Molecular Dynamics Simulations
We are interested in how proteins' and enzymes' structures are related to their function. At Centenary, we are using the Schulten group's software NAMD to perform steered molecular dynamics simulations of various mutations of casein kinase. The simulations are meant to mimic experiments performed in Dr. Cynthia Brame's (Centenary biology) lab help us to understand which amino acids are responsible for activating/deactivating the enzyme through phosphorylation.
Fluorescence is a powerful tool for measuring structural changes in proteins. Combining steady state and time-dependent fluorescence, we obtain a good understanding of the number of structures among which a protein fluctuates. The state occupation can be biased by varying different experimental coordinates such as temperature (e.g., free energy), substrate (e.g., active vs. inactive protein), or time (e.g., amyloid formation).