Development of Improved Methods to Rapidly Characterize Protein Structure, Function and Dynamics

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This proposal is aimed at developing better, faster and cheaper methods for characterizing the structure, function and dynamics of proteins. Proteins are often called the “engines of life”. They are responsible for powering or performing most of the complex and essential activities inside cells. They assemble, move, synthesize, catalyze, clean and protect just about everything inside and outside the cell. Thousands of different proteins are required to perform these specialized functions and each function is determined by that protein’s unique 3D structure and its characteristic motions. Understanding the structure, function and dynamics of proteins has been the subject of intense research for the past 50 years. This interest is not just driven by scientific curiosity. Indeed, understanding protein structure and function is key to understanding disease, developing new drugs, creating new bioproducts, combating pests and enhancing crop productivity. It is little wonder then that a dozen Nobel prizes have been awarded for structural biology and >$10 billion has been spent determining the structure of ~90,000 different proteins. However, protein structure determination continues to remain difficult, expensive, time-consuming and often fraught with errors. For the past 20 years my research has focused on both devising and experimentally testing novel techniques for improving protein structure characterization. Over that time, we have come up with a number of very elegant and simple methods that have greatly helped accelerate and simplify protein structure determination via Nuclear Magnetic Resonance (NMR) spectroscopy. These novel NMR methods are now widely used by 1000s of structural biologists around the world. For this proposal, I plan to improve upon our earlier work and to start placing the final pieces of the puzzle together. I believe this “final push” will ultimately make many aspects of protein structural biology significantly faster and easier. Over the next 5 years my lab will work on 3 specific objectives: 1) create robust NMR chemical shift-based methods for consistent and rapid 3D protein structure determination; 2) devise new NMR-based approaches to comprehensively measure protein dynamics and thermodynamics; and 3) most interestingly, implement a mass spectrometry-based method for determining the 3D structure of proteins and protein complexes. Each of the objectives has clear performance goals and, based on our preliminary data, each objective appears to be attainable. Details of the methods and of our preliminary results are contained within the proposal. All of the approaches we will use are unique, original and build on some important breakthroughs we achieved through our 2009-14 NSERC funding. If we achieve our first 2 goals we expect protein structure determination, dynamic assessments and thermodynamic evaluations could be sped up by 3-4X and costs reduced by 50-90%. These new methods could be particularly useful for structure-based drug or pesticide design. If we achieve our third goal we could open a whole new field of structural biology that might someday rival X-ray crystallography or NMR spectroscopy. Over its 5-year lifetime, this project will provide superb interdisciplinary training opportunities for ~10-12 trainees (summer students, grad students, PDFs). All trainees will have the chance to work in cutting edge areas of structural biology, to operate high-end NMR instruments and mass spectrometers, to work in both wet (chemistry/biochemistry) labs and “dry” (computer) labs and to learn the latest techniques in machine learning and protein chemistry. They will also be able to apply this newly acquired knowledge to solve important problems that could profoundly affect the future of structural biology.