Department of Bioengineering, University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, Illinois 60607, USA.
J Am Chem Soc. 2012 Jan 25;134(3):1775-81. doi: 10.1021/ja209895m. Epub 2012 Jan 12.
β-Barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They are important for pore formation, membrane anchoring, and enzyme activity. These proteins are also often responsible for bacterial virulence. Due to difficulties in experimental structure determination, they are sparsely represented in the protein structure databank. We have developed a computational method for predicting structures of the transmembrane (TM) domains of β-barrel membrane proteins. Based on physical principles, our method can predict structures of the TM domain of β-barrel membrane proteins of novel topology, including those from eukaryotic mitochondria. Our method is based on a model of physical interactions, a discrete conformational state space, an empirical potential function, as well as a model to account for interstrand loop entropy. We are able to construct three-dimensional atomic structure of the TM domains from sequences for a set of 23 nonhomologous proteins (resolution 1.8-3.0 Å). The median rmsd of TM domains containing 75-222 residues between predicted and measured structures is 3.9 Å for main chain atoms. In addition, stability determinants and protein-protein interaction sites can be predicted. Such predictions on eukaryotic mitochondria outer membrane protein Tom40 and VDAC are confirmed by independent mutagenesis and chemical cross-linking studies. These results suggest that our model captures key components of the organization principles of β-barrel membrane protein assembly.
β-桶状膜蛋白存在于革兰氏阴性菌的外膜、线粒体和叶绿体中。它们对于孔形成、膜锚定和酶活性很重要。这些蛋白质也常常与细菌的毒力有关。由于实验结构测定的困难，它们在蛋白质结构数据库中代表较少。我们开发了一种用于预测β-桶状膜蛋白跨膜（TM）结构域结构的计算方法。基于物理原理，我们的方法可以预测具有新型拓扑结构的β-桶状膜蛋白的 TM 结构域，包括来自真核线粒体的结构域。我们的方法基于物理相互作用模型、离散构象状态空间、经验势能函数以及考虑链间环熵的模型。我们能够从一组 23 种非同源蛋白的序列中构建 TM 结构域的三维原子结构（分辨率为 1.8-3.0 Å）。包含 75-222 个残基的 TM 结构域中，预测结构与实测结构之间主链原子的均方根偏差（rmsd）中位数为 3.9 Å。此外，还可以预测稳定性决定因素和蛋白质-蛋白质相互作用位点。真核线粒体外膜蛋白 Tom40 和 VDAC 的这些预测结果通过独立的诱变和化学交联研究得到了证实。这些结果表明，我们的模型捕获了β-桶状膜蛋白组装的组织原则的关键组成部分。
