Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
J Biomol NMR. 2012 Aug;53(4):281-92. doi: 10.1007/s10858-012-9644-3. Epub 2012 Jun 23.
Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.
残基偶极耦合（RDC）有可能提供有关蛋白质构象波动的详细信息。然而，由于 RDC 与蛋白质结构之间的复杂关系，提取这些信息极具挑战性。一种有前途的解码这种关系的方法涉及基于结构的蛋白质构象对准张量的计算。通过实施该策略在分子动力学模拟中生成结构约束，我们表明可以有效地提取 RDC 提供的关于蛋白质天然状态下构象波动的信息。我们提出的方法可以在广泛的对准介质中使用，包括 Pf1、带电双胶束和凝胶。该方法的准确性通过分析未用作计算约束的 RDC 的 Q 因子来证明，这些 Q 因子明显低于现有高分辨率结构和结构集合的 Q 因子，从而表明我们有效地捕获了构象波动对 RDC 的贡献。
