ENZYME SPECIFICITY USING NORMAL MODE ANALYSIS

我们计算正常模式的α-裂解蛋白酶，无论是为 野生型和M190 A突变体，以研究如何 酶的内部振动可能会导致 其催化特性。 而野生型则高度 在其主要特异性口袋中特异于小底物， M190 A突变体具有更广泛的特异性，催化大的和 小基板。 我们假设对于排列在细胞壁上的原子来说 在特异性口袋中，野生型正常模式具有更多的 对称的性格，与壁振动的相位，和大小 口袋保持相对固定。 这是符合 先前的X射线晶体学结果。 相反，我们预计， 突变模式具有更多的反对称特征， 异相振动，并且口袋能够膨胀和收缩。 这些结果表明分子的内部振动 可能在决定结合和催化特异性方面起作用。 资源的使用对于详细的 我们的简正模结果的图形分析。 的示例 我们所做的计算类型是活性位点的变化 体积和表面积，因为蛋白质结构是 沿其每个正常模式被扰动沿着。 这些 使用算法进行计算密集型计算 包括在计算机图形实验室的MidasPlus软件包中。 在 除了这些计算之外，我们还广泛使用了CGL， 详细的三维渲染我们的晶体和 蛋白质结构模型

We calculate normal modes of alpha-lytic protease, both for the wild type and for the M190A mutant, in order to investigate how internal vibrations in the enzyme might contribute to a characteristic feature of its catalytic specificity. While the wild type is highly specific for small substrates in its primary specificity pocket, the M190A mutant has a much broader specificity, catalyzing both large and small substrates. We hypothesize that for the atoms lining the walls of the specificity pocket, the wild-type normal modes have a more symmetric character, with the walls vibrating in phase, and the size of the pocket remaining relatively fixed. This is in agreement with previous X-ray crystallographic results. In contrast, we expect that the mutant modes have a more antiymmetric character, with the walls vibrating out of phase, and the pocket able to expand and contract. These results would suggest that the internal vibrations of a molecule may play a role in determining both binding and catalytic specificity. The use of resources has been very important for the detailed graphical analyses of our normal-mode results. An example of the types of calculations we make is that of the changes in active-site volume and surface area that take place as the protein structure is perturbed along each of its normal modes. These computationally-intensive calculations are made using an algorithm included in the Computer Graphics Labroatory's MidasPlus package. In addition to such calculations, we have used the CGL extensively for detailed three-dimensional rendering of both our crystallographic and modeled protein structures.