Cummings M D, Hart T N, Read R J
Department of Biochemistry, University of Alberta, Edmonton, Canada.
Proteins. 1998 May 15;31(3):282-98.
We describe a novel application of a fragment-based ligand docking technique; similar methods are commonly applied to the de novo design of ligands for target protein binding sites. We have used several new flexible docking and superposition tools, as well as a more conventional rigid-body (fragment) docking method, to examine NAD binding to the catalytic subunits of diphtheria (DT) and pertussis (PT) toxins, and to propose a model of the NAD-PT complex. Docking simulations with the rigid NAD fragments adenine and nicotinamide revealed that the low-energy dockings clustered in three distinct sites on the two proteins. Two of the sites were common to both fragments and were related to the structure of NAD bound to DT in an obvious way; however, the adenine subsite of PT was shifted relative to that of DT. We chose adenine/nicotinamide pairs of PT dockings from these clusters and flexibly superimposed NAD onto these pairs. A Monte Carlo-based flexible docking procedure and energy minimization were used to refine the modeled NAD-PT complexes. The modeled complex accounts for the sequence and structural similarities between PT and DT and is consistent with many results that suggest the catalytic importance of certain residues. A possible functional role for the structural difference between the two complexes is discussed.
我们描述了一种基于片段的配体对接技术的新应用；类似的方法通常用于从头设计与靶蛋白结合位点结合的配体。我们使用了几种新的灵活对接和叠加工具，以及一种更传统的刚体（片段）对接方法，来研究烟酰胺腺嘌呤二核苷酸（NAD）与白喉毒素（DT）和百日咳毒素（PT）催化亚基的结合，并提出NAD-PT复合物的模型。用刚性的NAD片段腺嘌呤和烟酰胺进行对接模拟表明，低能量对接聚集在这两种蛋白质上的三个不同位点。其中两个位点是两个片段共有的，并且与以明显方式结合到DT上的NAD的结构相关；然而，PT的腺嘌呤亚位点相对于DT的腺嘌呤亚位点发生了偏移。我们从这些簇中选择了PT对接的腺嘌呤/烟酰胺对，并将NAD灵活地叠加到这些对上。基于蒙特卡罗的灵活对接程序和能量最小化被用于优化模拟的NAD-PT复合物。模拟的复合物解释了PT和DT之间的序列和结构相似性，并且与许多表明某些残基具有催化重要性的结果一致。讨论了两种复合物结构差异可能的功能作用。
