Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures.
Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures.
复制标题
葡萄球菌核酸酶变性状态下长程结构的表征。
DOI：
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发表时间：
1997
影响因子：
5.6
通讯作者：
D. Shortle
中科院分区：
文献类型：
--
作者：
Joel R. Gillespie;D. Shortle
δ 131 δ，葡萄球菌核酸酶的变性状态的片段模型的结构分析，已被扩展通过获得链段之间的长程距离的限制，顺磁弛豫增强。十四个独特的PROXYL自旋标签被引入的网站，是溶剂暴露在天然状态，并通过NMR光谱测量所产生的增强T2的酰胺质子。当这些数据与测量或估计的相关时间τ（c）结合时，可以计算每个自旋标记蛋白质的自旋标记和30至60个酰胺质子之间的r（-6）加权、时间和整体平均距离。在大约700个这样的松散距离约束的基础上，通过组合距离几何/分子动力学方法生成了相容结构的集合。由于这些距离约束的物理基础存在很大的不确定性，因此进行了大量计算，以确定计算结构对这些约束中的系统误差的灵敏度。总体而言，顺磁弛豫数据中反映的结构特征是稳健的; tau（c）、允许距离的边界窗口或所用约束距离的数量的较大变化对所有计算结构共有的一般特征影响较小。这种变性形式的葡萄球菌核酸酶的全局拓扑结构，如通过与数据一致的构象集合所描述的，与天然状态的全局拓扑结构惊人地相似，主要差异是在天然状态下形成β发夹的两个疏水片段的分离。这些发现表明，蛋白质折叠的拓扑结构是在变性状态下建立的，在没有涉及紧密堆积或稳定氢键的合作相互作用的情况下。疏水性相互作用单独可以编码全局拓扑结构。
Structural analysis of delta131delta, a fragment model of the denatured state of staphylococcal nuclease, has been extended by obtaining long-range distance restraints between chain segments by paramagnetic relaxation enhancement. Fourteen unique PROXYL spin labels were introduced at sites that are solvent-exposed in the native state, and the resulting enhancements of T2 for the amide protons were measured by NMR spectroscopy. When these data were combined with either measured or estimated correlation times tau(c), the r(-6)-weighted, time and ensemble-averaged distance between the spin label and 30 to 60 amide protons could be calculated for each spin-labeled protein. On the basis of approximately 700 such loose distance restraints, ensembles of compatible structures were generated by a combined distance geometry/molecular dynamics approach. Because of the large uncertainty in the physical basis of these distance restraints, a number of calculations were carried out to establish the sensitivity of the calculated structures to systematic errors in these restraints. Overall, the structural features reflected in the paramagnetic relaxation data were robust; large variations in tau(c), in the bounds window of allowed distances, or in the number of restraint distances used had small effects on the general features common to all calculated structures. The global topology of this denatured form of staphylococcal nuclease, as described by an ensemble of conformations consistent with the data, is strikingly similar to that of the native state, the major difference being the segregation of two hydrophobic segments that form a beta hairpin in the native state. These findings suggest that the topology of a protein's fold is established in the denatured state in the absence of cooperative interactions involving tight packing or stable hydrogen bonding. Hydrophobic interactions alone may encode global topology.
自旋标记溶菌酶中的距离测量。
影响因子：
2.9
作者：
Schmidt,PG;Kuntz,ID
通讯作者：
Kuntz,ID
葡萄球菌核酸酶的平衡折叠途径：通过 NMR 和 CD 光谱鉴定最稳定的链-链相互作用。
影响因子：
2.9
作者：
Wang,Y;Shortle,D
通讯作者：
Shortle,D