扩散控制酶表面配体定向通过的元胞自动机模型
Directed Ligand Passage Over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model
摘要：
某些酶促反应的限速步骤是物理步骤，即扩散。这种反应的效率可以通过增加底物分子的到达速率来提高，例如通过底物（配体）在与酶表面随机相遇后定向通过活性位点。在此，我们引入了一个元胞自动机模型，模拟配体通过蛋白质表面到达其指定的活性位点。该系统的模拟使用概率转移规则的格子气自动机。不同分布的氨基酸在蛋白质表面进行检查。对于每个分布，实现水合模式，并计算配体到达活性位点所需的迭代步骤的平均数。结果的比较表明，配体到达活性位点的速率明显受到活性侧外氨基酸分布的影响。这样的过程可以促进配体向活性位点扩散，从而提高酶作用的效率。
英文摘要：
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of substrate (ligand) to active site after its random encounter with the enzyme surface. Herein, we introduce a cellular automata model simulating the ligand passage over the protein surface to its destined active site. The system is simulated using the lattice gas automata with probabilistic transition rules. Different distributions of amino acids over the protein surface are examined. For each distribution, the hydration pattern is achieved and the mean number of iteration steps needed for the ligand to arrive at the active site calculated. Comparison of results indicates that the rate at which ligand arrives at the active site is clearly affected by the distribution of amino acids outside the active side. Such a process can facilitate the ligand diffusion towards the active site thereby enhancing the efficiency of the enzyme action.
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