Studies on the principle of protein architecture by the simplification of amino acid sequence

从氨基酸序列简化研究蛋白质结构原理

基本信息

批准号：
16370074
负责人：
KATAOKA Mikio
金额：
$ 8.83万
依托单位：
NARA INSTITUTE OF SCIENCE AND TECHNOLOGY
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2004
资助国家：
日本
起止时间：
2004 至 2005
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-16370074/
关键词：
photoactive yellow protein simplification of sequence circular dichroism structure-function relationship amyloid chromoprotein PAS family β scaffold 色素蛋白質

项目摘要

In order to understand the information encoded in an amino-acid sequence, we have created variants of photoactive yellow protein (PYP) with simplified amino-acid sequences. We simplified the amino-acid sequence of PYP using a simple set of rules to reduce overlapping structural information. The simplified PYP protein (sPYP0), which was composed of only nine species of amino acids (Ser,Val,Asp,Lys,Phe,Met,Gly,Pro, and Cys), showed a completely different structure than the native conformation. Even after the evolutionarily conserved residues were restored in the simplified protein (sPYPI), the PYP variant did not properly fold. Additional restorations of the substituted hydrophobic (sPYPII) or hydrophilic residues (sPYPIII) did not lead to a variant that formed the native structure. sPYPIII only shows the tendency of helical formation by TFE. Partial simplification was successfully performed by creating chimeric proteins composed of combinations of wild-type PYP and sPYPIII. Hybrid mutants containing a wild-type β scaffold adopted native-like structures. In contrast, the hybrid mutants that contained the simplified β scaffold demonstrated a tendency to adopt non-native conformations, suggesting that there is a wealth of information about the formation of the structure in the β scaffold. 5 hydrophobic residues in the β scaffold were identified to be responsible for the structure formation. It is also demonstrated that sPYPII takes amyloid-like fibril structure.

为了理解氨基酸序列中编码的信息，我们创建了具有简化氨基酸序列的光敏黄色蛋白（PYP）变体。我们使用一组简单的规则来简化 PYP 的氨基酸序列，以减少重叠。简化的PYP蛋白(sPYP0)仅由9种氨基酸(Ser、Val、Asp、Lys、Phe、Met、Gly、Pro和Cys)组成，显示了完整的结构信息。即使在简化蛋白（sPYPI）中恢复了进化上保守的残基后，PYP 变体也没有正确折叠取代的疏水性（sPYPII）或亲水性残基（sPYPIII）。形成天然结构的变体仅显示出通过TFE形成螺旋的趋势，通过创建由野生型组合组成的嵌合蛋白成功地进行了部分简化。含有野生型β支架的杂交突变体采用了类似天然的结构，相比之下，含有简化β支架的杂交突变体表现出采用非天然构象的倾向，这表明存在大量关于其的信息。 β支架中的结构的形成经鉴定，β支架中的5个疏水残基负责结构的形成。还证明sPYPII具有淀粉样蛋白原纤维结构。