Professor Joseph Johnson

UMD Swenson Col of Sci & Eng
UM Duluth
Duluth
Project Title: 
Computational Biochemistry and Proteomics

This research group is involved in two major projects using MSI:

  • One project focuses on anti-cancer and antimicrobial drug design that target enzymes like the proteasome or integral membrane proteins like cell surface growth receptors and transporters. For example, inhibition of the proteasome leads to cancer cell apoptosis or programmed cell death. This project requires access to the molecular modeling and simulation resources to perform molecular docking (e.g., with AUTODOCK and DOCK) and QSAR studies (e.g., with Tripos Sybyl , GAUSSIAN, and the Cambridge Structural Database) to guide the synthesis of novel hybrid inhibitors with some similarity to known scaffolds. Similar methods will be applied to other anti-microbial compounds.
  • The second project is to identify the structure and function of a novel family of membrane-bound aspartyl proteases. This uses molecular modeling and simulation resources and will use structural biology resources designed for biomolecular systems, biological force fields, and docking software in the future to perform docking studies in order to elucidate the preferred protein substrates for these proteases. In addition, this lab collaborates with the Center for Mass Spectrometry and their data are being stored on shared MSI/Mass Spec resources. They use a variety of the proteomics software packages for analyzing mass spectrometry data to identify proteins cleaved by their proteases.

In routine applications, the lab uses a variety of software packages, including the Vector NTI software package for molecular biology and genetic engineering applications; software for data analysis, curve fitting, and graphing; and MATLAB and Mathematica for numerical computation.

Project Investigators

Professor Joseph Johnson
Hyojung Kim
 
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