Folded state dynamics and hydration in transcriptional regulation

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This research is aimed broadly at understanding fundamental principles that govern genetic regulation along the evolutionary tree of life. Higher-order organisms, such as animals, have complex body plans and well-defined developmental stages. To meet these complicated physiologic demands, gene expression in high order organisms is controlled by finely tuned molecular mechanisms that are absent in single-cell counterparts. To date, many basic details of these mechanisms remain unknown. The objective of this project is to elucidate the role of dynamics in gene regulation. Dynamics represent a fundamental property of biological molecules and are intimately related to their interactions with their water-filled environment. The knowledge gained from this project will advance our understanding of emerging concepts in gene regulation that have thus far received little attention. While completing this project, the PI will also develop novel methods of computation and data analysis that will apply to tackling other scientific problems, thus benefiting the wider research community. This project will introduce young students to topics and careers in the physical sciences by a coordinated effort through Science ATL, a local nonprofit organization that produces events and community-building activities that enhance access to STEM opportunities. The folded states of proteins, nucleic acids and their complexes exist as conformational ensembles in dynamic fluctuation. Folded state dynamics play a major role in the affinity and specificity of protein/DNA interactions. As binding in solution also involves a redistribution of water-accessible surface area, hydration and dynamics are coupled contributors in protein/DNA recognition. In contrast with prokaryotic gene regulators, eukaryotic transcription factors form distinct complexes with cognate DNA sequences that invoke divergent biological outcomes. These complexes assume discrete structures that vary in a discontinuous, non-continuum manner with binding affinity. This property, which we term sequence-directed tuning, is central to the regulation of complex eukaryotic genomes. The objective of this project is to unveil the dynamic and hydration contributions to sequence-directed tuning. To achieve this objective, 1) the project will establish a volumetric framework to analyze the hydration and dynamics contributions to protein/DNA recognition. 2) A joint solution NMR and molecular dynamics approach to dissect the transduction pathways and the relevant DNA dynamics that initiate sequence-directed tuning, 3) the dynamic constraints that drive the evolution of sequence-directed tuning in eukaryotic transcription factors will be defined. Using ancient helix-turn-helix (HTH) motifs as models, the project will query the dynamic requirements for non-continuum DNA binding in characteristic HTH-based motifs that are conserved across the kingdoms of life. This project is supported by the Molecular Biophysics Cluster of the Molecular and Cellular Biosciences Division in the Biological Sciences Directorate.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.