Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA.
Structure. 2012 Mar 7;20(3):464-78. doi: 10.1016/j.str.2012.01.023.
Electron density maps of membrane proteins or large macromolecular complexes are frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo-electron microscopy or X-ray crystallography. In these density maps, the general arrangement of secondary structure elements (SSEs) is revealed, whereas their directionality and connectivity remain elusive. We demonstrate that the topology of proteins with up to 250 amino acids can be determined from such density maps when combined with a computational protein folding protocol. Furthermore, we accurately reconstruct atomic detail in loop regions and amino acid side chains not visible in the experimental data. The EM-Fold algorithm assembles the SSEs de novo before atomic detail is added using Rosetta. In a benchmark of 27 proteins, the protocol consistently and reproducibly achieves models with root mean square deviation values <3 Å.
膜蛋白或大型大分子复合物的电子密度图通常仅在 4 Å 到 10 Å 之间的中分辨率下通过冷冻电子显微镜或 X 射线晶体学确定。在这些密度图中，揭示了二级结构元件（SSE）的总体排列，而它们的方向性和连接性仍然难以捉摸。我们证明，当与计算蛋白质折叠方案结合使用时，多达 250 个氨基酸的蛋白质的拓扑结构可以从这些密度图中确定。此外，我们准确地重建了实验数据中不可见的环区和氨基酸侧链的原子细节。EM-Fold 算法在使用 Rosetta 添加原子细节之前从头开始组装 SSE。在 27 种蛋白质的基准测试中，该方案始终如一地、可重复地获得均方根偏差值 <3 Å 的模型。
