A systematic approach to the comparison of protein structures.
A systematic approach to the comparison of protein structures.
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比较蛋白质结构的系统方法。
DOI：
10.1016/0022-2836(80)90357-5
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发表时间：
1980
影响因子：
5.6
通讯作者：
Brian W. Matthews
中科院分区：
文献类型：
--
作者：
S. Remington;Brian W. Matthews
已经开发了一种比较蛋白质主链构象的系统方法（Remington & Matthews, 1978）。通过依次优化一种蛋白质中所有可能的选定长度片段与另一种蛋白质中所有可能的相同长度片段之间的一致性来比较两种蛋白质。该方法揭示了两种蛋白质之间的任何相似性，并提供了对所获得的任何给定结构协议的统计显著性的估计。该方法已在许多情况下进行了测试，包括脱氢酶和胰腺和细菌丝氨酸蛋白酶的比较。选择这些例子是为了测试比较方法在存在大插入和删除时检测结构相似性的能力。结果表明，脱氢酶中“核苷酸结合折叠”的检测是其原始形式比较技术能力的极限，尽管有可能推广该方法以允许蛋白质中的插入和缺失。总结了用不同探针长度进行的许多蛋白质比较的结果。对于中等和较长的探针长度，结构一致性的平均值不太取决于所比较的蛋白质的类型。结构一致性的平均值随探针长度的平方根而增加，但对于超过40个残基的探针长度，标准差与探针长度无关。从这些观察结果中，可以构造一个广义概率图来评估在比较两种蛋白质时可能获得的任何结构一致性的意义。
A systematic method has been developed for comparing the backbone conformations of proteins (Remington & Matthews, 1978). Two proteins are compared by successively optimizing the agreement between all possible segments of a chosen length from one protein, and all possible segments of the same length from the other protein. The method reveals any similarities between the two proteins, and provides an estimate of the statistical significance of any given structure agreement that is obtained.The method has been tested in a number of cases, including comparisons of the dehydrogenases and of the pancreatic and bacterial serine proteases. These examples were chosen to test the ability of the comparison method to detect structural similarities in the presence of large insertions and deletions. The results suggest that the detection of the “nucleotide binding fold” in the dehydrogenases is at the limit of the capability of the comparison technique in its original form, although it may be possible to generalize the method to allow for insertions and deletions in proteins.The results of many protein comparisons, made with different probe lengths, are summarized. For medium and long probe lengths, the average value of the structural agreement does not depend very much on the type of protein being compared. The average value of the structure agreement increases with the square root of the probe length, but for probe lengths above about 40 residues, the standard deviation is independent of probe length. From these observations it is possible to construct a generalized probability diagram to evaluate the significance of any structure agreement that might be obtained in comparing two proteins.