Mechanism of the CD2/CD58 complex formation in immune system

通过计算机模拟研究了CD2/CD58络合物的形成机理。我们这个项目的目的是：1)研究与复合体形成有关的蛋白质动力学；2)通过自由能分析估计氨基酸残基和能量项对蛋白质的贡献；3)研究CD2/CD58复合体的形成在信号传递中的作用。为了达到第一个目的，发展了一种新的方法，利用核磁共振约束和驰豫参数来精炼蛋白质在溶液中的结构和动力学。该方法基于最小跳跃(JAM)模型的概念：在该模型中，我们假设蛋白质动力学由两种类型的运动组成：子态内运动和子态间运动。在~10PSEC的时间尺度上，用力场能量项的分子动力学计算模拟了子态内的运动。通过创建与几何…一致的结构集合来包括子状态间运动更多的核磁共振限制。确定了构象亚态的统计权重，以再现核磁共振弛豫参数。这些运动主要影响略微凹陷的反受体结合部位的曲率，并代表凹面(封闭的)和平坦的(开放的)结合面之间的过渡。通过将溶液中的结构与对抗受体CD58的复杂结构进行比较，我们发现这两种类型的转变与对抗受体结合时的变化相似。为了实现第二个目的，我们开发了REUS(副本交换伞采样)来进行自由能计算。该方法是副本交换法和加权直方图分析法的结合。这使我们能够更准确地估计结合自由能。各种突变的自由能分析正在进行中，但尚未完成。我们计划继续进行这种计算，以进一步研究免疫系统中的信号传递机制。较少

The mechanism of the CD2/CD58 complex formation was investigated by computer simulation. Our purposes of this project are 1) Investigate protein dynamics involved with the complex formation, 2) Estimate contribution from amino acid residues and energy terms by free energy analysis, 3) Investigate the role of CD2/CD58 complex formation in signal transfer. In order to attain the first purpose, a novel method has been developed in order to refine structure and dynamic of proteins in solution by using NMR restraints and relaxation parameters. This method is based on the concept of Jumping-Among-Minima (JAM) model: In this model we assume that protein dynamics consists of two types of motions, intra-substate motion and inter-substate motion. Intra-substate motions, which occur in the time scale of~ 10 psec, are simulated with molecular dynamics calculations with force field energy terms. Inter-substate motions are included by creating an ensemble of structures consistent with the geometric … More NMR restraints. Statistical weights of the conformational substates are determined to reproduce the NMR relaxation parameters. The motions affect primarily the curvature of the slightly concave counter-receptor-binding site and represent transitions between a concave (closed) and flat (open) binding face. By comparing the ensemble of structures in solution to the complex structure with counter receptor CD58, we found that these two types of transitions resemble the change upon counter-receptor binding. To achieve the second purpose, we have developed the REUS (Replica Exchange Umbrella Sampling) to carry out free energy calculation. This method is the combination of the replica exchange method and WHAM (Weighted Histogram Analysis Method). This enables us to estimate binding free energy more accurately. Free energy analysis of various mutations are being carried out but not yet finished. We are planning to continue this kind of calculation to further investigate the signal transfer mechanisms in immune system. Less