A space-time structure determination of human CD2 reveals the CD58-binding mode.
A space-time structure determination of human CD2 reveals the CD58-binding mode.
复制标题
DOI：
10.1073/pnas.030540397
复制
发表时间：
2000-02
影响因子：
11.1
通讯作者：
A. Kitao;G. Wagner
中科院分区：
文献类型：
--
作者：
A. Kitao;G. Wagner
我们描述了蛋白质结构时空描述的程序。该方法能够确定构象亚状态的群体以及内部蛋白质运动的幅度和方向。这是通过拟合静态和动态 NMR 数据来实现的。该方法基于跳跃最小值概念。首先，对与结构 NMR 数据兼容的宽构象空间进行采样，以找到大量子状态。随后，通过使用具有力场能量项的分子动力学计算来对基内运动进行采样。接下来，将亚态总体拟合到 NMR 弛豫数据。通过对二阶矩矩阵进行对角化，可以识别运动的方向和幅度。该方法应用于人CD2的粘附结构域。我们发现很少有子状态可以解释大部分实验数据。此外，只有两种类型的集体运动具有高振幅。它们代表凹面（闭合）和平坦（开放）结合面之间的过渡，类似于反受体（CD58）结合时的变化。
We describe a procedure for a space-time description of protein structures. The method is capable of determining populations of conformational substates, and amplitudes and directions of internal protein motions. This is achieved by fitting static and dynamic NMR data. The approach is based on the jumping-among-minima concept. First, a wide conformational space compatible with structural NMR data is sampled to find a large set of substates. Subsequently, intrasubstate motions are sampled by using molecular dynamics calculations with force field energy terms. Next, the populations of substates are fitted to NMR relaxation data. By diagonalizing a second moment matrix, directions and amplitudes of motions are identified. The method was applied to the adhesion domain of human CD2. We found that very few substates can account for most of the experimental data. Furthermore, only two types of collective motions have high amplitudes. They represent transitions between a concave (closed) and flat (open) binding face and resemble the change upon counter-receptor (CD58) binding.