Floating stereospecific assignment revisited: Application to an 18 kDa protein and comparison with J-coupling data
Floating stereospecific assignment revisited: Application to an 18 kDa protein and comparison with J-coupling data
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DOI：
10.1023/a:1018670623695
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发表时间：
1997-04-01
影响因子：
2.7
通讯作者：
Nilges, M
中科院分区：
文献类型：
--
作者：
Folmer, RHA;Hilbers, CW;Nilges, M
我们报告了一种浮动手性程序，用于使用限制分子动力学和模拟退火从 NMR 数据计算蛋白质结构中处理非立体特异性指定的亚甲基或异丙基。该协议利用两种策略来诱导前手性中心的正确构象：在评估 NOE 能量项后进行显式原子“交换”，以及通过减少角度和不适当的力常数来实现原子“浮动”，从而在前手性中心强制执行定义的手性。对两种方法的各自贡献进行了调查。此外，还研究了质子间距离约束对准确度和精密度的影响。所采用的模型系统是由假单胞菌噬菌体 Pf3 编码的 18 kDa 单链 DNA 结合蛋白。将浮动手性应用于所有产生非简并 NMR 信号的亚甲基和异丙基，并将其中 34 个基团的结果与 J 耦合数据进行比较。我们得出的结论是，浮动立体特异性分配是蛋白质结构计算中的可靠工具。它的使用是有益的，因为它允许直接从测量的峰值体积中提取距离限制，而不需要平均或添加伪原子校正。因此，计算出的结构的质量几乎与通过立体定向分配获得的结构相当。此外，由于浮动手性是处理前手性中心的唯一方法，可确保单个结构中两个质子频率的一致分配，因此它似乎比使用伪原子或 (R-6) 平均更可取。
We report a floating chirality procedure to treat nonstereospecifically assigned methylene or isopropyl groups in the calculation of protein structures from NMR data using restrained molecular dynamics and simulated annealing. The protocol makes use of two strategies to induce the proper conformation of the prochiral centres: explicit atom 'swapping' following an evaluation of the NOE energy term, and atom 'floating' by reducing the angle and improper force constants that enforce a defined chirality at the prochiral centre. The individual contributions of both approaches have been investigated. In addition, the effects of accuracy and precision of the interproton distance restraints were studied. The model system employed is the 18 kDa single-stranded DNA binding protein encoded by Pseudomonas bacteriophage Pf3. Floating chirality was applied to all methylene and isopropyl groups that give rise to nondegenerate NMR signals, and the results for 34 of these groups were compared to J-coupling data. We conclude that floating stereospecific assignment is a reliable tool in protein structure calculation. Its use is beneficial because it allows the distance restraints to be extracted directly from the measured peak volumes without the need for averaging or adding pseudoatom corrections. As a result, the calculated structures are of a quality almost comparable to that obtained with stereospecific assignments. As floating chirality furthermore is the only approach treating prochiral centres that ensures a consistent assignment of the two proton frequencies in a single structure, it seems to be preferable over using pseudoatoms or (R-6) averaging.