Molecular Dynamics Simulation Studies On The Conformational Transition Of Prion Protein And Regulation Of Antiprion Inhibitors On Its Conformational Transition

Prion diseases are fatal neurodegenerative diseases of humans and animials which caused by the misfolding and aggregation of prion protein?PrP?.Former studies indicate that the conformational transition from the cellular prion protein?PrP^C?into the pathological form of PrP^Scc is closely related to the cytotoxicity of PrP.Moreover,the pathological form of PrP^Sc is known to be infectious and protease-resistant,as thus,the conformational conversion from PrP^C into PrP^Sc is believed to be the key event in the infection of prion disease.Therefore,studying the mechanism of conformational transition of PrP is of much importance for us to understand the pathogenesis of prion disease and to seek the potential effecitive drug therapy.In the exploration of conformational transition mechanism of PrP^C,it is very hard to capture the detailed structural change of PrP by the conventional experimental method due to the rapid conformational transition of PrP^C?PrP^Sc.In comparison,as a supplementary method,it is very convenient for the molecular dynamics?MD?simulation to provide the structural change of protein at atomic level.With the advantages,the MD simulations have been largely applied to the mechanism studies of PrP misfolding and aggregation.In this work,combing MD simulation and several analysis methods,we have investigated the structural transition mechanism of PrP misfolding and the potential stabilization mechanism of antiprion melcules to regulate the PrP^C conformation.Recent studies indicated that the novel protective G127V mutation of PrP is intrinsically resistant to the propagation of Kuru and Creutzfeld-Jakob disease.As thus,to unravel the potential protective molecular mechanism of the G127V mutation on prion disease propagation is significant importance,which may provide valuable theoretical and applied guidance for the effective treatment of prion disease.Therefore,by using MD simulation,we first explored the influences of the protective G127V mutation of PrP on two key processes during the prion propagation,including dimerization and fibril formation to study its protective mechanism at molecular level.Our obtained results indicate that V127 variant of PrP is unfavorable to form dimer by reducing the main-chain hydrogen-bond interactions.Moreover,simulations on formed fibrils consisting of?1 strand prove that V127 variant decreases the stability of the formed fibrils and disrupt the order of it,this result mainly reflects on two aspects:?a?reducing the binding free energy between fibril layers,especially the van der Waals interation for layer stacking;?b?deacrease the hydrogen-bond interactions in the same layer.This study can deepen the understanding of prion propagation and may guide the design of peptide mimetics or small molecule to mimic the protective effect of V127 variant.Then,using the fragment 127-147 of PrP?PrP127-147?as a simplified model,we studied the conformational change of this fragment that could be relevant to the PrP^C?PrP^Sc transition by combing MD simulation and Markov state model?MSM?.The fragment PrP127-147 has been previously reported to be a critical region for PrP^Sc formation in Gerstmann-Straussler-Scheinker?GSS?syndrome,and has the similar properties as the full-length prion.Thus,PrP127-147 can serve as a simplified model of full-length prion.The resulting MSM reveals the PrP127-147monomer is likely to adopt the disordered coil and turn structures.Additionally,a key metastable folded state with typical extended?-sheet structure is identified with Pro137 being located in a turn region.Further conformational analysis suggests that intrapeptide hydrophobic interaction and key residue interaction Arg136–His140 and Pro137–His140,contribute a lot to the formation of the key metastable state.Meanwhile,from the disordered states,there are heterogeneous folding pathways can lead to the formation of the extended?-sheet states,however,the formation timescale is quite long?at the millisecond level?which may attribute to the large structural rearrangement.The results of our study provide insights into the molecular details of the early stage of prion aggregation.Later,we have investigated the pH-induced misfolding mechanism of PrP90-231.Experiment results have been reported that the acidic environment can promote the structural transition of PrP and trigger its misfolding,however,the pH-induced misfolding mechanism of PrP remains unclear.In this chapter,we then investigated the pH-induced PrP misfolding mechanism of PrP90-231 by performing microsecond simulation at acidic condition with the accelerated molecular dynamics simulation?AMD?together with MSM analysis.We found that at an acidic pH,the globular domain of PrP is partially unfolded,particularly the?2 C-terminus.Structural characterization of the key intermediate states obtained by MSM indicates that the C-terminal of the?2 C-terminus and?2-?2 loop may serve as initiating sites for the early PrP misfolding.Moreover,considering the large equilibrium probability of main macrostates,we conclude that the partially unfolding structures are the main misfolded states.The dynamical network analysis suggesting that the protonated H187 weakens the interactions between the?2C-terminus,?1-?2 loop,and?2-?3 loop,leading these domains especially the?2 C-terminus become unstable and begin to misfold.Therefore,the?2 C-terminus plays a key role in the early PrP misfolding process and serves as a potential drug targeting site.Finally,based on the MD simulation,we explored the specific stabilization mechanism of antiprion molecules on the native PrP^C.Presently,among the strategies of antiprion drug designing,specific stabilizing the native conformation of PrP^C is believed to be the relatively safe approach.Investigating the specific bingding and stabilization mechanism of antiprion compounds is valuable for the further design and discovery of new antiprion inhibitors.Therefore,in the last chapter of this thesis,we investigated the stabilizing mechanism of several antiprion compounds on PrP^C that were previously reported to have specific binding to the“hot spot”region of PrP^C.We found that the stabilization mechamism of our studied compounds can be classified into three categories:?a?to stabilize both the flexible C-terminal of?2 and the hydrophobic core;?b?to strongly stabilize the hydrophobic core;?c?to stabilize the overall structure of PrP^C by high binding affinity.Additionally,the residues N159 and Q160 play an important role in the specific binding of the studied Antiprion molecules.We also found that despite the different structure of studied compounds,they interct with residues of PrP^C in a similar way,including L130 in the?1strand,P158,N159,Q160 in the?1-?1 loop and H187,T190,T191 in the?2 C-terminus.As a whole,our obtained result may provide valuable guidance for the design of effective Antiprion drugs or modify the present antiprion molecules in the future.