My research interests are focused on the application of high field NMR spectroscopic methods to determine novel protein structures in order to gain insight into function at the molecular level. Related to this area, I am also interested in probing the complex relationship between protein sequence and structure. While NMR spectroscopy plays a key role in most of our studies, my laboratory also uses a number of other biophysical tools as well as bioinformatics, chemistry, biochemistry, and molecular biology techniques. Two main projects currently underway in the lab are summarized briefly here.

I. The Protein Folding Code - Conformational Switching and the Evolution of New Folds
How does the amino acid sequence of a protein determine its three-dimensional structure? Understanding the relation between protein sequence and structure is a significant issue in structural genomics and deciphering the protein folding code remains one of the fundamental unsolved problems in structural biology. We have been using small IgG- and albumin-binding domains from Streptococcal Protein G as model systems to study conformational switching between alpha and beta structures with a range of genetic and biophysical tools. A key question we are investigating is what is the minimum number of amino acids required to specify one fold over another? Our present work has important implications for understanding how new protein folds evolve and may also provide novel insight into the prediction of 3D structures from sequence data.

II. Microbial and Eukaryotic Structural Genomics
The first organism to have its genome sequenced entirely was the human pathogen, Haemophilus influenzae, a causative agent in diseases including meningitis, sepsis, and upper respiratory infections. Approximately 25% of the 1740 genes in this genome had no known function. These genes were termed conserved "hypotheticals" or orphan genes. As the number of sequenced genomes grew, a recurring observation was that a significant proportion (as high as 70% in some cases) of prokaryotic, archaeal, and eukaryotic genomes had unknown function. This lack of functional annotation represents a significant gap in our understanding of biology and biochemistry. Since 3D protein structure is more highly conserved than sequence, it was thought that a genome-wide effort to determine 3D structures - termed structural genomics - may assist in the annotation of function for these unknowns as well as provide structures for other incompletely characterized proteins. That is, structural homology might reveal connections to function that are hidden by analysis of sequence data. Our structural genomics targets have included hypotheticals from Gram-negative bacteria as well as splice variants of human proteins. Many of the 3D structures have provided valuable insights into molecular function. As an extension to this work, we are currently developing methods for determining the substrate specificity of putative enzymes using a combination of knockouts, metabolomics, and ligand screening.

Support from the NIH, NSF, DOE and Keck Foundation is gratefully acknowledged.