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 transitionfrom PrP - D1c - D1 to PrP - D1Sc - D1. The NMR structure of PrP contains two β-strands and threeα-helices. The presence of β-strands is in contrast with model predictions of an all-helicalPrP structure of PrP D1c . The present problems are as follows：the packing simulation of two β-strands and three α-helices，(2) the improvement of our statistical mechamical method for protein secondary structure predictionto predict the initial secondary structures of PrP.Our previous works showed that the tertiary结构的several proteins可以预测预测the positions of secondary结构are known. The packing simulation of PrP, howeverdid not yield the tertiary structure similar to the NMR structure. This indicates that the presenceβ-strands may be important for the initiation of the transition from PrP d - 1c toPrP - 1 - 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，however,have not optimized properly, thus the prediction results of proteins for estimation havereached the accuracy of only 68%，它可能不会sufficient for packing secondary structures into the correct tertiary structure。improvement is in progress。

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.