Duran Amanda M, Meiler Jens
Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37235.
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37240.
Protein Sci. 2018 Jan;27(1):341-355. doi: 10.1002/pro.3335. Epub 2017 Nov 15.
Computational membrane protein design is challenging due to the small number of high-resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high-throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo-oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native-like amino acid property composition. While leucine was overrepresented in the inner and outer-hydrophobic regions of RosettaMembrane designs, it resulted in a native-like surface hydrophobicity indicating that it is currently the best option for designing membrane proteins with Rosetta.
由于可用于阐明膜蛋白结构物理基础的高分辨率结构数量较少、存在多个功能重要的构象状态以及用于监测功能的高通量生物物理测定数量有限，计算膜蛋白设计具有挑战性。然而，在过去几年中，膜蛋白的结构测定取得了巨大进展。与此同时，可溶性计算设计领域也取得了令人瞩目的进展。这些进展使我们能够应对设计功能性膜蛋白这一艰巨挑战。在此，我们对用于膜蛋白设计的Rosetta进行了基准测试。我们评估了应对实验性膜蛋白结构质量通常较低的策略。此外，我们测试了设计方案中对称性的使用，这一点尤为重要，因为许多膜蛋白以同型寡聚体形式存在。我们将一种可溶性评分函数与针对膜蛋白优化的评分函数RosettaMembrane进行了比较。当完全重新设计膜蛋白时，这两种评分函数都恢复了约一半的天然序列。然而，RosettaMembrane恢复了最接近天然的氨基酸性质组成。虽然亮氨酸在RosettaMembrane设计的内部和外部疏水区域中过度富集，但它导致了类似天然的表面疏水性，这表明它目前是使用Rosetta设计膜蛋白的最佳选择。
