Abstract
A major challenge in designing proteins de novo to bind user-defined ligands with high affinity is finding backbones structures into which a new binding site geometry can be engineered with high precision. Recent advances in methods to generate protein fold families de novo have expanded the space of accessible protein structures, but it is not clear to what extend de novo proteins with diverse geometries also expand the space of designable ligand binding functions. We constructed a library of 25,806 high-quality ligand binding sites and developed a fast protocol to place (“match”) these binding sites into both naturally occurring and de novo protein families with two fold topologies: Rossman and NTF2. Each matching step involves engineering new binding site residues into each protein “scaffold”, which is distinct from the problem of comparing already existing binding pockets. 5,896 and 7,475 binding sites could be matched to the Rossmann and NTF2 fold families, respectively. De novo designed Rossman and NTF2 protein families can support 1,791 and 678 binding sites that cannot be matched to naturally existing structures with the same topologies, respectively. While the number of protein residues in ligand binding sites is the major determinant of matching success, ligand size and primary sequence separation of binding site residues also play important roles. The number of matched binding sites are power law functions of the number of members in a fold family. Our results suggest that de novo sampling of geometric variations on diverse fold topologies can significantly expand the space of designable ligand binding sites for a wealth of possible new protein functions.
Highlights
Ligand binding is a major class of protein functions, and the ability to design ligand binding de novo has many important applications [1] such as engineering of biosensors and ligand-controlled protein functions [2, 3]
Because ligand binding site geometries need to be accommodated by protein backbone scaffolds at high accuracy, the diversity of scaffolds is a major limitation for designing new ligand binding functions
Advances in computational protein structure design methods have significantly increased the number of accessible stable scaffold structures
Summary
Ligand binding is a major class of protein functions, and the ability to design ligand binding de novo has many important applications [1] such as engineering of biosensors and ligand-controlled protein functions [2, 3]. Designing new ligand binding proteins requires the ability to build binding sites with defined geometries into stable protein scaffolds that can accommodate the desired interaction geometry with high accuracy. While this approach has led to the successful design of enzymatic activity [7, 8], ligand binding proteins [9, 10], and biosensors [2, 3, 11], it has been limited by both the availability of defined binding site geometries and stable protein scaffolds into which these binding sites can be designed [3]. Other methods [13, 14] use statistics from the protein data bank (PDB) to find three-dimensional placements of amino acid residues that form favorable interactions with fragments of a ligand, which can be assembled into complete binding site geometries. Protein-ligand interactions defined by these methods have been built successfully into a de novo designed beta barrel [12], and a parametrically designed helical bundle [14]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
