In the genomic era, with high throughput screening and sequence comparisons, biological research is dependent upon computational power. The Wackett laboratory strives to answer important biological questions, which requires the use of computational tools. They have a number of projects using the computational abilities at MSI.
- Data mining of genomes for proteins whose functions were elucidated in this lab. To determine function and relatedness to other experimentally determined proteins, the researchers utilize sequence alignment programs like ClustalW and T-Coffee, phylogenetic programs like RaxML and Phylip, and structure analysis programs like Schrodinger and Discovery Studios. This computational work allows the researchers to make hypotheses that they can further investigate in the laboratory via detailed biochemical analysis.
- Using protein crystallization to answer questions about enzyme mechanisms and substrate binding. MSI resources are used to solve crystallographic coordinates and visualize solved structures.
- Structural comparison and substrate docking experiments.
- Project 1: modeling protein mutants with varying substrate specificity to allow for a larger substrates to facilitate mechanistic studies.
- Project 2: determining which substances in tracking fluids have the potential to dock into biodegradative enzyme active sites. This project will use large-scale docking methods for analysis and target determinations.
- Whole-genome sequencing. The lab has initiated a new whole-genome sequencing project and are looking to scale up to metagenomic sequencing.