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

Abstract

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 bondingmore » 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.« less

Authors:

Chu, Alexander E.  ^[1];

• Search DOE PAGES for author "Chu, Alexander E."
• Search DOE PAGES for ORCID "0000-0002-6219-7887"

Fernandez, Daniel  ^[2];

• Search DOE PAGES for author "Fernandez, Daniel"
• Search DOE PAGES for ORCID "0000-0002-6221-152X"

Liu, Jingjia  ^[3];

• Search DOE PAGES for author "Liu, Jingjia"
• Search DOE PAGES for ORCID "0000-0002-6038-593X"

Eguchi, Raphael R.  ^[4];

• Search DOE PAGES for author "Eguchi, Raphael R."
• Search DOE PAGES for ORCID "0000-0002-2704-8464"

Huang, Po-Ssu  ^[5]

• Search DOE PAGES for author "Huang, Po-Ssu"
• Search DOE PAGES for ORCID "0000-0002-7948-2895"

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+ Show Author Affiliations

1. Biophysics Program, Stanford University, Stanford, CA, USA, Department of Bioengineering, Stanford University, Stanford, CA, USA
2. Program in Chemistry, Engineering, And Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA, Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
3. Department of Bioengineering, Stanford University, Stanford, CA, USA
4. Department of Bioengineering, Stanford University, Stanford, CA, USA, Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA, Department of Biochemistry, Stanford University, Stanford, CA, USA
5. Biophysics Program, Stanford University, Stanford, CA, USA, Department of Bioengineering, Stanford University, Stanford, CA, USA, Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA, Bio-X Institute, Stanford University, Stanford, CA, USA

Publication Date:

Tue Oct 11 00:00:00 EDT 2022

Sponsoring Org.:

USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:

1909309

Grant/Contract Number:  

AC02-76SF00515

Resource Type:

Published Article

Journal Name:

BioDesign Research

Additional Journal Information:

Journal Name: BioDesign Research Journal Volume: 2022; Journal ID: ISSN 2693-1257

Publisher:

American Association for the Advancement of Science (AAAS)

Country of Publication:

India

Language:

English