7Q6B image
Deposition Date 2021-11-06
Release Date 2023-04-12
Last Version Date 2024-02-07
Entry Detail
PDB ID:
7Q6B
Title:
mRubyFT/S148I, a mutant of blue-to-red fluorescent timer in its blue state
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:mRubyFT S148I, a mutant of blue-to-red fluorescent timer
Mutations:S147I
Chain IDs:A
Chain Length:241
Number of Molecules:1
Biological Source:Entacmaea quadricolor
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
VUB A MET chromophore
Primary Citation
Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form.
Int J Mol Sci 24 ? ? (2023)
PMID: 37175610 DOI: 10.3390/ijms24097906

Abstact

The mRubyFT is a monomeric genetically encoded fluorescent timer based on the mRuby2 fluorescent protein, which is characterized by the complete maturation of the blue form with the subsequent conversion to the red one. It has higher brightness in mammalian cells and higher photostability compared with other fluorescent timers. A high-resolution structure is a known characteristic of the mRubyFT with the red form chromophore, but structural details of its blue form remain obscure. In order to obtain insight into this, we obtained an S148I variant of the mRubyFT (mRubyFTS148I) with the blocked over time blue form of the chromophore. X-ray data at a 1.8 Å resolution allowed us to propose a chromophore conformation and its interactions with the neighboring residues. The imidazolidinone moiety of the chromophore is completely matured, being a conjugated π-system. The methine bridge is not oxidized in the blue form bringing flexibility to the phenolic moiety that manifests itself in poor electron density. Integration of these data with the results of molecular dynamic simulation disclosed that the OH group of the phenolic moiety forms a hydrogen bond with the side chain of the T163 residue. A detailed comparison of mRubyFTS148I with other available structures of the blue form of fluorescent proteins, Blue102 and mTagBFP, revealed a number of characteristic differences. Molecular dynamic simulations with the combined quantum mechanic/molecular mechanic potentials demonstrated that the blue form exists in two protonation states, anion and zwitterion, both sharing enolate tautomeric forms of the C=C-O- fragment. These two forms have similar excitation energies, as evaluated by calculations. Finally, excited state molecular dynamic simulations showed that excitation of the chromophore in both protonation states leads to the same anionic fluorescent state. The data obtained shed light on the structural features and spectral properties of the blue form of the mRubyFT timer.

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Primary Citation of related structures