Content area
Full Text
ABSTRACT
The transmembrane (TM) domains of many integral membrane proteins are composed of α-helix bundles. Structure determination at high resolution (<4 [Angstrom]) of TM domains is still exceedingly difficult experimentally. Hence, some TM-protein structures have only been solved at intermediate (5-10 [Angstrom]) or low (>10 [Angstrom]) resolutions using, for example, cryo-electron microscopy (cryo-EM). These structures reveal the packing arrangement of the TM domain, but cannot be used to determine the positions of individual amino acids. The observation that typically, the lipid-exposed faces of TM proteins are evolutionary more variable and less charged than their core provides a simple rule for orienting their constituent helices. Based on this rule, we developed score functions and automated methods for orienting TM helices, for which locations and tilt angles have been determined using, e.g., cryo-EM data. The method was parameterized with the aim of retrieving the native structure of bacteriorhodopsin among near- and far-from-native templates. It was then tested on proteins that differ from bacteriorhodopsin in their sequences, architectures, and functions, such as the acetylcholine receptor and rhodopsin. The predicted structures were within 1.5-3.5 [Angstrom] from the native state in all cases. We conclude that the computational method can be used in conjunction with cryo-EM data to obtain approximate model structures of TM domains of proteins for which a sufficiently heterogeneous set of homologs is available. We also show that in those proteins in which relatively short loops connect neighboring helices, the scoring functions can discriminate between near- and far-from-native conformations even without the constraints imposed on helix locations and tilt angles that are derived from cryo-EM.
INTRODUCTION
TM proteins are crucial mediators of cell-to-cell signaling and transport processes, and constitute some 50% of contemporary drug targets (Fleming, 2000). In recent years the pace of structural determination of TM proteins has increased, but technical problems related to protein purification and crystallization still hamper TM-protein structure determination. Thus, despite their biomedical importance, <40 distinct folds of TM proteins have been solved to date by high-resolution methods such as x-ray crystallography. The lack of a large set of solved TM proteins also restricts the usefulness of computational methods based on the statistics of solved protein structures, and in particular, of comparative or homology modeling, which has been a very successful...