Structural diversity of oligomeric β-propellers with different numbers of identical blades

Abstract

β-Propellers arise through the amplification of a supersecondary structure element called a blade. This process produces toroids of between four and twelve repeats, which are almost always arranged sequentially in a single polypeptide chain. We found that new propellers evolve continuously by amplification from single blades. We therefore investigated whether such nascent propellers can fold as homo-oligomers before they have been fully amplified within a single chain. One- to six-bladed building blocks derived from two seven-bladed WD40 propellers yielded stable homo-oligomers with six to nine blades, depending on the size of the building block. High-resolution structures for tetramers of two blades, trimers of three blades, and dimers of four and five blades, respectively, show structurally diverse propellers and include a novel fold, highlighting the inherent flexibility of the WD40 blade. Our data support the hypothesis that subdomain-sized fragments can provide structural versatility in the evolution of new proteins.

Structural plasticity of a designer protein sheds light on β‐propeller protein evolution

“…A similar shift in symmetry is brought about by making tandem copies of the protein [25]. Similar structural plasticity in fragment assembly has also been shown in β‐propellers in a study last year by the group of Lupas, which addressed the question of structural diversity in propellers with different numbers of identical blades [16]. Stable proteins were created by expressing tandem copies of a blade, based on the natural 7‐bladed propeller PkwA, as a single polypeptide.…”

“…The multimeric WRAP assemblies were not symmetrically arranged around a central axis, and it seems that the interface between fragments also provides some structural flexibility. Although fragments could assemble into 8‐ and 9‐bladed propellers, it is unclear whether monomeric constructs would adopt the same conformations [16].…”

“…It can be imagined that such malleability may greatly increase the ease of evolving a wide variety of b-propellers with either odd or even symmetry. Structural plasticity has recently been observed in the assembly of fragments containing two to five repeats of a 7-bladed WD40 propeller [16], but to date it has not been demonstrated in a single polypeptide that forms a complete propeller.…”

The Taming of the Screw: the natural and artificial development of β-propeller proteins

“…As repeat proteins, β-propellers provide us with both analytic and synthetic approaches to understanding their evolutionary origins. In a recent paper, for example, Lupas and colleagues used WRAP to show that β-propellers built from identical repeat sequences can show remarkable structural plasticity [21]. They expressed tandem repeats of this blade with up to six copies per polypeptide.…”

The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins

“…Despite their wide sequence diversity ( Fig. 1e, f ), most β-propeller families are related to each other and emerged by independent amplification from a set of homologous ancestral blades, in a process that is still visibly ongoing ( Afanasieva et al , 2019 ; Alva et al , 2015 ; Chaudhuri et al , 2008 ; Dunin-Horkawicz et al , 2014 ; Kopec and Lupas, 2013 ). Classification studies ( Chaudhuri et al , 2008 ; Kopec and Lupas, 2013 ) suggested that most β-propeller families form a supercluster centred on WD40 β-propellers, a large superfamily characterized by a Trp-Asp motif at the end of strand C (in position 40).…”