De novo design of functional proteins for biomedical applications
2Cardiovascular Research Institute, University of California, San Francisco, USA
Proteins are amazing macromolecules that carry out a myriad of roles. While traditional protein engineering is limited by naturally occurring building blocks, de novo protein design enables us to build proteins completely from scratch, custom designed to carry out predetermined functionalities.
We have developed a computational method that enables the de novo design of bespoke proteins, by generating precise geometric matches to a chosen target backbone, chosen from highly prevalent structural motifs, as surveyed across the Protein Data Bank. This nature-inspired approach is complemented by our newly developed protein-protein interface design algorithms.
Using this method, we designed two distinct classes of protein materials, spanning different sizes, structural requirements, and design complexities: protein nanopores and therapeutic binders. Protein nanopores are large membrane-bound, channel-forming complexes primarily utilized for long-read nucleic acid sequencing. Nanopore sequencing is reliant on the ion flow through the channel, which is governed by the physical dimensions of the protein complex. We accurately designed two generations of protein nanopores with distinct predetermined structural features. These de novo nanopores are readily incorporated into industrial nanopore sequencing devices, and display optimal conductance and high stability and enhanced signal-to-noise ratio.
Furthermore, we designed a small protein binder, with tight and specific binding to IL-6, a pleiotropic cytokine. with non-ideal structural features. This was achieved without display-based optimization, directly from computational design to a validated binder, with sub-micromolar KD, a rare and exciting accomplishment. This widely applicable approach enables the future design of new classes of functional proteins and biomaterials.