Three-Dimensional Structure of the Orange-Red Fluorescent Biomarker DiB3-F53L

Objective: The 3D structure of the fluorescent protein DiB3-F53L, an orange-red fluorescent non-covalent complex of a genetically engineered variant of the bacterial protein lipocalin Blc with a synthetic GFP-like chromophore M739, was studied by the molecular dynamics (MD) computational method. The fluorescence brightness of the complex has increased by ~1.16 times compared to the parent DiB3 biomarker, which makes it a promising biomarker for cell biology for labeling biological objects, as well as a starting object for the subsequent design of new brighter biological markers. Methods: Molecular dynamics (MD). Results and discussion: The 3D structure of the fluorescent protein DiB3-F53L, an orange-red fluorescent non-covalent complex of a genetically engineered variant of the bacterial protein lipocalin Blc with a synthetic GFP-like chromophore M739, has been studied by the computational molecular dynamics method. Calculations revealed the amino acids surrounding the chromophore at the binding site that contribute most strongly to the chromophore-protein interaction energy. Conclusions: The DiB3-F53L protein complex with the M739 chromophore has an increased fluorescence brightness compared with the parent biomarker DiB3, which makes it a promising biomarker for labeling biological objects in cell biology, as well as a starting object for the subsequent design of new brighter biomarkers.