Protein Functional Dynamics and Energy Landscapes

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We are interested in how biological macromolecules, such as proteins, function. Specifically, we propose the following lines of study: 1) Protein Folding. Once synthesized in a cell, proteins, spontaneously adopt a specific 3D shape (i.e. fold) in millionths of a second. Moreover, they accomplish this usually without error. We propose a folding mechanism in which the protein adopts an intermediate which is expanded, yet devoid of water. There are profound consequences of such intermediates to diseases associated with protein misfolding, such as Alzheimer's. 2) Amyloidosis and Protein Aggregation. We are interested in the forces at play which give rise to protein aggregation, as it applies to disease. We have devised a way to detect states of proteins involved in aggregation. 3) Enzyme Functional Dynamics. While much is known about enzymes in their inactive and active states, the current challenge is to piece together how enzymes speed up chemical reactions. How do very fast (picoseconds) and very slow (micro and millisecond) motions conspire to allow the enzyme to engage its substrate and churn out product? Understanding these motions is key to understanding function. Using NMR we can capture conformations of a bacterial dehalogenase enzyme (a homodimeric defluorinase, consisting of 304 amino acids per domain) along the reaction pathway and see how spontaneous motions aid the enzyme in its function. The results allow us to greatly advance our understanding of enzyme mechanism, conformational preselection, and induced fit, and 4) G protein coupled receptor (GPCR) dynamics. Half of all drugs target these complex membrane proteins responsible for cell signaling. We are proposing to study the role of drugs on the complex energy landscape of a well-known GPCR. How do specific drugs cause the GPCR to adopt states that ultimately speed up or slow down signalling? The proposed work has the potential to transform our understanding of GPCR activation, and the influence of pharmacophores.