Narita Mitsuaki, Narita Masakuni, Itsuno Yasuko, Itsuno Shinichi
Department of Biotechnology & Life Science, Tokyo University of Agriculture and Technology, Naka-machi 2-24-16, Koganei, Tokyo 183-8588, Japan.
Research Laboratory, Nihon Pharmaceutical Co., Ltd., Shinizumi 34, Narita 286-0825, Japan.
ACS Omega. 2016 Dec 22;1(6):1355-1366. doi: 10.1021/acsomega.6b00206. eCollection 2016 Dec 31.
To the best of our knowledge, this is the first study that shows that the X-ray structures of proteins can be dissected into their continuous folding structure units. Each folding structure unit was designed such that both the terminal di- or tri-peptide sequences shared common sequences with the two adjacent folding structure units. To encode the folding structure information of proteins into their amino acid sequences, we proposed 44 kinds of folding elements, which covered all of the amino acids in the protein chains, and defined all folding structure units. The folding element was defined to mean a minimum structural piece, which covered the frame of the main chain of each amino acid in a protein chain. A folding structure unit of a local sequence could be fully characterized by the sequential combination of individual folding elements assigned to each amino acid. The folding structure information showed amino acid preferences in various positions in folding structure units. Folding structure formation proceeded on the basis of probability theory. Strikingly, relative formation ability analysis clearly indicated that we can decode the types and the chain length of folding structure units from the amino acid sequence of a protein.
据我们所知，这是第一项表明蛋白质的X射线结构可以被分解为其连续折叠结构单元的研究。每个折叠结构单元的设计使得其末端的二肽或三肽序列与两个相邻的折叠结构单元共享共同序列。为了将蛋白质的折叠结构信息编码到其氨基酸序列中，我们提出了44种折叠元件，这些元件覆盖了蛋白质链中的所有氨基酸，并定义了所有的折叠结构单元。折叠元件被定义为一个最小的结构片段，它覆盖了蛋白质链中每个氨基酸主链的框架。局部序列的折叠结构单元可以通过分配给每个氨基酸的单个折叠元件的顺序组合来完全表征。折叠结构信息显示了折叠结构单元中各个位置的氨基酸偏好。折叠结构的形成基于概率论进行。引人注目的是，相对形成能力分析清楚地表明，我们可以从蛋白质的氨基酸序列中解码出折叠结构单元的类型和链长。
