Poster abstracts

Poster number 16 submitted by Johann Roque

Selective Covalent Ligand Targeting of Differential Dynamics in RNA-Binding Protein

Johann M. Roque (Department of Chemistry & Biochemistry, University of Notre Dame), Julia A. Hass (Department of Chemistry & Biochemistry, University of Notre Dame), Beth P. Anderson (Department of Chemistry & Biochemistry, University of Notre Dame), Will P. Ford (Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine), Blanton S. Tolbert (Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine), Brittany S. Morgan (Department of Chemistry & Biochemistry, University of Notre Dame)

Abstract:
Intrinsically dynamic protein regions are challenging to target with traditional small molecules due to their conformational heterogeneity and shallow binding surfaces. Covalent ligands provide an alternative strategy for engaging these dynamic regions by coupling molecular recognition with irreversible bond formation. Here, we investigate how protein conformational dynamics influence covalent ligand recognition using the highly homologous RNA-binding proteins heterogeneous nuclear ribonucleoproteins H and F (hnRNP H/F) as a model system. Despite >85% sequence conservation and similar tertiary structures, hnRNP H/F exhibit distinct dynamics within their quasi-RNA recognition motifs (qRRMs), including loops containing conserved cysteine residues. A proteome-wide screen identified covalent fragments that label hnRNP H/F qRRMs 1,2, with all reactive fragments preferentially labeling hnRNP H. Nuclear magnetic resonance studies further revealed slower conformational exchange within the dynamic loops of hnRNP H compared to hnRNP F. These results suggest that differences in local conformational dynamics contribute to selective covalent ligand engagement between highly homologous RNA-binding proteins. We hypothesize that slower dynamics favor pocket-like conformations that facilitate productive molecular recognition and subsequent covalent bond formation. Together, this work provides a framework for leveraging protein dynamics to develop selective covalent ligands for challenging RNA-binding proteins.

Keywords: Covalent Ligands, RNA-Binding Protein, Dynamic Loops