Residual dipolar couplings (RDCs) are NMR parameters that provide both structural and dynamic information concerning inter-nuclear vectors, such as N–HN and Cα–Hα bonds within the protein backbone. Two approaches for extracting this information from RDCs are the model free analysis (MFA) (Meiler et al. in J Am Chem Soc 123:6098–6107, ; Peti et al. in J Am Chem Soc 124:5822–5833, ) and the direct interpretation of dipolar couplings (DIDCs) (Tolman in J Am Chem Soc 124:12020–12030, ). Both methods have been incorporated into iterative schemes, namely the self-consistent RDC based MFA (SCRM) (Lakomek et al. in J Biomol NMR 41:139–155, ) and iterative DIDC (Yao et al. in J Phys Chem B 112:6045–6056, ), with the goal of removing the influence of structural noise in the MFA and DIDC formulations. Here, we report a new iterative procedure entitled Optimized RDC-based Iterative and Unified Model-free analysis (ORIUM). ORIUM unifies theoretical concepts developed in the MFA, SCRM, and DIDC methods to construct a computationally less demanding approach to determine these structural and dynamic parameters. In all schemes, dynamic averaging reduces the actual magnitude of the alignment tensors complicating the determination of the absolute values for the generalized order parameters. To readdress this scaling issue that has been previously investigated (Lakomek et al. in J Biomol NMR 41:139–155, ; Salmon et al. in Angew Chem Int Edit 48:4154–4157, ), a new method is presented using only RDC data to establish a lower bound on protein motion, bypassing the requirement of Lipari–Szabo order parameters. ORIUM and the new scaling procedure are applied to the proteins ubiquitin and the third immunoglobulin domain of protein G (GB3). Our results indicate good agreement with the SCRM and iterative DIDC approaches and signify the general applicability of ORIUM and the proposed scaling for the extraction of inter-nuclear vector structural and dynamic content.Electronic supplementary materialThe online version of this article (doi:10.1007/s10858-013-9775-1) contains supplementary material, which is available to authorized users.
展开▼
机译：残留偶极偶合（RDC）是NMR参数，可提供有关核间载体的结构和动态信息，例如蛋白质骨架内的N–H N 和Cα–Hα键。从RDC提取此信息的两种方法是无模型分析（MFA）（Meiler等人，J Am Chem Soc 123：6098-6107； Peti等人，J Am Chem Soc 124：5822-5833，）和直接解释偶极耦合（DIDC）（Tolman in J Am Chem Soc 124：12020–12030，）。两种方法都已合并到迭代方案中，即基于自洽RDC的MFA（SCRM）（Lakomek等人，J Biomol NMR 41：139-155，）和迭代DIDC（Yao等人，J Phys Chem B 112 ：6045-6056，），目的是消除MFA和DIDC配方中结构噪声的影响。在这里，我们报告了一个新的迭代过程，名为“基于RDC的优化迭代和无模型统一分析（ORIUM）”。 ORIUM统一了MFA，SCRM和DIDC方法中开发的理论概念，以构建计算量较少的方法来确定这些结构和动态参数。在所有方案中，动态平均都会减小对齐张量的实际大小，这会使确定广义阶参数的绝对值变得复杂。为了解决以前已经研究过的缩放问题（Lakomek等人，J Biomol NMR 41：139–155； Salmon等人，Angew Chem Int Edit 48：4154-4157，），提出了一种仅使用RDC数据建立了蛋白质运动的下限，绕过了Lipari–Szabo顺序参数的要求。 ORIUM和新的缩放程序适用于蛋白质泛素和蛋白质G（GB3）的第三个免疫球蛋白结构域。我们的结果表明与SCRM和DIDC迭代方法具有良好的一致性，并表明ORIUM的普遍适用性以及拟议的缩放比例用于提取核间矢量结构和动态内容。电子补充材料本文的在线版本（doi：10.1007 / s10858） -013-9775-1）包含补充材料，授权用户可以使用。
展开▼
