Berlin Konstantin, O'Leary Dianne P, Fushman David
Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742-3360, USA.
J Magn Reson. 2009 Nov;201(1):25-33. doi: 10.1016/j.jmr.2009.07.028. Epub 2009 Aug 5.
We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.
我们描述了一种基于分子形状计算分子排列张量的全新且计算效率高的方法。通过将问题重新表述为数值积分问题（而非像PALES方法那样进行简单的均匀采样），以及使用凸包而非分子表面的详细表示，实现了速度的提升。该方法适用于双分子层、聚乙二醇/己醇以及其他可通过平面屏障引入的空间限制进行建模的排列介质。此方法用于通过等效椭球体进一步探索和比较蛋白质形状的各种表示。我们还使用各种从头算方法检验了排列张量和剩余偶极耦合（RDC）预测的准确性。我们分别量化了由于排列张量的方向和大小不准确导致的RDC预测中的不准确性，得出结论：在准确预测RDC时，方向准确性更为重要。
