Koehler Leman Julia, D'Avino Andrew R, Bhatnagar Yash, Gray Jeffrey J
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland.
Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York.
Proteins. 2018 Jan;86(1):57-74. doi: 10.1002/prot.25402. Epub 2017 Nov 8.
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo-chemical correctness, and are more tightly packed. After quantifying these differences, we used high-resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.
膜蛋白的研究颇具挑战性，由于围绕它们的膜环境会引发各种实验难题，用于结构测定的限制条件通常较少或分辨率较低。当膜蛋白结构在不同环境中通过不同技术测定时，一个自然而然的问题是“哪种结构与生物学关系最为密切？”为了回答这个问题，我们汇编了一个膜蛋白数据集，这些膜蛋白的已知结构是通过溶液核磁共振（NMR）和X射线晶体学两种方法测定的。通过研究这些结构之间的差异，我们发现晶体结构与NMR结构在膜区域的均方根偏差（RMSD）低于5 Å，NMR集合在膜区域具有更高的收敛性，晶体结构的跨膜区域通常更笔直，具有更高的立体化学正确性，并且堆积更紧密。在量化这些差异之后，我们使用NMR结构的高分辨率精修来减轻这些差异，这为鉴定和提高膜蛋白的结构质量铺平了道路。
