Chemical and Biological Systems Optimization Lab

The Chemical and Biological Systems Optimization lab focuses on the development of algorithms and optimization techniques to support the analysis and redesign of biological systems at different scales including the protein, organism and community level.

At the metabolic network level, the lab focuses on the generation and analysis of genome-scale metabolic networks. The use of additional –omics data allows for further model curation along with the development of kinetic models. The optimization techniques developed within the lab are applied to these models to determine metabolic engineering strategies to optimize the production of industrially relevant products.

At the protein level, we use the Iterative Protein Redesign and Optimization procedure (IPRO) to predict enzyme variants within these metabolic pathways that exhibit improved catalysis. We also use IPRO for various other applications, including de novo antibody design, protein specificity alteration, and grafting of novel binding sites into existing protein architectures.

Current research focuses in the lab include:

• Development of computational tools for both protein and metabolic engineering
• Creation and curation of genome-scale metabolic models, along with the incorporation of –omics data for a number of industrially relevant organisms
• Elucidating organism or tissue interactions using metabolic models
• Prediction of metabolic engineering intervention strategies to optimize yields of industrially relevant bioproducts
• De novo design of high-affinity antibody variable regions for various antigen epitiopes
• Redesign of enzymes with improved catalytic properties using transition state analogue stabilization
• Establishment of stable, water-selective transmembrane proteins