9YVZ

Crystal structure of red fluorescent protein mScarlet, 277 K

Summary for 9YVZ

• Entry DOI: 10.2210/pdb9yvz/pdb
• Descriptor: Red fluorescent protein mScarlet, SULFATE ION (3 entities in total)
• Functional Keywords: red fluorescent protein, fluorescent protein
• Biological source: Discosoma sp.
• Total number of polymer chains: 1
• Total formula weight: 27445.85

Authors

Damry, A.M.,Hunt, S.E.,Legault, S.,Thompson, M.C.,Goto, N.K.,Chica, R.A. (deposition date: 2025-10-23, release date: 2026-07-15, Last modification date: 2026-07-22)

Primary citation

Damry, A.M.,Hunt, S.E.,Legault, S.,Thompson, M.C.,Goto, N.K.,Chica, R.A.
Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis.
Protein Eng.Des.Sel., 39:-, 2026

PubMed Abstract: 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.

PubMed: 42402021
DOI: 10.1093/protein/gzag014

Experimental method

X-RAY DIFFRACTION (1.35 Å)