1Biophysics Program, Stanford University, Stanford, CA, USA
2Department of Bioengineering, Stanford University, Stanford, CA, USA
3Program in Chemistry, Engineering, And Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
4Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Stanford, CA, USA
5Department of Biochemistry, Stanford University, Stanford, CA, USA
6Bio-X Institute, Stanford University, Stanford, CA, USA
| Received 15 Feb 2022 |
Accepted 26 May 2022 |
Published 11 Oct 2022 |
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.
