Computational design of a modular protein sense/response system

Glasgow, Anum; Huang, Yao-Ming; Mandell, Daniel J.; Thompson, Michael C.; Ritterson, Ryan; Loshbaugh, Amanda L.; Pellegrino, Jenna; Krivacic, Cody; Pache, Roland A.; Barlow, Kyle; Ollikainen, Noah; Jeon, Deborah; Fraser, James S.; Kortemme, Tanja

doi:10.1101/648485

Cited by 20 publications

(33 citation statements)

References 52 publications

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“…Using the new fast match protocol introduced here as well as the Rosetta matcher, we were able to match a library of high-quality binding sites to de novo protein fold families. To engineer new ligand binding proteins, the matching step is typically followed by sequence design (3,8) to optimize the binding site protein environment. Ligand binding site design is a challenging problem because the designed sequence must simultaneously be compatible with the protein fold and precisely place binding site residues in their desired geometries for favorable interactions with the ligand.…”

Section: Discussionmentioning

confidence: 99%

“…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). Naturally occurring proteins recognize their cognate ligands with high affinity and specificity using defined three-dimensional geometries of binding sites with high shape complementarity between ligands and proteins.…”

Section: Introductionmentioning

confidence: 99%

“…Designing new ligand binding proteins therefore 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(6, 7), ligand binding proteins(8, 9), and biosensors(2, 3, 10), it has been limited by both the availability of defined binding site geometries and stable protein scaffolds into which these binding sites can be placed(3).…”

Section: Introductionmentioning

confidence: 99%

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De novoprotein fold families expand the designable ligand binding site space

Pan

Kortemme

2021

Preprint

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A major challenge in designing proteins de novo to bind user-defined ligands with high specificity and affinity is finding backbones structures that can accommodate a desired binding site geometry 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. 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.Author summaryDe novo design of proteins that can bind to novel and highly diverse user-defined small molecule ligands could have broad biomedical and synthetic biology applications. 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. Understanding how many new ligand binding sites can be accommodated by the de novo scaffolds is important for designing novel ligand binding proteins. To answer this question, we constructed a large library of ligand binding sites from the Protein Data Bank (PDB). We tested the number of ligand binding sites that can be accommodated by de novo scaffolds and naturally existing scaffolds with same fold topologies. The results showed that de novo scaffolds significantly expanded the ligand binding space of their respective fold topologies. We also identified factors that affect difficulties of binding site accommodation, as well as the relationship between the number of scaffolds and the accessible ligand binding site space. We believe our findings will benefit future method development and applications of ligand binding protein design.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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De novoprotein fold families expand the designable ligand binding site space

Pan

Kortemme

2021

Preprint

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“…These were also shown to regulate cellular activities in vivo, but the crystal structures of the designs evidenced substantial differences to the predicted binding modes. Remarkable computational design work was performed by Glasgow and colleagues, where a CID was rationally designed by transplanting the binding sites of a ligand to an existing protein dimer 13 . However, the precise design of key interaction residues to mediate small molecule interactions and control CIDs remain an extremely challenging computational design problem.…”

Section: Introductionmentioning

confidence: 99%

“…All these approaches focus on chemically induced dimerization systems 1,[11][12][13] , yet chemical disruption systems also have important applications in synthetic biology and remain much less explored 14,15 .…”

Section: Introductionmentioning

confidence: 99%

A rational blueprint for the design of chemically-controlled protein switches

Shui

Gainza

Scheller

et al. 2021

Preprint

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Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. However, the repertoire of small-molecule protein switches is insufficient for many applications, including those in the translational spaces, where properties such as safety, immunogenicity, drug half-life, and drug side-effects are critical. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions as OFF- and ON-switches. The designed binders and drug-receptors form chemically-disruptable heterodimers (CDH) which dissociate in the presence of small molecules. To design ON-switches, we converted the CDHs into a multi-domain architecture which we refer to as activation by inhibitor release switches (AIR) that incorporate a rationally designed drug-insensitive receptor protein. CDHs and AIRs showed excellent performance as drug responsive switches to control combinations of synthetic circuits in mammalian cells. This approach effectively expands the chemical space and logic responses in living cells and provides a blueprint to develop new ON- and OFF-switches for basic and translational applications.

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The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology

Bojar

Fussenegger

2019

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Engineered proteins with enhanced or altered functionality, generated for example by mutation or domain fusion, are at the core of nearly all synthetic biology endeavors in the context of precision medicine, also known as personalized medicine. From designer receptors sensing elevated blood markers to effectors rerouting signaling pathways to synthetic transcription factors and the customized therapeutics they regulate, engineered proteins play a crucial role at every step of novel therapeutic approaches using synthetic biology. Here, we discuss recent developments in protein engineering, aided by advances in directed evolution, de novo design and machine learning. Building on clinical successes already achieved with chimeric antigen receptor (CAR-) T cells and other cellbased therapies, these developments are expected to further enhance the capabilities of mammalian synthetic biology in biomedical and other applications.

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Computational design of a modular protein sense/response system

Cited by 20 publications

References 52 publications

De novoprotein fold families expand the designable ligand binding site space

De novoprotein fold families expand the designable ligand binding site space

A rational blueprint for the design of chemically-controlled protein switches

The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology

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