfolding related to the conformational properties of?2 C-terminus,metadynamics simulations of 500 ns were performed on the?2 C-terminus of PrP.For comparison,three different systems were designed:neutral system?pH⁷?,acidic system?pH⁵?,and H187R mutation system?pH⁷?.The results of free energy surfaces obtained from metadynamics simulations indicate that acidic conditions and H187R mutation can promote prion misfolding by decreasing the free energy barriers for conformational transitions and forming more stable metastable conformations.Further analysis aimed at?2 C-terminus shows that due to the increase of positive charge of residue 187 in both acidic and H187R systems,the electrostatic repulsion of residue187 and R136/R156 increases largely,which disrupts the electrostatic interaction network around?2 C-terminus and makes the hydrophobic core exposed to the solvent.Taken together,the acidic conditions and H187R mutation can accelerate PrP misfolding mainly by forming more stable metastable conformations with lower free energy barriers,and electrostatic network disruption involving residue 187 drives the initial misfolding of?2 C-terminus.This study provides a quantitative insight into the related function of the?2 C-terminus in the PrP misfolding process,which may guide the?2 C-terminus mediated drug design in the future.In the second work,we designed a series of peptides that are able to inhibit the aggregation of PrP using molecular simulations.The treatment of prion disease has been a difficult problem for researchers all the time.To date,it has been reported that small molecule compounds,antibodies and peptides have good inhibitory effects for prion disease at the experimental level.Among them,peptide is a kind of promising drug due to its advantage of low side effects,low immunogenicity,high specificity,and high success rate of clinical trial.In addition,it has been reported that peptide molecules containing the original sequence in PrP can reverse misfolding and aggregation process of PrP.The reported crystal structures of several PrP^Schave revealed?1-mediated intermolecular sheets,suggesting that the?1 strand may contribute to a possible initiation site for?-sheet mediated PrP^Scc propagation.Therefore,on the basis of the reported?1 strand sequences of PrP structures,we designed 24 initial?-hairpin peptide sequences after the turns and caps added.The three-dimensional structures of these peptides were obtained through the structure prediction by I-TASSER online program.Then,200 ns conventional molecular dynamics simulations were performed to acquire stable structure of peptides,and a series of analysis were performed to monitor the structural change of peptides.Among these,the peptides with superior structural stability were selected for the following Thioflavin T experiment to obtain template peptides that could inhibit PrP aggregation.Overall,our results provide a relatively complete prospect for PrP misfolding from the insight of the structure,thermodynamics and conformational transition properties of the?2 C-terminus in PrP,which are valuable to understand the potential pathogenesis of prion disease and to find effective inhibitors for prion disease in the future by focusing on the?2 C-terminus related functions.In addition,through molecular dynamics simulation method and Thioflavin T screening experiments,it is expected to obtain the peptides with high inhibitory activity for protein aggregation after subsequently structural modification.In conclusion,our research is of great significance in elucidating the pathogenesis of prion disease and discovering inhibitors for prion diseases.