Computational design of symmetrical eight-bladed β-propeller proteins

Noguchi, Hideyuki; Addy, Christine; Simoncini, David; Wouters, Staf; Mylemans, B.; Meervelt, Luc Van; Schiex, Thomas; Zhang, Kam Y. J.; Tame, J.R.H.; Voet, Arnout

doi:10.1107/s205225251801480x

Cited by 36 publications

(40 citation statements)

References 55 publications

(50 reference statements)

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“…Alternatively, they may have just retained the closure present in the ancestral motif prior to duplication and fusion. Future experiments using different recently designed proteins, such as Tako8 and Cake9, belonging to different propeller families may shed further light on the matter 29,30 . Nevertheless, the propeller fold may be highly successful because of an intrinsic adaptability that allows individual proteins to adopt different permutations to regulate their flexibility.…”

Section: Discussionmentioning

confidence: 99%

Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein

et al. 2020

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The β-propeller fold is adopted by a sequentially diverse family of repeat proteins with apparent rotational symmetry. While the structure is mostly stabilized by hydrophobic interactions, an additional stabilization is provided by hydrogen bonds between the N-and C-termini, which are almost invariably part of the same β-sheet. This feature is often referred to as the "Velcro" closure. The positioning of the termini within a blade is variable and depends on the protein family. In order to investigate the influence of this location on protein structure, folding and stability, we created different circular permutants, and a circularized version, of the designer propeller protein named Pizza. This protein is perfectly symmetrical, possessing six identical repeats. While all mutants adopt the same structure, the proteins lacking the "Velcro" closure were found to be significantly less resistant to thermal and chemical denaturation. This could explain why such proteins are rarely observed in nature. Interestingly the most common "Velcro" configuration for this protein family was not the most stable among the Pizza variants tested. The circularized version shows dramatically improved stability, which could have implications for future applications.

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Section: Discussionmentioning

confidence: 99%

Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein

et al. 2020

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“…We have explored the structural versatility of propeller blades, which represent one of the ancestral peptides predating folded proteins (Alva et al 2015). For this we used two symmetrical β-propellers of the WD40 family, one of which has clearly been amplified extremely recently in evolution and naturally shows an almost perfect internal symmetry (Chaudhuri et al 2008, Dunin-Horkawicz et al 2014), obviating the need to bring it about computationally (Voet et al 2014, Noguchi et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Provided that the PkwA-derived constructs did form the expected structures, this blade would thus potentially have been even more versatile, since the WRAP constructs did not produce any 6-bladed form. A counterpoint to the view that WD40 blades may be particularly versatile is however provided by recent results with a computationally symmetrized 8-bladed WD40 propeller, Tako8 (Noguchi et al 2019). A version with 7 blades, Tako7, could not be expressed and one with 9 blades, Tako9, formed an 8-bladed structure with a single unfolded blade.…”

Section: Discussionmentioning

confidence: 99%

“…Many folds, spanning all levels of complexity (fibrous, solenoid, toroid, and globular), clearly originated in this way. β-Propellers offer an attractive model system to study this process (Nikkhah et al 2006, Yadid and Tawfik 2007, Chaudhuri et al 2008, Yadid et al 2010, Yadid and Tawfik 2011, Voet et al 2014, Smock et al 2016, Noguchi et al 2019. They are toroids formed by sequential supersecondary structure units of typically 40-50 residues, each consisting of four anti-parallel b-strands.…”

Section: Introductionmentioning

confidence: 99%

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

Afanasieva

Chaudhuri

Martin

et al. 2019

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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.

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“…In a related study, Voet and co-workers were recently able to exploit the modular structure of WD40 proteins to design a symmetrical 8-bladed β-propeller protein through pure computational design. 56 …”

Section: Repeating Structural Motifs Facilitate the Emergence Of Novementioning

confidence: 99%

Harnessing Conformational Plasticity to Generate Designer Enzymes

2020

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Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.

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Computational design of symmetrical eight-bladed β-propeller proteins

Abstract: Two artificial β-propeller proteins with eight identical blades were designed, purified and crystallized. X-ray crystallography confirmed the perfectly symmetrical structures of these highly stable proteins.

Cited by 36 publications

References 55 publications

Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein

Influence of circular permutations on the structure and stability of a six‐fold circular symmetric designer protein

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

Harnessing Conformational Plasticity to Generate Designer Enzymes

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