Molecular Dynamics Simulations On Structure And Function Of The Saccharomyces Cerevisiae Ssa1 N-terminal Domain

Amyloid diseases are a class of neurological diseases,its pathogenesis has a commoc characterized that misfolded proteins cause the formation of amyloid fibril protein.Previous studies have shown that molecular chaperones have assisted other protein correct folding and degradated abnormal protein,and molecular chaperones is critical regulator of amyloid diseases and potential cures target.Hsp70 is an important type of molecular chaperone,and directly involved in correct protein folding and abnormal protein degradating.And it has an important influence to form the amyloid protein.Numerous studies found that yeast cytoplasmic matrix Hsp70 mutants of yeast prion[PSI+]proliferation with varying degrees of influence.But just from yeast genetics to study and experiment with these mutant proteins Hsp70 dapage[PSI+]adjustment mechanism is not comprehensive,not well explained the unique relationship between the mutant Hsp70 conformational change and function,so the current regulation of Hsp70 amyloid formation mechanism is not well described.To better described the mechanism of yeast cytoplasmic Hsp70 damage proliferation of yeast prions,thus adjusting the mechanism to Hsp70 amyloid gradual expansion in the present study,we first used E.coli Hsp70 DnaK as based model by molecular dynamics learning simulation method for the molecular chaperone Hsp70 NBD mutant ATP activity area causing a conformational change and functional relationships exploratory research.The results showed that the apo state DnaK mutants DnaKA17v,DnaKT23H,DnaKG32S(homologous Ssal mutant SsalA17V,SsalR23H,Ssalc32S)through the influence loopl in the ATP binding pocket(the first corner,connecting β1 and(32)changes in the structure of the hydrogen bond network area,enhancing the flexiblility in the loopl region Three-dimensional structure,causing significant residues T11 hydroxyl side chains easier and y-phosphate group to ATP.Explains the reasons that Ssal NBD different point mutations damage[PSI+]proliferation from the three-dimensional structure of the protein.In order to further improve the lack of subsequent experiments and further validate these conclusions through homology modeling method was successfully constructed Ssal NBD structural model with a small molecule ADP*Pi,and conducted a series of mutant MD simulations,to further study the impact on Ssal NBD conformation and function because of drefferent point mutations.The results show that:(1)the positive mutations(SsalA17V,SsalR23H,SsalG32D,SsalG32S and SsalR34K)enhance the stability of the ADP by enhancing the interaction of ADP hydrogen bonding and hydrophobic with the Ssal NBD,thus affecting the ATPase cycle,damage[PSI+]proliferation,the negative models SsalV372I will weaken the interaction of ADP hydrogen bonding and hydrophobic with the Ssal NBD.(2)catastrophe model SsalA17V,SsalR23H,SsalG32D,SsalR34K enhanced stabilizing effect of ADP is ADP phosphorylated and ADP nucleoside part,synergistic conducted while the model SsalG32S mainly through enhanced adp nucleoside enhance the ADP stability,and the hydrogen enhanced obvious,to some extent confirmed our Ssal NBD SsalG32S mutants in apo state characteristic.Finally,in this paper we study the cross-domain signal transmission by study the conservative Inter-Domain linker in Ssal,mainly focused on the Inter-Domain linker binding or not the function of Ssal and conformation of the relationship.We study the ssal NBD binding Inter-Domain linker and not binding Inter-Domain linker respectively in ATP state,and use the ways of molecular dynamics simulations and double-template modeling..The results showed that:(1)Inter-Domain linker Ssal NBD binding protein can enhance the stability of the small molecule substrates ATP,while promoting the importance of ATP hydrolysis to form hydrogen bonds Lys69-γPi;(2)Inter-Domain linker can combine Ssal NBD the stability of hydrophobic amino acids Arg169 and adjacent auxiliary chaperone Hsp40 plays an important role in the docking studies further found Inter-Domain linker binding Ssal NBD Hsp40 binding pair can be enhanced,but also has been reported with the experimental protein structure close.In this paper,molecular dynamics simulation study conclusions from protein conformation further complements previous genetic test and biochemical tests reported Ssal NBD mutant prejudice[PSI+]ability to breed,while further from the molecular level elaborated Ssal NBD mutant conformation changes in the relationship and function.This cycle is adjusted to enhance binding Hsp70 SBD peptide substrate can weaken[PSI+]propagation theory provides further support.In addition,our study also reflects how the molecular dynamics simulations and docking analysis as an effective analytical tool to speculate and verified to weaken[PSI+]proliferation of Hsp70 NBD mutants mechanisms within the cell.In the same time,because Hsp70 is highly conserved family and consistency.The results of this paper study can be selectively used to explore other types of amyloid diseases,and to further study relational mechanisms.