Role of electric fields and a dynamic local environment in protein-RNA molecular recognition

Ribonucleic acids (RNA) are biopolymers with substantial amounts of negative electrical charge, and the surfaces of proteins that bind them often contain amino acid residues with electrical charge that can help attract, direct, and bind their targets. Importantly, these are large and flexible molecules so fluctuations in their structure and local environment play a significant role in their function.

This project seeks to understand how the process of molecular recognition between RNA and proteins is influenced by their electrostatic interactions and by the dynamic environment in which binding occurs by developing a multimodal instrumentation that combines a variety of spectroscopic techniques. This research will train students in a multidisciplinary skillset at the interface of physical chemistry and biophysics, with broader impacts that include the development of transferrable methods for quantitative characterization of biomolecular interactions.

In this project, scalable and quantitative experiment kits for remote learning will be designed and implemented with the goal of expanding hands-on, experience-based education beyond typical teaching laboratory settings.

Interactions between proteins and RNA show significant diversity – proteins can recognize their RNA targets in ways that are specific to their sequence, to their structure, to both, or to neither. To uncover the molecular-scale mechanisms that tune substrate recruitment, complex stability, and cooperative target recognition by multiple protein domains, this project integrates electrochemical and spectroscopic tools to measure the dynamic signatures of protein-RNA binding, their conformational fluctuations, and their response to non-equilibrium perturbations – all under the effects of a controlled electrostatic environment.

RNA substrates will be localized at an electrode surface to tune their electrostatic interactions with proteins in solution, and the resulting protein-RNA complexes will be probed with a multimodal instrument that combines electrochemistry with mid-infrared plasmonics, ultrafast multi-channel fluorescence, and pump-probe spectroscopies. The outcomes of this research will reveal the way electrostatic interactions and fast dynamics of biomolecular structure and solvation affect the thermodynamics and kinetics of formation, stability, and dissociation of protein-RNA complexes.

This project is supported by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.