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Theoretical Research on Protein Folding Problem by the island Model

岛模型对蛋白质折叠问题的理论研究

基本信息

批准号：
10680644
负责人：
KOBAYASHI Yukio
金额：
$ 0.96万
依托单位：
Soka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
1998
资助国家：
日本
起止时间：
1998 至 1999
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-10680644/
关键词：
island model protein structure prediction secondary structure tertiary structure prion

项目摘要

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.

我通过岛模型模拟了朊病毒蛋白的折叠过程，以阐明从PrPィイD1cィエD1到PrPィイD1ScエD1的转变。 PrP 的 NMR 结构包含两个 β 链和三个 α 螺旋。 β 链的存在与 PrPィイD1cィD1 全螺旋结构的模型预测相反。目前的问题如下：（1）两个β-链和三个α-螺旋的堆积模拟，（2）改进蛋白质二级结构预测的统计力学方法，以预测PrP的初始二级结构。我们之前的工作表明，只要已知二级结构的位置，就可以预测多种蛋白质的三级结构。然而，PrP 的堆积模拟并未产生与 NMR 结构相似的三级结构。这表明β链的存在可能对于从PrPィイD1cィエD1到PrPィイD1ScィエD1的转变的启动很重要。为了通过我们的统计力学方法预测蛋白质二级结构，α-螺旋和β-链中残基对的统计权重是必要的。然而，这些参数尚未得到适当的优化，因此用于估计的蛋白质的预测结果仅达到68%的准确度，这可能不足以将二级结构包装成正确的三级结构。改进正在进行中。