Research Article: Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

Date Published: March 01, 2020

Publisher: International Union of Crystallography

Author(s): Jens M. H. Thomas, Ronan M. Keegan, Daniel J. Rigden, Owen R. Davies.

http://doi.org/10.1107/S2059798320000443

Abstract

The solution of coiled-coil crystal structures may be achieved by AMPLE through the use of ensembled ab initio models in molecular replacement. Improvements in ab initio modelling of elongated helices and oligomeric coiled-coils allow AMPLE to solve a greater number of coiled-coil structures and at lower resolution than previously achieved.

Partial Text

The coiled-coil is perhaps the best understood protein fold, and in its ideal form constitutes a highly geometric structure that has been defined computationally (Lupas & Gruber, 2005 ▸). A theoretical model of the coiled-coil was first postulated in 1952 by Francis Crick (Crick, 1952 ▸, 1953a ▸,b ▸), guided by the characteristic α-form X-ray diffraction patterns of natural fibres, including hair and wool, that were previously collected by William Astbury (Astbury & Street, 1931 ▸; Astbury & Woods, 1933 ▸). In this classic model, the coiled-coil was described as two or three parallel α-helices that twist around one another at a crossing angle of approximately 20°, such that their hydrophobic side chains become interlocked in a ‘knobs-into-holes’ pattern that repeats every seven amino acids in a ‘heptad repeat’. An isolated α-helix has 3.6 amino acids per turn, with a rise of 1.5 Å per amino acid, providing an α-helical pitch of 5.4 Å per turn. Within the classic coiled-coil model, the interhelical crossing angle provides a periodicity of seven amino acids across two turns, with a pitch along the coiled-coil axis of 5.1 Å per α-helical turn (Lupas & Gruber, 2005 ▸; Hartmann, 2017 ▸; Lupas et al., 2017 ▸). However, whilst this classical model proved to be correct, subsequent experimental evidence demonstrated that it represents only part of a large family of highly divergent structures. These include larger oligomers, parallel and antiparallel orientations, a range of inter-helical crossing angles, left or right super-helical handed­ness, interruptions by skips, stammers and stutters, non-heptad periodicities, deviation from ‘knobs-into-holes’ packing and variations of these parameters along the coiled-coil length (Lupas & Gruber, 2005 ▸; Parry et al., 2008 ▸; Moutevelis & Woolfson, 2009 ▸; Lupas et al., 2017 ▸; Hartmann, 2017 ▸). Thus, the modern definition of a coiled-coil encompasses a highly diverse family of elongated α-helical structures that exhibit a wide range of geometries and topologies.

Here, we describe an enhanced functionality for AMPLE in coiled-coil structure solution through improvements in the ab initio modelling of coiled-coils as either elongated monomeric α-helices or as full oligomers, which we have implemented in a new automated ‘coiled-coil’ mode.

 

Source:

http://doi.org/10.1107/S2059798320000443

 

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