Proteins are molecular machines that contribute to virtually every activity of every biological system. Regulation of their activity is a principal goal of drug and protein design. But we do not yet know enough about how proteins function to efficiently design molecules that modulate their activities. We know that to function they need to change their shape - alter their conformation - but visualizing these changes in shape is a substantial experimental challenge. The approach we will take here is to attempt to characterize the set of all shapes a protein can take on - its full conformational ensemble. This will provide a critical link between structure, dynamics and function. The problem is that in a drop of solution, there is a multitude of proteins, each of which may have a different conformation. We will alter the relative abundance of each conformation under many different experimental conditions and collect wide-angle x-ray solution scattering (WAXS) data from the protein under each of those conditions. Using advanced signal processing techniques, we will then extract from these data the scattering due to each conformation individually. This will provide direct structural information on the conformations of functional intermediates that never occur in solution in the absence of other conformations. The result will be a map of the conformational changes that occur during protein action, providing direct experimental evidence for understanding the way proteins use conformational changes to carry out their functions.
The project will make extensive use of state-of-the-art signal processing techniques that are well known in engineering but used sparingly in biophysics. This exemplifies a rapidly accelerating trend to data-rich scientific inquiry powered by increasing use of automatic data capture. Science is becoming ever more dependent on sophisticated methods of signal and data analysis. Training of scientists in advanced data processing techniques will be an essential part of this transition. In this project, success will depend on cross-disciplinary training of both scientists and engineers; training that starts with the PI's - who are already learning from one another - continues with graduate students involved in the research, and extends to graduate students and undergraduates who will benefit from the cross-disciplinary courses that we will create. Underrepresented groups will be introduced to this approach through research experiences for undergraduates and K12 teachers and outreach to K12 students - activities that will constitute an integral part of this project and be designed to encourage and prepare students for careers in science or science teaching.
