Compact units in proteins.
Compact units in proteins.
复制标题
DOI：
10.1021/bi00367a062
复制
发表时间：
1986-09
期刊：
影响因子：
2.9
通讯作者：
Michael H. Zehfus;George D. Rose
中科院分区：
文献类型：
--
作者：
Michael H. Zehfus;George D. Rose
引入了几何紧度的显式度量，称为紧度系数。这个单值的优点图确定了多肽链的那些连续片段，它们的体积具有最小的溶剂可接近的表面积。这些片段是蛋白质最紧密的单位，较大的片段对应于传统的蛋白质结构域。为了证明这种方法作为一种鉴定蛋白质结构域的方法的合理性，该措施被应用于溶菌酶和核糖核酸酶，以发现它们的组成紧密单位。然后将这些单元与其他方法找到的域、子域和模块进行比较。为了显示该方法的灵敏度，该方法被用于成功区分天然和故意错误折叠的蛋白质[Novotný， J., Bruccoleri， R., & Karplus， M. (1984) J. Mol. Biol. 177, 787-818]。仅利用主链原子来定义结构域的方法无法区分真实的和错误折叠的分子，因为它们的主链构象实际上是重叠的。用这种方法确定的紧凑单元表现出层次结构。这样的组织暗示了可能的折叠途径，可以通过实验进行测试。
An explicit measure of geometric compactness called the coefficient of compactness is introduced. This single value figure of merit identifies those continuous segments of the polypeptide chain having the smallest solvent-accessible surface area for their volume. These segments are the most compact units of the protein, and the larger ones correspond to conventional protein domains. To demonstrate the plausibility of this approach as a method of identifying protein domains, the measure is applied to lysozyme and ribonuclease to discover their constituent compact units. These units are then compared with domains, subdomains, and modules found by other methods. To show the sensitivity of the method, the measure is used to successfully differentiate between native and deliberately misfolded proteins [Novotný, J., Bruccoleri, R., & Karplus, M. (1984) J. Mol. Biol. 177, 787-818]. Methods that utilize only backbone atoms to define domains cannot distinguish between authentic and misfolded molecules because their backbone conformations are virtually superimposable. Compact units identified by this method exhibit a hierarchic organization. Such an organization suggests possible folding pathways that can be tested experimentally.