Aromatic Ring Flips and Local Volume Fluctuations in BPTI

Sammanfattning: Aromatic ring flips are a classic example of a dynamic process in proteins. Discovered decades ago, methodological limitations hindered progress at the time. Ring flips have gained new interest and experimentalists can measure the flip rate and thermodynamic quantities associated with it. Molecular Dynamics (MD) simulations provide atomic resolution data and can complement the experimental work since it allows us to 1) compare theoretical and experimental values, 2) distinguish between local and global activation volumes and 3) elucidate the ring flip mechanism. Ring flips are slow processes and an enhanced sampling technique is necessary to sample them in reasonable computational times. Metadynamics, an enhanced sampling technique, works by applying a bias potential which “fills up” energy minima for a system coordinate, often called Collective Variable (CV) and while the dynamics are inherently non-physical, rare events can be sampled, thus creating extended ensembles. I have calculated the local activation volumes for buried residues in Bovine Pancreatic Trypsin Inhibitor(BPTI) in metadynamics trajectories and found qualitative agreement with experimental studies, showing that there is a positive activation volume associated with flips. I have also calculated the compressiblity of the transition state ‡κ=5.40'10−4 bar−1, developed an indirect CV that can force ring flips if biased and showed that solvation may be associated with flip kinetics.