Proteins & Enzyme Mechanisms

We investigate the structure, dynamics, and function of proteins and enzymes using a suite of computational approaches. Our goal is to understand how molecular architecture encodes biological function.

Topics

• Conformational dynamics and allostery in proteins
• Enzyme catalytic mechanisms (serine proteases, hydrolases, oxidoreductases)
• Protein–ligand binding and drug discovery applications
• Effect of mutations on protein stability and function
• Intrinsically disordered proteins

Approaches

• All-atom and coarse-grained MD simulations
• Umbrella sampling and metadynamics for free energy profiles
• Normal mode analysis
• Network-based analysis of protein dynamics