Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.
Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.
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作者：
Koehler Leman J;D'Avino AR;Bhatnagar Y;Gray JJ
膜蛋白的研究是具有挑战性的，结构测定的限制通常是稀疏的或低分辨率的，因为它们周围的膜环境导致各种实验挑战。当膜蛋白结构在不同的环境中由不同的技术确定时，一个自然的问题是“哪种结构最具生物学相关性？”为了回答这个问题，我们编制了一个由溶液NMR和X射线晶体学确定的已知结构的膜蛋白数据集。通过研究结构之间的差异，我们发现晶体和NMR结构之间的RMSD在膜区域低于5 μ m，NMR系综在膜区域具有更高的收敛性，晶体结构通常具有更直的跨膜区域，具有更高的立体化学正确性，并且更紧密地堆积。在量化这些差异后，我们使用NMR结构的高分辨率细化来减轻它们，这为识别和改善膜蛋白的结构质量铺平了道路。
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.
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