Light-Activated Reversible Imine Isomerization: Towards a Photochromic Protein Switch

Regulation of Absorption and Emission in a Protein/Fluorophore Complex

Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.

Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins

Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.

A chromatography-free total synthesis of a ferrocene-containing dendrimer exhibiting the property of recognizing 9,10-diphenylanthracene

Molecules comprising several ferrocene residues constitute an intriguing group of compounds for various applications. Here, the total synthesis of a new example of a ferrocene-containing dendrimer is presented. The target compound was obtained in excellent combined yield (65%) employing facile, chromatography-free methods at each step. Interesting findings, meeting the dynamic covalent chemistry concept, are reported. Cyclic voltammetry analyses revealed one pair of current signals for the ferrocene moieties. Ultimately, the synthesized ferrocene-containing dendrimer has been used as an innovative recognition material for 9,10-diphenylanthracene, a polycyclic aromatic hydrocarbon, with the limit of detection value equal to 0.06 μM.

Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin

The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems, but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal protonated Schiff base (rPSB) and all-trans to 15-cis isomerization of unprotonated Schiff base (rUSB). Here we use hybrid quantum mechanics/molecular mechanics (QM/MM) tools coupled with transient absorption and cryokinetic UV-vis spectroscopies to investigate these isomerization processes. The results suggest that primary rPSB photoisomerization of M2 occurs around the C13═C14 double bond within 2 ps following an aborted-bicycle pedal (ABP) isomerization mechanism similar to natural microbial rhodopsins. The rUSB isomerization is much slower and occurs within 48 ps around the C15═N double bond. Our findings reveal the possibility to engineer naturally occurring mechanistic features into artificial rhodopsins and also constitute a step toward understanding the photoisomerization of UV pigments. We conclude by reinforcing the idea that the presence of the retinal chromophore inside a tight protein cavity is not mandatory to exhibit ABP mechanism.

Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches

Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.

Mechanosynthesis of Photochromic Oligophenyleneimines: Optical, Electrochemical and Theoretical Studies

In this work, two oligophenyleneimines type pentamers with terminal aldehydes, designated as DAFCHO (4,4′-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis(azanyl ylidene))bis(9H-fluorene-7,2-diyl))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) and FDACHO (4,4′-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis (azanylylidene))bis(4,1-phenylene))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) were synthesized by mechanochemistry method using 2,5-bis(octyloxy) terephtal aldehyde and 2,7-diaminofluorene or 1,4-phenylenediamine. All compounds were spectroscopically characterized using ¹H and ¹³C-NMR, FT-IR and mass spectrometry MALDITOF. The optical properties of the compounds were analyzed by UV-vis spectroscopy using different solvents. We observed that DAFCHO and FDACHO exhibit interesting photochromic properties when they are dissolved in chloroform and exposed to sunlight for 3, 5 and 10 min. The value of the energy band gap was calculated from the absorption spectra without irradiation E_gap(optical). It was 2.50 eV for DAFCHO in chloroform solution, and it decreased to 2.34 eV when it is in films. For FDACHO, it was 2.41 eV in solution and 2.27 eV in film. HOMO (Highest Occupied Molecular Orbital), LUMO (Lowest Unoccupied Molecular Orbital) and E_{gap(electrochemical)} values were obtained by electrochemical studies. The results indicate that the compounds can be considered as organic semiconductors since their values are 2.35 eV for DAFCHO and 2.06 eV for FDACHO. The structural and electronic properties of the compounds were corroborated with a DFT (Density Functional Theory) study.

Mimicking Microbial Rhodopsin Isomerization in a Single Crystal

Bacteriorhodopsin represents the simplest, and possibly most abundant, phototropic system requiring only a retinal-bound transmembrane protein to convert photons of light to an energy-generating proton gradient. The creation and interrogation of a microbial rhodopsin mimic, based on an orthogonal protein system, would illuminate the design elements required to generate new photoactive proteins with novel function. We describe a microbial rhodopsin mimic, created using a small soluble protein as a template, that specifically photoisomerizes all- trans to 13- cis retinal followed by thermal relaxation to the all- trans isomer, mimicking the bacteriorhodopsin photocycle, in a single crystal. The key element for selective isomerization is a tuned steric interaction between the chromophore and protein, similar to that seen in the microbial rhodopsins. It is further demonstrated that a single mutation converts the system to a protein photoswitch without chromophore photoisomerization or conformational change.

A Near-Infrared Photoswitchable Protein-Fluorophore Tag for No-Wash Live Cell Imaging

FR-1V, a fluorene-based aldehydic chromophore, binds its target protein as an imine to yield a highly bathochromic pigment, CF-2, a prototypic protein-dye tagging system whose NIR emission can be spatiotemporally switched ON by rapid UV-light activation. This is achieved through photoisomerization of the imine and its subsequent protonation. We demonstrate a no-wash protocol for live cell imaging of subcellular compartments in a variety of mammalian cell lines with minimal fluorescence background.

A Genetically Encoded Ratiometric pH Probe: Wavelength Regulation-Inspired Design of pH Indicators

Mutants of human cellular retinol-binding protein II (hCRBPII) were engineered to bind a julolidine retinal analogue for the purpose of developing a ratiometric pH sensor. The design relied on the electrostatic influence of a titratable amino acid side chain, which affects the absorption and, thus, the emission of the protein/fluorophore complex. The ratio of emissions obtained at two excitation wavelengths that correspond to the absorption of the two forms of the protein/fluorophore complex, leads to a concentration-independent measure of pH.

Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates

Human Cellular Retinol Binding Protein II (hCRBPII), a member of the intracellular lipid-binding protein family, is a monomeric protein responsible for the intracellular transport of retinol and retinal. Herein we report that hCRBPII forms an extensive domain-swapped dimer during bacterial expression. The domain-swapped region encompasses almost half of the protein. The dimer represents a novel structural architecture with the mouths of the two binding cavities facing each other, producing a new binding cavity that spans the length of the protein complex. Although wild-type hCRBPII forms the dimer, the propensity for dimerization can be substantially increased via mutation at Tyr60. The monomeric form of the wild-type protein represents the thermodynamically more stable species, making the domain-swapped dimer a kinetically trapped entity. Hypothetically, the wild-type protein has evolved to minimize dimerization of the folding intermediate through a critical hydrogen bond (Tyr60-Glu72) that disfavors the dimeric form.

A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution

The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.