Molecular Dynamics Simulations For The Site Mutant In NBD Of Protein Ssa1 And The Cycle Of ATPase

Ssa1 protein is an important member of the family of Heat shock protein 70 (Hsp70), it is mainly distributed in yeast cells and play a role of molecular chaperone, it can help the right folding of new protein and repair the misfolding protein, it is also can disaggregation the complex folding aggregated proteins and manage the activity of regulatory proteins, and help the proteins translocation from the organelles and across the cell membrane. Therefore, Ssa1 protein in yeast cell is the core of the protein homeostasis network and the study of the structure and function of Ssa1 has great significance and value. In a cell, many new protein folding is dependent on the function of molecular chaperone, which can prevent the cytoplasmic protein misfolding and aggregation in the crowded environment, a large number of studies have shown that molecular chaperone in the cytoplasm, especially the members of the Hsp70 family, can be applied to repair the misfolded proteins and the aggregates formation of them. So they are very useful to the neurodegenerative diseases which caused by amyloid protein accumulation and protect the cell to resist the pressure environment, such as Alzheimer’s and Huntington’s disease, the Parkinson’s disease and the strong survival ability of cancer cells.But in the experiments, there are some various problems in the directly research in the Hsp70 disease in human body. Because of Hsp70 protein family are very conservative, the research of Hsp70 often take the eukaryotes yeast cells as an alternative research materials for the study of human Hsp70. The study of Hsp70 protein Ssa1 in the yeast cytoplasm are very mature and convenient, so through the research of Ssa1, it is very useful for the research of Hsp70 protein in the human body, the relationship between molecular chaperone and amyloid disease, in a word, the study has very important referential significance for the regulation and mechanism of human Hsp70.This study start from the genetics experiments of yeast Hsp70 (Ssa1) of Jones and Masison et al that the positive site mutant A17V, R23H, G32D, G32S, R34K in NBD of Ssa1 damaged the breeding of yeast prions [PSI+], and the negative site mutant V372I in NBD of Ssa1 recovered the breeding of yeast prions [PSI+]. The reasons for this change is still not clear, because of the ATPase cycle in NBD is the major cause of the control function of Hsp70 protein, and the release of ADP is the limiting step of it, so the genetic experimental results of yeast may be influenced by its ATPase cycle, and the study take the ways of molecular dynamics simulation to study it. First, it is homology modeling to build the ADP-NBD initial model containing the small molecules and the other mutant model, to study the molecular mechanisms and reasons for such changes in the NBD of yeast Hsp70 protein; then use the same method to argument if other site mutant in NBD of Ssa1 is conform to the mechanism; at the last, it is homology modeling to build the ATP-NBD initial model containing the small molecules and the other mutant model, to further study the effect of the site mutant in NBD for the ATPase cycle, to look for and explain the mechanism that the site mutant in NBD of Hsp70 affect the ATPase cycle.Study found that in the ADP binding state, the site mutant in NBD of Ssa1 mainly affect the ATPase cycle through the hydrophobic interaction between NBD and ADP, the residue Tyr13, Cys15 of Loop1 (7-16), the residue Lys268, Arg269 of a-Helix8 (255-273), the residue Gly336, Ser337, Arg339, Ile340 of Loop23 (335-341) and the residue Asp363 of a-Helixll (361-375) is the most important interaction residues in this interaction. And this regulation is also found in other site mutant in NBD of Ssa1, such as the T36A and T36E model. In addition, the further study of site mutant in NBD of Ssa1 that containing the ATP how to affect the ATPase cycle, it is found that in the ATP binding state, the electrostatic interaction between NBD and ATP increases greatly, the electrostatic interaction becomes the main interaction between NBD and ATP, which about 1-2 times than the hydrophobic interaction. The main interaction residue is Gly10, Thrll, Thr12, Tyr13, Cys15 of Loopl (7-16), the residue Lys69 of a-Helix2 (68-75), the residue Gly198, Gly199, Gly200 of Loop16 (198-201), the residue Lys268, Arg269, Ser272 of a-Helix8 (255-273), the residue Gly336, Ser337, Arg339, Ile340 of Loop23 (335-341) and the residue Asp363 of a-Helix11 (361-375).