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De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the...

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Autores principales: Chu, Alexander E., Fernandez, Daniel, Liu, Jingjia, Eguchi, Raphael R., Huang, Po-Ssu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AAAS 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521652/
https://www.ncbi.nlm.nih.gov/pubmed/37850141
http://dx.doi.org/10.34133/2022/9842315
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author Chu, Alexander E.
Fernandez, Daniel
Liu, Jingjia
Eguchi, Raphael R.
Huang, Po-Ssu
author_facet Chu, Alexander E.
Fernandez, Daniel
Liu, Jingjia
Eguchi, Raphael R.
Huang, Po-Ssu
author_sort Chu, Alexander E.
collection PubMed
description The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.
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spelling pubmed-105216522023-10-17 De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design Chu, Alexander E. Fernandez, Daniel Liu, Jingjia Eguchi, Raphael R. Huang, Po-Ssu Biodes Res Research Article The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels. AAAS 2022-10-10 /pmc/articles/PMC10521652/ /pubmed/37850141 http://dx.doi.org/10.34133/2022/9842315 Text en Copyright © 2022 Alexander E. Chu et al. https://creativecommons.org/licenses/by/4.0/Exclusive Licensee Nanjing Agricultural University. Distributed under a Creative Commons Attribution License (CC BY 4.0). (https://creativecommons.org/licenses/by/4.0/)
spellingShingle Research Article
Chu, Alexander E.
Fernandez, Daniel
Liu, Jingjia
Eguchi, Raphael R.
Huang, Po-Ssu
De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title_full De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title_fullStr De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title_full_unstemmed De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title_short De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design
title_sort de novo design of a highly stable ovoid tim barrel: unlocking pocket shape towards functional design
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521652/
https://www.ncbi.nlm.nih.gov/pubmed/37850141
http://dx.doi.org/10.34133/2022/9842315
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