Structural determinant of protein designability
Structural determinant of protein designability
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DOI：
10.1103/physrevlett.90.218101
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发表时间：
2003-05-30
影响因子：
8.6
通讯作者：
Shakhnovich, EI
中科院分区：
文献类型：
--
作者：
England, JL;Shakhnovich, EI
本文给出了氨基酸序列空间中蛋白质结构的接触矩阵与其能谱形状之间关系的近似解析理论。我们证明了结构中低能序列的数目与结构接触矩阵的特征值的依赖关系，然后用蒙特卡罗模拟测试了这一分析结果对立方晶格蛋白质的适用性。我们发现，具有最多低能序列的晶格结构与理论预测的结果相同。我们认为，在对可折叠性有足够严格的要求的情况下，这些结构是最可设计的，我们提出了一个简单的方法来测试本文的结果是否适用于真实的蛋白质。
Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of low energy in a structure on the eigenvalues of the structure's contact matrix, and then use a Monte Carlo simulation to test the applicability of this analytical result to cubic lattice proteins. We find that the lattice structures with the most low-energy sequences are the same as those predicted by the theory. We argue that, given sufficiently strict requirements for foldability, these structures are the most designable, and we propose a simple means to test whether the results in this paper hold true for real proteins.