High-resolution structure prediction ofβ-barrel membrane proteins

Abstract

β-Barrel membrane proteins (βMPs) play important roles, but knowledge of their structures is limited. We have developed a method to predict their 3D structures. We predict strand registers and construct transmembrane (TM) domains of βMPs accurately, including proteins for which no prediction has been attempted before. Our method also accurately predicts structures from protein families with a limited number of sequences and proteins with novel folds. An average main-chain rmsd of 3.48 Å is achieved between predicted and experimentally resolved structures of TM domains, which is a significant improvement (>3 Å) over a recent study. For βMPs with NMR structures, the deviation between predictions and experimentally solved structures is similar to the difference among the NMR structures, indicating excellent prediction accuracy. Moreover, we can now accurately model the extended β-barrels and loops in non-TM domains, increasing the overall coverage of structure prediction by>30%. Our method is general and can be applied to genome-wide structural prediction of βMPs.