The beast pictured at right is staphylococcal nuclease (SNase), a bacterial enzyme that cleaves DNA and RNA and has been implicated in several diseases. Of greater interest to me than its insidious or benign function is that SNase serves as a prototype protein for the study of protein folding and, more generally, protein dynamics. My interest is in a fundamental characterization of proteins, namely in how they move (protein dynamics) and how their motions relate to their biochemical function.
My specific concern is to apply computational tools to interpret certain quantities - called order parameters and correlation times - obtained from NMR and thereby obtain a detailed model of protein side-chain motions. NMR has been a powerful tool in elucidating backbone motion in proteins, and more recently it has been applied to the study of protein side-chain motions. However, while NMR can quantify the magnitude and time scale of motions, it cannot provide a precise model of motion - hence the need for MD simulation, which can provide such a model.
Specific projects underway include simulation of small proteins such as SNase in a solution environment to characterize motions of selected short side-chains, and simulation of small peptides in a crystalline environment to validate methods.