Computational Biochemistry and Proteomics

Abstract: 

Computational Biochemistry and Proteomics

This research group is involved in two major projects. One focuses on anti-cancer and antimicrobial drug design that target the proteasome, a barrel-shaped ATP requiring protease that is responsible for proteostasis in cells. Inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. For this project, the researchers perform molecular docking and QSAR studies to guide the synthesis of novel hybrid proteasome inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.

The other project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. The researchers use the Discovery Studio software package (Accelrys, Inc.) and other molecular dynamics software (Gromacs and NAMD) designed for biomolecular systems to perform docking studies in order to elucidate the preferred protein substrates for these proteases. In addition, they are collaborating with the Center for Mass Spectrometry and Proteomics and their data are being stored on shared MSI/Mass Spec resources. They use proteomics software packages for analyzing mass spectrometry data to identify proteins cleaved by their proteases. 

Group name: 
johnsonj