Download MendeleyDe novo design of cavity-containing proteins with a backbone-centered neural network energy function.
Xu, Y., Hu, X., Wang, C., Liu, Y., Chen, Q., Liu, H.(2024) Structure 32: 424
- PubMed: 38325370
- DOI: https://doi.org/10.1016/j.str.2024.01.006
- Primary Citation of Related Structures:
8HDU, 8HDV - PubMed Abstract:
The design of small-molecule-binding proteins requires protein backbones that contain cavities. Previous design efforts were based on naturally occurring cavity-containing backbone architectures. Here, we designed diverse cavity-containing backbones without predefined architectures by introducing tailored restraints into the backbone sampling driven by SCUBA (Side Chain-Unknown Backbone Arrangement), a neural network statistical energy function. For 521 out of 5816 designs, the root-mean-square deviations (RMSDs) of the Cα atoms for the AlphaFold2-predicted structures and our designed structures are within 2.0 Å. We experimentally tested 10 designed proteins and determined the crystal structures of two of them. One closely agrees with the designed model, while the other forms a domain-swapped dimer, where the partial structures are in agreement with the designed structures. Our results indicate that data-driven methods such as SCUBA hold great potential for designing de novo proteins with tailored small-molecule-binding function.
Organizational Affiliation:
Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Centre for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
