580 California St., Suite 400
San Francisco, CA, 94104
Key research themes
1. How can computational methods reshape enzyme conformational landscapes to enhance catalytic efficiency and substrate selectivity?
This research theme explores the use of computational protein design, particularly multistate and multiconformational modeling, to rationally tune enzyme conformational ensembles. Since enzyme function is inherently linked to their structural plasticity and ability to adopt multiple conformations, remodeling these energy landscapes towards catalytically productive states can significantly improve activity and alter substrate specificity. Such computational strategies enable targeted stabilization of reactive conformations, providing a more efficient pathway to engineer enzymes beyond traditional single-state design methods.
Key finding: Utilizing multistate computational protein design, the authors redesigned E. coli aspartate aminotransferase to stabilize the less-populated but catalytically active closed conformation, thereby increasing catalytic... Read more
Key finding: By adapting computational protein design methods with Monte Carlo exploration and free energy landscape flattening, the study ranked thousands of DHFR mutants predicting those that reduce binding affinity to the antibiotic... Read more
Key finding: The study used transition path sampling and molecular dynamics to design a mutant of aromatic amine dehydrogenase that introduces favorable subpicosecond protein motions coupled to catalysis, preserving essential fast... Read more
2. What structural and mechanistic insights into substrate binding and enzyme dynamics facilitate the engineering of efficient, thermostable enzymes for industrial applications?
This theme focuses on elucidating the detailed substrate binding modes, dynamic behavior, and stabilization mechanisms of enzymes, especially thermophilic variants, to inform rational engineering aimed at improving activity and stability under industrially relevant conditions. Understanding multiple substrate binding conformations, allosteric regulation, and structural plasticity enables the identification of mutational hotspots and the design of variants with enhanced thermostability and substrate turnover rates, critical for processes like plastic degradation and biocatalysis.
Key finding: High-resolution crystal structures of PES-H1 and PES-H2 hydrolases complexed with PET substrate analogues, combined with molecular dynamics simulations, revealed multiple substrate binding modes and key residues governing... Read more
Key finding: Through detailed analysis of protein motions spanning femtoseconds to milliseconds, the review highlights how targeted mutations and chimeric enzyme creation can modulate enzyme flexibility to influence ligand binding and... Read more
Key finding: The review synthesizes practical approaches to enhance enzyme stability under harsh industrial conditions including high temperature, extreme pH, and presence of surfactants. It underscores how molecular interactions such as... Read more
3. How can cell-free and in vitro prototyping platforms accelerate enzyme pathway optimization for industrially relevant non-model organisms?
This research area investigates the development and application of cell lysate-based in vitro systems to bypass slow, iterative in vivo metabolic engineering cycles. By enabling combinatorial assembly and rapid evaluation of enzyme variants and pathways ex vivo, these platforms provide scalable and high-throughput workflows particularly amenable to engineering complex biosynthetic pathways in genetically intractable or slow-growing organisms. The approach facilitates data-driven design and accelerates identification of high-performing enzyme combinations essential for industrial bioproduction.
Key finding: The iPROBE platform integrates cell-free protein synthesis with combinatorial metabolic pathway assembly from crude lysates for rapid screening and ranking of enzyme variants. Application to the 3-hydroxybutyrate pathway... Read more