Our lovely group


- NMRPipe
- Sparky
- Ploticus
- MolMol
- PyMol
- MestreC

Research Interests

The research in Professor Andersen’s group focuses on both the fundamental thermodynamics and structural features associated with biorecognition phenomena and practical applications in drug and protein design. The primary biophysical tools employed are spectroscopic: NMR determinations of polypeptide structure and dynamics, IR- and fluorescence-monitored T-jump kinetics for folding pathways, CD studies of the melting of secondary and tertiary structure. Drug design efforts are supported by NMR structural data for protein hormones and enzymes for key steps required for the viability of bacteria. Active programs in mutant protein over-expression, peptide synthesis, and combinatorial synthesis of small molecule inhibitor libraries support this effort. Illustrative projects are briefly outlined in the following paragraphs.

The earliest stages of protein folding are studied by designing helices and beta hairpins with specific labeling patterns that allow the definition of the thermodynamics, kinetics, and pathways of structuring using NMR and T-jump methods. These studies have already determined the time scales of helix (200 ns) and hairpin (4 – 10 µs) formation and have established that helix formation, but not sheet formation, occurs too rapidly to contribute during the rapid hydrophobic collapse phase of protein folding. The mechanistic details of secondary structure formation will be addressed.

‘Minimalist’ proteins (< 25 residues) that display the diagnostic folding features of much larger native proteins are being designed. These systems should provide an atom-level understanding of the factors that yield stable protein folds and are small enough to allow for computational simulations that can be experimentally tested. To date, fully cooperative folding driven by the hydrophobic effect has been realized with systems as small as 20 residues.

Potent, selective inhibitors of the LpxC enzyme of Pseudomonas aeruginosa are viewed as a potential medicinals for treating Cystic Fibrosis. Solving the structure of this 288 residue protein with a tightly bound inhibitor at the active site using multi-dimensional NMR methods and the design of inhibitors based on this structure are the ultimate aims of the research. In the meantime, fluorine NMR is being used to determine the relative affinities of leads from combi-synthesis libraries. The other medicinal chemistry project is the design of more stable versions of leptin, the obese protein. Leptin mutants will be used to define the recognition requisites at leptin receptors.