OUR SCIENCE
Representative peer-reviewed scientific papers that used our academic methods to design superior enzymes, antibodies, and vaccine immunogens.
Selected peer-reviewed papers that use protein stability and expression optimization:
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Goldenzweig, A. et al. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol. Cell 2016.
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Campeotto, I. et al. One-Step Design of a Stable Variant of the Malaria Invasion Protein RH5 for Use as a Vaccine Immunogen. Proc. Natl. Acad. Sci. U. S. A. 2017.
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Sherkhanov, S. et al. Isobutanol Production Freed from Biological Limits Using Synthetic Biochemistry. Nat. Commun. 2020.
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Hettiaratchi, M. H. et al. Reengineering Biocatalysts: Computational Redesign of Chondroitinase ABC Improves Efficacy and Stability. Sci Adv 2020.
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Peleg, Y. et al. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J. Mol. Biol. 2021.
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Kriegel, M. et al. A PROSS-Designed Extensively Mutated Estrogen Receptor α Variant Displays Enhanced Thermal Stability While Retaining Native Allosteric Regulation and Structure. Sci. Rep. 2021.
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Barber-Zucker, S. et al. Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences. J. Am. Chem. Soc. 2022.
Selected peer-reviewed papers that use enzyme activity optimization:
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Khersonsky, O. et al. Automated Design of Efficient and Functionally Diverse Enzyme Repertoires. Mol. Cell 2018.
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Bengel, L. L. et al. Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles with Simple Haloalkanes. Angew. Chem. Int. Ed Engl. 2021.
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Vos, P. D. et al. Computationally Designed Hyperactive Cas9 Enzymes.
Nat. Commun. 2022.
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Barber-Zucker, S. et al. Designed High-Redox Potential Laccases Exhibit High Functional Diversity. ACS Catal. 2022.
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Gomez de Santos, P. et al. Repertoire of Computationally Designed Peroxygenases for Enantiodivergent C-H Oxyfunctionalization Reactions.
J. Am. Chem. Soc. 2023.
Selected peer-reviewed papers that use protein-protein interactions optimization:
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Netzer, R. et al. Ultrahigh Specificity in a Network of Computationally Designed Protein-Interaction Pairs. Nat. Commun. 2018.
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VanDrisse, C. M. et al. Computationally Designed Pyocyanin Demethylase Acts Synergistically with Tobramycin to Kill Recalcitrant Pseudomonas Aeruginosa Biofilms. Proc. Natl. Acad. Sci. U. S. A. 2021.
Selected peer-reviewed papers that show the successful humanization of therapeutic antibodies:
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Tennenhouse, A. et al. Reliable energy-based antibody humanization and stabilization. Nat. Biomed. Eng. (2023)
See additional peer-reviewed papers
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Lipsh-Sokolik, R. et al. Combinatorial Assembly and Design of Enzymes. Science 2023.
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Yang, S. et al. Improving the Thermostability of Glycosyltransferase YojK by Targeting Mutagenesis for Highly Efficient Biosynthesis of Rebaudioside D. Molecular Catalysis 2023.
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Borgert, S. R. et al. Moonlighting Chaperone Activity of the Enzyme PqsE Contributes to RhlR-Controlled Virulence of Pseudomonas Aeruginosa.
Nat. Commun. 2022.
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Lv, Y. et al. Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals. Applied Biosciences 2022.
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Joho, Y. et al. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella Sakaiensis PETase and Variants with Improved Stability and Activity. Biochemistry 2022.
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Whitefield, C. et al. Computational Design and Experimental Characterisation of a Stable Human Heparanase Variant. RSC Chemical Biology 2022.
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Beltrán, J. et al. Rapid Biosensor Development Using Plant Hormone Receptors as Reprogrammable Scaffolds. Nat. Biotechnol. 2022.
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Leonard, A. C. et al. Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning.
Protein Eng. Des. Sel. 2022.
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Allouche-Arnon, H. et al. Computationally Designed Dual-Color MRI Reporters for Noninvasive Imaging of Transgene Expression.
Nat. Biotechnol. 2022.
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Dong, F. et al. Insights of Conformational Dynamics on Catalytic Activity in the Computational Stability Design of Bacillus Subtilis LipA.
Arch. Biochem. Biophys. 2022.
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Listov, D. et al. Assessing and Enhancing Foldability in Designed Proteins. Protein Sci. 2022.
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Ospina, F. et al. Selective Biocatalytic N-Methylation of Unsaturated Heterocycles.
Angew. Chem. Int. Ed Engl. 2022. -
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Vongsouthi, V. et al. A Rationally and Computationally Designed Fluorescent Biosensor for D-Serine. ACS Sens 2021.
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Hsieh, C. L. et al. Stabilized Coronavirus Spike Stem Elicits a Broadly Protective Antibody. Cell Rep. 2021.
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Dietler, J. et al. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J. Mol. Biol. 2021.
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Mao, G. et al. Sustainable Approach for Degradation and Detoxification of Malachite Green by an Engineered Polyphenol Oxidase at High Temperature. J. Clean. Prod. 2021.
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Adams, E. M. et al. Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction. JACS Au 2021.
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Ben-Sasson, A. J. et al. Design of Biologically Active Binary Protein 2D Materials. Nature 2021.
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Wang, J. et al. Enzyme Engineering and in Vivo Testing of a Formate-Reduction Pathway. Synthetic Biology 2021.
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Dermouche, S. et al. Optimizing the First TPR Domain of the Human SPAG1 Protein Provides Insight into the HSP70 and HSP90 Binding Properties. Biochemistry 2021.
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Badri, A. et al. Complete Biosynthesis of a Sulfated Chondroitin in Escherichia Coli. Nat. Commun. 2021.
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Xu, J. et al. Computational Design of Highly Stable and Soluble Alcohol Dehydrogenase for NADPH Regeneration.
Bioresources and Bioprocessing 2021.
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Zurek, P. J. et al. Growth Amplification in Ultrahigh-Throughput Microdroplet Screening Increases Sensitivity of Clonal Enzyme Assays and Minimizes Phenotypic Variation. Lab Chip 2021.
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Lajoie, M. J. et al. Designed Protein Logic to Target Cells with Precise Combinations of Surface Antigens. Science 2020.
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Lee, K. B. et al. Generation of Highly Selective Monoclonal Antibodies Inhibiting a Recalcitrant Protease Using Decoy Designs.
Biotechnol. Bioeng. 2020.
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Rezan, G. et al. Increasing Thermal Stability and Improving Biodistribution of VEGFR2-Binding Affibody Molecules by a Combination of in Silico and Directed Evolution Approaches. Scientific Reports 2020.
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Valliere, M. A. et al. A Bio-Inspired Cell-Free System for Cannabinoid Production from Inexpensive Inputs. Nat. Chem. Biol. 2020.
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Morrison, C. S. et al. Improved Soluble Expression and Use of Recombinant Human Renalase. PLoS One 2020.
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Georgoulia, P. S. et al. Deciphering the Molecular Mechanism of FLT3 Resistance Mutations. FEBS J. 2020.
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Lambert, A. R. et al. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Structure 2020.
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Malladi, S. K. et al. One-Step Sequence and Structure-Guided Optimization of HIV-1 Envelope gp140. Current Research in Structural Biology 2020.
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Tullman, J. et al. A ClpS-Based N-Terminal Amino Acid Binding Reagent with Improved Thermostability and Selectivity. Biochem. Eng. J. 2020.
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Klaus, M. et al. Ketosynthase Domain Constrains the Design of Polyketide Synthases. ACS Chem. Biol. 2020.
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Risso, V. A. et al. Enhancing a DE Novo Enzyme Activity by Computationally-Focused, Ultra-Low-Throughput Sequence Screening. Chem. Sci. 2020.
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Lei, Y. et al. Engineering Chromosome Region Maintenance 1 Fragments That Bind to Nuclear Export Signals. Protein Sci. 2019.
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Zahradník, J. et al. Flexible Regions Govern Promiscuous Binding of IL-24 to Receptors IL-20R1 and IL-22R1. FEBS J. 2019.
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Lee, K. B. et al. Reducing Proteolytic Liability of a MMP-14 Inhibitory Antibody by Site-saturation Mutagenesis. Protein Sci. 2019.
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Buldun, C. M. et al. SnoopLigase Catalyzes Peptide–Peptide Locking and Enables Solid-Phase Conjugate Isolation. J. Am. Chem. Soc. 2018.
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Lapidoth, G. et al. Highly Active Enzymes by Automated Combinatorial Backbone Assembly and Sequence Design. Nat. Commun. 2018.
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Trudeau, D. L. et al. Design and in Vitro Realization of Carbon-Conserving Photorespiration. Proc. Natl. Acad. Sci. U. S. A. 2018.
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Gan, J. et al. Native Mass Spectrometry of Recombinant Proteins from Crude Cell Lysates. Anal. Chem. 2017.
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Goldsmith, M. et al. Overcoming an Optimization Plateau in the Directed Evolution of Highly Efficient Nerve Agent Bioscavengers.
Protein Eng. Des. Sel. 2017.
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Vernon, R. M. et al. Stabilization of a Nucleotide-Binding Domain of the Cystic Fibrosis Transmembrane Conductance Regulator Yields Insight into Disease-Causing Mutations. J. Biol. Chem. 2017.
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Brazzolotto, X. et al. Bacterial Expression of Human Butyrylcholinesterase as a Tool for Nerve Agent Bioscavengers Development. Molecules 2017.