Integrated Structural Biology for Alpha-Helical Membrane Protein Structure Determination

Abstract

While great progress has been made, only 10% of the nearly 1,000 integral, a-helical, multi-span membrane protein families are represented by at least one experimentally determined structure in the PDB. We developed the algorithm BCL::MP-Fold, which samples the large conformational space of membrane proteins de novo by assembling predicted secondary structure elements guided by knowledge-based potentials. We present a case study of rhodopsin fold determination by integrating sparse and/or low-resolution restraints from multiple experimental techniques including electron microscopy, electron paramagnetic resonance spectroscopy, and nuclear magnetic resonance spectroscopy. Simultaneous incorporation of orthogonal experimental restraints not only significantly improved the sampling accuracy but also allowed identification of the correct fold, which is demonstrated by a protein size-normalized transmembrane root-mean-square deviation as lowas 1.2 A. We further illustrate application of these technologies for GPCR structure determination.