Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

Jens M H Thomas,Daniel J Rigden,Yang Zhang,Olga Mayans,Felix Simkovic,Chengxin Zhang,Ronan Keegan

doi:10.1107/s2059798317016436

Abstract

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Highlights

Transmembrane proteins are an important class of proteins that are estimated to comprise about 30% of the proteome (Tusnady et al, 2004)
Considering that transmembrane proteins are considered to be relatively hard targets to solve, that so many of this set can be solved using a small library of ideal helices and a simple molecular replacement (MR) protocol is an encouraging result to set alongside other advances in the use of ideal helices (Millan et al, 2015)
The solution of target 2o9g is different as the addition of the contact information has explicitly resulted in the modelling, albeit in an intramolecular fashion, of the intermolecular interface. This exploration of the ability of AMPLE to solve -helical transmembrane proteins was prompted by our earlier successes solving small globular proteins, where 80% of the entirely -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

Summary

Introduction

Transmembrane proteins are an important class of proteins that are estimated to comprise about 30% of the proteome (Tusnady et al, 2004). They reside, at least partly and often predominantly, within the hydrophobic cell membrane, sandwiched between the aqueous cell interior and exterior. 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. As studied here, are thought to represent around 14% of the human proteome (Almen et al, 2009; Fagerberg et al, 2010)

Methods

Results

Conclusion