Rules for connectivity of secondary structure elements in protein: Two-layer αβ sandwiches
Rules for connectivity of secondary structure elements in protein: Two-layer αβ sandwiches
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DOI：
10.1002/pro.3285
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发表时间：
2017-11-01
期刊：
影响因子：
8
通讯作者：
Ota, Motonori
中科院分区：
文献类型：
--
作者：
Minami, Shintaro;Chikenji, George;Ota, Motonori
在蛋白质结构中，折叠是根据二级结构元件（SSE：α-螺旋和α-链）的空间排列及其连接性来描述的。SSE之间的连接或连接模式是理解蛋白质折叠多样性的最重要因素之一。在这项研究中，我们介绍了连接字符串编码的连接性，通过使用类型，位置和连接的SSE，并计算列举了所有的连接性的两层α-β三明治。计算出的连接性进行了比较，在天然蛋白质中使用MICAN，非序列结构比较方法确定。对于2 alpha-4 beta，在所有连通性中的23，000个中，只有48个没有不规则的连通性，例如循环交叉。其中，只有20个是在天然蛋白质中发现的，并且超家族偏向于某些类型的连接性。一个类似的不成比例的分布被确认为大多数其他空间安排的SSE在两层的α-β三明治。我们发现了两个连接规则，很好地解释了偏见：在不同的层中桥接SSE的层间连接环的丰度;和非局部β链对，两个空间相邻的β链位于氨基酸序列中的不连续位置。这两个属性的二维图表明，这两个连接规则不是独立的，这可以解释为蛋白质的协同性的规则。
In protein structures, the fold is described according to the spatial arrangement of secondary structure elements (SSEs: alpha-helices and alpha-strands) and their connectivity. The connectivity or the pattern of links among SSEs is one of the most important factors for understanding the variety of protein folds. In this study, we introduced the connectivity strings that encode the connectivities by using the types, positions, and connections of SSEs, and computationally enumerated all the connectivities of two-layer alpha beta sandwiches. The calculated connectivities were compared with those in natural proteins determined using MICAN, a nonsequential structure comparison method. For 2 alpha-4 beta, among 23,000 of all connectivities, only 48 were free from irregular connectivities such as loop crossing. Of these, only 20 were found in natural proteins and the superfamilies were biased toward certain types of connectivities. A similar disproportional distribution was confirmed for most of other spatial arrangements of SSEs in the two-layer alpha beta sandwiches. We found two connectivity rules that explain the bias well: the abundances of interlayer connecting loops that bridge SSEs in the distinct layers; and nonlocal beta-strand pairs, two spatially adjacent beta-strands located at discontinuous positions in the amino acid sequence. A two-dimensional plot of these two properties indicated that the two connectivity rules are not independent, which may be interpreted as a rule for the cooperativity of proteins.