Institute for Tuberculosis Research
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The genome projects yielded the sequences of tens of thousands of proteins. Elucidating the roles these proteins play in health and disease, and also how they can be used and/or modified for the development of novel therapeutics, biomaterials, biosensors, methods for energy production and methods for environmental remediation, will be aided by a better understanding of how a protein's amino acid sequence determines its structure and how a structure determine function. In the Jeffery lab we are using biophysical and biochemical methods along with computer-based structure analysis in several projects to study the connections between protein sequences, structures, and functions.
(1) Analysis of protein sequences and structures to elucidate the connections between sequence, structure and function. This information might help in the future in developing better methods to predict a protein's function(s) from its sequence or structure. Two current projects in this area include an analysis of ligand binding sites in protein crystal structures and a study of the sequences and structures of "moonlighting proteins". Many protein functions can be inferred from the known functions of homologous proteins, but determining protein functions is complicated by an increasing number of "moonlighting proteins", proteins that have more than one function where the multiple functions are not a result of splice variants, gene fusions, or multiple isoforms (Jeffery, C. J. Moonlighting Proteins. (1999) Trends in Biochemical Sciences. 24: 8-11). We are preparing a database of the known moonlighting proteins and performing an analysis of their sequences and structures. Knowing more about moonlighting proteins could help in predicting which additional proteins might also have a second function, which would be useful in determining the function(s) of the thousands of proteins identified through the genome projects and the functions of the "unknown" proteins whose structures were solved as part of the Protein Structure Initiative. In addition, since the ability of proteins to moonlight can complicate interpretation of the results of proteomics projects, identifying the roles of proteins in disease, and the selection of biomarkers, understanding which proteins moonlight can be important for both basic research and medicine.
(2) The development of novel approaches to increase the expression of transmembrane proteins for biochemical analysis and structure determination. Membrane proteins play key roles in health and disease and are the targets of the majority of pharmaceuticals in use today, but much less is known about their structures and mechanisms of function than for soluble proteins because of the challenges in their expression, purification, and structure determination. The goal of our new approaches is to alleviate the bottleneck in protein expression.
(3) In a previous project, we elucidated the reaction mechanism of a glycolytic enzyme that moonlights as a tumor cell motility factor in breast cancer cells: phosphoglucose isomerase/autocrine motility factor (PGI/AMF). By solving six structures of PGI/AMF with different ligands bound, we developed a model of the multistep catalytic mechanism for this multifunctional enzyme/growth factor.