Research Article: Approaches to ab initio molecular replacement of α-helical transmembrane proteins

Date Published: December 01, 2017

Publisher: International Union of Crystallography

Author(s): Jens M. H. Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J. Rigden.


Homology-independent methods for ab initio phasing of α-helical transmembrane proteins are explored.

Partial Text

Transmembrane proteins are an important class of proteins that are estimated to comprise about 30% of the proteome (Tusnády et al., 2004 ▸). They reside, at least partly and often predominantly, within the hydrophobic cell membrane, sandwiched between the aqueous cell interior and exterior. Transmembrane proteins come in two main forms, α-helical and β-barrel, with the overwhelming majority being of the α-helical form (White & Wimley, 1999 ▸). Estimates of the number of transmembrane proteins encoded in the human genome vary. Most studies agree that roughly 26% of proteins are transmembrane proteins, but this includes a large number of single-pass transmembrane proteins. Polytopic proteins, as studied here, are thought to represent around 14% of the human proteome (Almén et al., 2009 ▸; Fagerberg et al., 2010 ▸).

The weighted mean phase error for all of the final rebuilt models was measured to confirm that the structure had been correctly determined. In all cases the error was less than 30°.

This exploration of the ability of AMPLE to solve α-helical transmembrane proteins was prompted by our earlier successes solving small globular proteins, where 80% of the entirely α-helical structures could be solved (Bibby et al., 2012 ▸), and with coiled-coil proteins (Thomas et al., 2015 ▸), where again 80% of the structures could be solved. A notably positive outcome of this work is the solution of all bar one of the targets with a resolution of better than 2.0 Å using a small library of eight ideal helices.




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