Ortega Alvaro, García de la Torre Jose
Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain.
J Am Chem Soc. 2005 Sep 21;127(37):12764-5. doi: 10.1021/ja053080l.
The calculation of the rotational diffusion tensor and NMR relaxation times of quasi-rigid macromolecular structures with atomic detail can be made by means of bead/shell models. The computing time required for calculation of these properties for a single structure using rigorous hydrodynamic methods requires a moderate computing time. In possible applications of the methodology in which such a calculation had to be repeated for many structures, a faster method would be welcome. We have studied the effect of introducing a simplifying approximation in the treatment of hydrodynamic interaction, comparing the rigorous and approximate results for a set of 30 globular proteins. When the NMR relaxation times are combined in some relative form, the rigorous and approximate results are practically coincident. For absolute quantities, such as the correlation time, we find that the bias introduced by the approximation can be closely predicted and corrected. The differences between the results of the approximate-corrected and rigorous procedures are not greater than usual experimental errors, and the typical computing time is reduced from 5 min to 1 s.
借助珠/壳模型可以计算具有原子细节的准刚性大分子结构的旋转扩散张量和核磁共振弛豫时间。使用严格的流体动力学方法计算单个结构的这些性质所需的计算时间适中。在该方法可能的应用中，若必须对许多结构重复进行此类计算，那么更快速的方法将大受欢迎。我们研究了在流体动力学相互作用处理中引入简化近似的效果，比较了一组30种球状蛋白质的严格结果和近似结果。当以某种相对形式组合核磁共振弛豫时间时，严格结果和近似结果几乎一致。对于诸如相关时间等绝对量，我们发现近似引入的偏差可以被精确预测并校正。近似校正结果与严格程序结果之间的差异不大于通常的实验误差，并且典型计算时间从5分钟减少到了1秒。
