Mapping Functional Dynamics Hotspots for Protein Engineering with NMR Peak Intensity Analysis

Structural dynamics play a crucial role in protein function, and tuning these dynamics through mutagenesis has emerged as a promising strategy for enhancing activity. However, identifying dynamics hotspots for protein engineering remains a labor-intensive challenge. Here, we demonstrate that NMR peak intensity analysis‒a rapid, qualitative method with residue-level resolution‒can identify functionally relevant dynamic regions with high precision. Using a family of red fluorescent proteins (RFPs) as a case study, we reveal that flexibility in specific regions of their structures correlates with function. Specifically, as quantum yield increases, the side of the β-barrel closest to the chromophore phenolate moiety becomes more rigid, while the opposite side, closest to the acylimine group, gains flexibility. Notably, the phenolate face corresponds to a mutational hotspot frequently targeted in directed evolution campaigns aimed at enhancing brightness, underscoring its functional significance. B-factor analysis of non-cryogenic X-ray crystal structures further supports our findings. Our results establish NMR peak intensity analysis as a promising tool for mapping functional dynamics hotspots to guide protein engineering campaigns.