Berjanskii Mark, Wishart David S
Department of Computing Science, 2-21 Athabasca Hall, University of Alberta, Edmonton, Alberta T6G 2E8, Canada.
Nat Protoc. 2006;1(2):683-8. doi: 10.1038/nprot.2006.108.
We present a protocol for predicting protein flexibility from NMR chemical shifts. The protocol consists of (i) ensuring that the chemical shift assignments are correctly referenced or, if not, performing a reference correction using information derived from the chemical shift index, (ii) calculating the random coil index (RCI), and (iii) predicting the expected root mean square fluctuations (RMSFs) and order parameters (S2) of the protein from the RCI. The key advantages of this protocol over existing methods for studying protein dynamics are that (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone assignments. When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1-2 h using a spreadsheet program.
我们提出了一种从核磁共振（NMR）化学位移预测蛋白质柔韧性的方案。该方案包括：（i）确保化学位移归属已正确校正，若未校正，则利用化学位移指数得出的信息进行校正；（ii）计算随机卷曲指数（RCI）；（iii）根据RCI预测蛋白质的预期均方根波动（RMSF）和序参数（S2）。与现有研究蛋白质动力学的方法相比，该方案的主要优点在于：（i）不需要蛋白质三级结构的先验知识；（ii）对蛋白质的整体翻滚不敏感；（iii）除了用于主链归属的标准实验外，不需要额外的NMR测量。当有化学位移归属时，使用电子表格程序可在1-2小时内计算出蛋白质柔韧性参数，如S2和RMSF。
