Theoretical Research on Protein Folding Problem by the island Model

I simulated the folding process of prion protein by the island model to elucidate the transition from PrPイD1 cイD1 to PrPイD1 ScイD1。PrP的NMR结构包括两条β-链和三条α-螺旋。使用模型预测的存在与模型的存在。当前的问题是如下的： （1）对两个β-strands和三个α-helices的封装模拟， （2）对我们的统计机械方法的改进，以预测蛋白质二级结构的初始二级结构的初始二级结构，我们展示了我们先前的工作，即几种蛋白质的三种结构可以预先提供已知的位置。PrP的包装模拟，如何，并没有将第三结构与核磁共振结构类似。This indicates that the presence of β-strands may be important for the initiation of the transition from PrP-D1c-D1到PrP-D1Sc-D1.To predict protein secondary structures by our statistical Mechanical method， the statistical weights of residue pairs in α-helix and β-strand are necessary。这些参数、方法、它们并没有被优化的特性，因此，蛋白质的预测结果估计达到了仅68%的准确性，而在正确的第三级结构中包装二级结构是不可行的。改进正在进行中。

I simulated the folding process of prion protein by the island model to elucidate the transition from PrPィイD1cィエD1 to PrPィイD1ScィエD1. The NMR structure of PrP contains two β-strands and three α-helices. The presence of β-strands is in contrast with model predictions of an all-helical structure of PrPィイD1cィエD1. The present problems are as follows : (1) the packing simulation of two β-strands and three α-helices, (2) the improvement of our statistical mechamical method for protein secondary structure prediction to predict the initial secondary structures of PrP.Our previous works showed that the tertiary structures of several proteins can be predicted provided that the positions of secondary structures are known. The packing simulation of PrP, however, did not yield the tertiary structure similar to the NMR structure. This indicates that the presence of β-strands may be important for the initiation of the transition from PrPィイD1cィエD1 to PrPィイD1ScィエD1.To predict protein secondary structures by our statistical mechanical method, the statistical weights of residue pairs in α-helix and β-strand are necessary. These parameters, however, have not been optimized properly and thus the prediction results of proteins for estimation have reached the accuracy of only 68%, which may not be sufficient for packing secondary structures into the correct tertiary structure. The improvement is in progress.