Castro G, Boswell C A, Northrup S H
Department of Chemistry, Tennessee Technological University, Cookeville 38505, USA.
J Biomol Struct Dyn. 1998 Oct;16(2):413-24. doi: 10.1080/07391102.1998.10508257.
The dynamics of the docking step in the electron transfer reaction between yeast cytochrome c peroxidase and iso-1-cytochrome c has been studied using the Brownian dynamics method. In particular we have calculated the bimolecular rate constant at which a specific complex, the xray crystalline complex, can form in solution by translational and rotational diffusion in a field of force. Complexation criteria have been assessed based on the simultaneous alignment of three atom-atom contacts, as well as alternative criteria. The proteins are able to align one or two contacts at remarkably high rates, in fact, at rates approaching the diffusion-controlled limit for two spheres reactive over their entire surfaces. Three contacts may align, and hence the specific complex may dock, at rates on the order of 10(8) M(-1) s(-1), which is quite representative of the experimental association rate constant for ET-competent complex(es). The formation of the specific complex is strongly influenced by the favorable electrostatic interaction between these proteins. It is striking that a specific protein-protein complex can form within one order of magnitude as fast as two spherical proteins can touch at any orientation. It remains plausible that the high ET tunneling rate in this system can take place through a single highly favorable specific complex using a single high efficiency pathway. Still the contribution from a nonspecific set of complexes is not ruled out, particularly considering the marginal reproduction of the ionic strength dependence in the formation of the xray complex.
利用布朗动力学方法研究了酵母细胞色素c过氧化物酶与异-1-细胞色素c之间电子转移反应中对接步骤的动力学。特别是，我们计算了特定复合物（即x射线晶体复合物）在溶液中通过在力场中的平移和旋转扩散形成的双分子速率常数。基于三个原子-原子接触的同时对齐以及其他标准评估了复合标准。蛋白质能够以非常高的速率对齐一个或两个接触，实际上，速率接近两个在整个表面上反应的球体的扩散控制极限。三个接触可能对齐，因此特定复合物可能对接，速率约为10(8) M(-1) s(-1)，这与具有电子转移能力的复合物的实验缔合速率常数相当具有代表性。这些蛋白质之间有利的静电相互作用对特定复合物的形成有很大影响。令人惊讶的是，特定的蛋白质-蛋白质复合物能够以与两个球形蛋白质在任何取向上接触的速度快一个数量级的速度形成。仍然有可能的是，该系统中的高电子转移隧穿速率可以通过使用单一高效途径的单个高度有利的特定复合物发生。不过，不排除非特定复合物组的贡献，特别是考虑到x射线复合物形成中离子强度依赖性的边际再现。
