My research uses molecular dynamics simulations, with complimentary computational methods such as docking and QM calculations, to understand the biological functions of proteins and peptides.

The ileal bile acid binding protein (I-BABP) shows cooperative binding comparable to hemoglobin and specific site selectivity of ligands that only differ by a single hydroxyl group. I-BABP re-absorbs bile salts in the ileum and is of interest due to its role in cholesterol regulation and because the bile salt taurocholic acid is a germinant of C. diff spores. MD simulations are being employed to examine the allosteric interactions associated with cooperativty and selectivity and to determine the role of external ligands in binding in the protein interior.

Nisin is a naturally occurring antimicrobial peptide with a structure of several macrocyclic rings closed by thioether bonds. MD simulations of D-cysteine analogues of the first 12-residues of nisin have shown that the peptide backbone favours conformations that correspond to a disulfide bond closing the rings. Further work on this system will use QM/MM calculations to explicitly study disulfide bond formation and docking methods to predict the biological activity of the analogues.