Chemical shift-based methods in NMR structure determination

Chemical shifts are highly sensitive probes that can be harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary automated and computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high-resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) conformational modeling of protein sidechains. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we hope to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems and point out emerging areas of development that lead us towards the next generation of tools.

Methods
The NMR dataset consisting of chemical shifts and NOEs used for structure calculations of Abl kinase regulatory module were obtained from BMRB ID: 30332. The protein structures deposited here were computed using RASREC-Rosetta.

化学位移（chemical shift）是一类高灵敏探针，可被核磁共振波谱学家与结构生物学家用作构象参数，以表征各类生物分子。传统上，化学位移归属是一项劳动密集型工作，需要大量样本与一系列多维核磁共振实验。近二十年来，互补性自动化与计算方法的发展推动了化学位移的分析、解读与应用，助力解析高分辨率蛋白质与核酸结构。
本文综述了基于化学位移的结构解析方法的发展与应用，重点涵盖从头算（ab initio）片段组装、比较建模、寡聚体系统以及自动化归属方法。在全文讨论中，我们将阐明化学位移用于结构建模的实际应用场景，以及其优势与局限。
此外，我们还重点介绍三类研究方向：(i) 将化学位移与其他类型核磁共振约束（残留偶极耦合、顺磁弛豫增强与假接触位移）相结合的混合方法，这类方法可提升所构建三维结构的精度与分辨率；(ii) 利用化学位移建模低占比激发态结构；(iii) 蛋白质侧链的构象建模。
最后，我们简要探讨了当代方法的优势：这类方法利用通过位点特异性同位素标记方案获取的稀疏核磁共振数据，实现基于化学位移的大分子量生物分子结构解析。藉由本综述，我们旨在强调化学位移在解析复杂生物系统结构时的可及性与通用性，并指明推动下一代结构解析工具发展的新兴研究方向。

方法
本研究用于Abl激酶调控模块结构计算的核磁共振数据集（包含化学位移与核Overhauser效应（NOE）数据）取自生物核磁共振数据库（Biological Magnetic Resonance Bank, BMRB）编号30332。本文所提交的蛋白质结构均通过RASREC-Rosetta算法计算得到。