CLOUDS, a protocol for deriving a molecular proton density via NMR
CLOUDS, a protocol for deriving a molecular proton density via NMR
复制标题
DOI：
10.1073/pnas.082114199
复制
发表时间：
2002-05-14
影响因子：
11.1
通讯作者：
Llinás, M
中科院分区：
文献类型：
--
作者：
Grishaev, A;Llinás, M
我们论证了从实验的核磁共振核Overhaser效应数据中计算蛋白质在溶液中的真实空间质子分布的可行性，并且只需最少的赋值。这种方法，云，依赖于精确和丰富的质子间距离约束计算，通过松弛矩阵分析的几组实验核Overhauser效应谱串音。MIDGE协议就是为此目的而修改的。在分子动力学模拟退火法中，原子核间距和范德华排斥项是唯一的活性约束条件，未分配的、未连接的氢原子气体凝聚成结构质子分布(云)。质子密度是通过组合大量这样的云来产生的，每个云都是从不同的轨道计算出来的。在参考最接近平均值的云进行过滤之后，识别出最小色散质子密度(FOC)。后者提供了一个准连续的纯氢概率分布，传达了与分子结构直接相关的蛋白质表面拓扑(凹槽、突起、潜在结合部位空洞等)的即时信息。对两个规则二级结构含量较低的球状蛋白结构域--人基质金属蛋白酶-2的Col-2结构域和人纤溶酶原的Kringle-2结构域--分别测定了60个和83个氨基酸残基，验证了该方法的可行性。
We demonstrate the feasibility of computing realistic spatial proton distributions for proteins in solution from experimental NMR nuclear Overhauser effect data only and with minimal assignments. The method, CLOUDS, relies on precise and abundant interproton distance restraints calculated via a relaxation matrix analysis of sets of experimental nuclear Overhauser effect spectroscopy crosspeaks. The MIDGE protocol was adapted for this purpose. A gas of unassigned, unconnected H atoms is condensed into a structured proton distribution (cloud) via a molecular dynamics simulated-annealing scheme in which the internuclear distances and van der Waals repulsive terms are the only active restraints. Proton densities are generated by combining a large number of such clouds, each computed from a different trajectory. After filtering by reference to the cloud closest to the mean, a minimal dispersion proton density (foc) is identified. The latter affords a quasi-continuous hydrogen-only probability distribution that conveys immediate information on the protein surface topology (grooves, protrusions, potential binding site cavities, etc.), directly related to the molecular structure. Feasibility of the method was tested on NMR data measured on two globular protein domains of low regular secondary structure content, the col 2 domain of human matrix metalloproteinase-2 and the kringle 2 domain of human plasminogen, of 60 and 83 amino acid residues, respectively.