Abstract by Wendy Billings
Chemistry and Biochemistry
Dennis Della Corte
Using molecular dynamics to structurally characterize cooperative protein interactions
Noncovalent interactions involving amino acid side chains play key roles in protein folding, function, and stability. Several of these include interactions between opposing charges (salt bridges), hydrophobic residues, and cation-pi or anion-pi side chain pairs. Recent experimental work demonstrates the ability of a central aromatic or hydrophobic residue to interact cooperatively with two distant opposing charges, stabilizing peptide tertiary structure by up to ~3kcal/mol. Experimental methods such as NMR and x-ray crystallography have been applied in an attempt to characterize the structural basis for the interaction; however, they have shown severe limitations. Here we explore the additional use of molecular dynamics simulations in understanding experimental results and discovering the mechanism of mediation for this cooperative interaction.