Revolutionizing Protein Structure Determination with Advanced SWAXS Analysis

Abstract The overall vision of our research program is to develop new methods and algorithms for probing the structure and dynamics of biological macromolecules to provide new insights that solve problems in human health. Our lab develops a combination of experimental tools and novel computational algorithms to maximize the efficiency and synergy of theory and experiment. One of the experimental tools we use is small and wide-angle X-ray scattering (SWAXS), which offers valuable insights into protein structures and dynamics in solution at room temperature. However, current methods for analyzing and interpreting SWAXS data have limitations. We propose the development of innovative tools to address these challenges. The goals of our research program over the next five years are to develop the following program areas. We will significantly improve the resolution of density reconstruction directly from SWAXS data by incorporating information about known protein structures. We will develop a new tool for modeling SWAXS data by incorporating the most recent advances in AI-based structure prediction. We will develop new algorithms for improving the accuracy and efficiency of SWAXS calculations from atomic models, as well as novel validation tools for objectively assessing the quality of models. We will also develop algorithms and tools for taking advantage of the high brightness and temporal resolution of X-ray free electron lasers. These advancements will lead to higher-resolution density maps, more accurate models, and robust methods for model validation. In the long term we will broaden the scope of these developments, including targeting protein dynamics, membrane proteins in detergent micelles and other membrane mimetic systems, RNA/DNA/complexes, and novel sample delivery modalities. Overall, our research program is developing a comprehensive approach that has the potential to revolutionize protein structure determination using SWAXS and transform the field of structural biology. This will yield new insights into biomedically relevant systems and improve models for drug discovery and design, enabling more rapid and effective treatments for many diseases.