An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data

Sarel J. Fleishman, Susan Harrington, Richard A. Friesner, Barry Honig, Nir Ben-Tal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


The transmembrane (TM) domains of many integral membrane proteins are composed of α-helix bundles. Structure determination at high resolution (<4 Å) of TM domains is still exceedingly difficult experimentally. Hence, some TM-protein structures have only been solved at intermediate (5-10 Å) or low (>10 Å) 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 evolutionarily 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 Å 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.

Original languageEnglish
Pages (from-to)3448-3459
Number of pages12
JournalBiophysical Journal
Issue number5
StatePublished - Nov 2004


FundersFunder number
Clore Israel Foundation
Constantiner Institute of Molecular Biology
National Science FoundationMCB-9808902
Israel Science Foundation
Tel Aviv University


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