Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step

Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins

The photochemically active sites of the proteins sfGFP66azF and Venus66azF, members of the green fluorescent protein (GFP) family, contain a non-canonical amino acid residue p-azidophenylalanine (azF) instead of Tyr66. The light-induced decomposition of azF at these sites leads to the formation of reactive arylnitrene (nF) intermediates followed by the formation of phenylamine-containing chromophores. We report the first study of the reaction mechanism of the reduction of the arylnitrene intermediates in sfGFP66nF and Venus66nF using molecular modeling methods. The Gibbs energy profiles for the elementary steps of the chemical reaction in sfGFP66nF are computed using molecular dynamics simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. Structures and energies along the reaction pathway in Venus66nF are evaluated using a QM/MM approach. According to the results of the simulations, arylnitrene reduction is coupled with oxidation of the histidine side chain on the His148 residue located near the chromophore.

Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen

Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer.

Fluorescent Proteins: Crystallization, Structural Determination, and Nonnatural Amino Acid Incorporation

Fluorescent proteins have revolutionized cell biology and cell imaging through their use as genetically encoded tags. Structural biology has been pivotal in understanding how their unique fluorescent properties manifest through the formation of the chromophore and how the spectral properties are tuned through interaction networks. This knowledge has in turn led to the construction of novel variants with new and improved properties. Here we describe the process by which fluorescent protein structures are determined, starting from recombinant protein production to structure determination by molecular replacement. We also describe how to incorporate and determine the structures of proteins containing non-natural amino acids. Recent advances in protein engineering have led to reprogramming of the genetic code to allow incorporation of new chemistry at designed residue positions, with fluorescent proteins being at the forefront of structural studies in this area. The impact of such new chemistry on protein structure is still limited; the accumulation of more protein structures will undoubtedly improve our understanding and ability to engineer proteins with new chemical functionality.

Why Are Gly31, Gly33, and Gly35 Highly Conserved in All Fluorescent Proteins?

Green fluorescent protein (GFP)-like fluorescent proteins have been found in more than 120 species. Although the proteins have little sequence identity, Gly31, 33, and 35 are 87, 100, and 95% conserved across all species, respectively. All GFP-like proteins have a β-barrel structure composed of 11 β-sheets, and the 3 conserved glycines are located in the second β-sheet. Molecular dynamics (MD) simulations have shown that mutating one or more of the glycines to alanines most likely does not reduce chromophore formation in correctly folded immature fluorescent proteins. MD and protein characterization of alanine mutants indicate that mutation of the conserved glycines leads to misfolding. Gly31, 33, and 35 are essential to maintain the integrity of the β_1-3 triad that is the last structural element to slot in place in the formation of the canonical fluorescent protein β-barrel. Glycines located in β-sheets may have a similar role in the formation of other non-GFP β-barrels.

Beyond protein tagging: Rewiring the genetic code of fluorescent proteins - A review

Fluorescent proteins (FP) are an integral part of modern biology due to its diverse biochemical and photophysical properties. The boundaries of FP have been extended through conventional mutagenesis and directed evolution approaches. Engineering of FP based on the standard genetic code consisting of 20 amino acids with limited functional groups restrict its diversification. Degeneracy of genetic code has helped in covering this substantial gap through genetic code engineering, wherein introduction of unnatural amino acid (UAA) analogues resulted in a collection of FP with varying properties. This review features the work carried till date in the area of FP incorporated with UAAs and explores strategies employed for incorporation, impact of UAAs in chromophore and surrounding residues and changes in inherent properties of FP. The long-standing association of FP as a tool for high throughput screening of orthogonal aaRS/tRNA pairs used in site specific incorporation of UAAs is expounded. Insertion of UAAs in FP has enabled their use in contemporary fields such as biophotovoltaics, bioremediation, biosensors, biomaterials and imaging of acidic vesicles. Thus, expansion of genetic code of FP is envisaged to rejig the existing spectra of colors and future research initiative in this direction is expected to glow brighter and brighter.

Site-Specific Fragmentation of Green Fluorescent Protein Induced by Blue Light

Green fluorescent protein (GFP) and related fluorescent proteins have multiple applications in cell biology, and elucidating their functions has been at the focus of biophysical research for about three decades. Fluorescent proteins can be bleached by intense irradiation, and a number of them undergo photoconversion. Rare cases have been reported where distant functional relatives of GFP exhibit UV-light-induced protein fragmentation. Here, we show that irreversible bleaching of two different variants of GFP (sfGFP, EGFP) with visible light is paralleled by successive backbone fragmentation of the protein. Mass spectrometry revealed that the site of fragmentation resides at the fluorophore, between residue positions 65 and 66.