A protein that absorbs near-infrared light can flip to absorbing ultraviolet instead. That's strange enough. But what happens when two of these molecular switches sit side by side, locked in a dimeric embrace just 29 angstroms apart?

They talk to each other. In light.

The discovery centers on Neorhodopsin, a recently identified fungal protein with properties that have startled researchers working at the frontiers of optogenetics. NeoR doesn't just sense light. It reversibly photoswitches between two wildly different states—one that absorbs maximally at 690 nanometers in the near-infrared, and another that peaks at 367 nanometers in the ultraviolet range. These aren't subtle shifts. They represent a dramatic reorganization of the protein's light-sensing chromophore, a retinal molecule tethered inside the protein pocket.

Most microbial rhodopsins bind a protonated retinal Schiff base. This gives them their characteristic absorption in the visible spectrum. NeoR's UV-absorbing state breaks that pattern. Here, the retinal Schiff base loses its proton. The electronic structure flips. What was once the lowest excited state becomes a higher one. An optically forbidden state drops below it.

The result? Unusual photophysics.

From Ultraviolet to Ultrafast

When ultraviolet light strikes the UV-absorbing form of NeoR—designated NeoR367—it excites the chromophore to what spectroscopists call the S3 state. This is an optically allowed excited state with specific symmetry properties. But it doesn't last.

In 39 femtoseconds, the system crashes down to a lower-lying excited state. Thirty-nine femtoseconds is 39 quadrillionths of a second. For context, light travels about 12 nanometers in that time—roughly the diameter of a small virus.

This lower excited state, termed S1, has different symmetry. It's optically forbidden, meaning it doesn't easily absorb or emit light. Researchers confirmed its identity using femtosecond stimulated Raman spectroscopy, which revealed an upshifted carbon-carbon stretch vibration at 1710 wavenumbers—a molecular fingerprint characteristic of this particular electronic configuration.

The S1 state persists much longer than S3. It decays over timescales ranging from about 1 to 100 picoseconds, with most molecules returning to their starting ground state. About 10 percent form a long-lived photoproduct that absorbs around 460 nanometers. The multiexponential decay suggests populations moving across a complex energy landscape with multiple pathways.

But something else happens during those picoseconds. Something unexpected.

The Energy Handoff

Using cryo-electron microscopy, researchers determined that NeoR exists as a homodimer—two identical protein units bound together. The retinal chromophores in each unit sit approximately 29 angstroms apart, center to center. Their beta-ionone rings, the bulky ends of the retinal molecules, face inward toward each other at an edge-to-edge distance of about 19 angstroms.

This is close. Close enough, it turns out, for quantum mechanical effects to bridge the gap.

The researchers prepared samples where some NeoR dimers contained one UV-absorbing unit and one near-IR-absorbing unit. When they excited the UV form with 360-nanometer light, they watched for what happened next using ultrafast transient absorption spectroscopy—a technique that tracks molecular changes on femtosecond-to-nanosecond timescales by probing with a second light pulse.

They saw the excited UV chromophore. They saw its decay. But they also saw something appear that shouldn't have been there: the excited state signature of the near-IR-absorbing chromophore, NeoR690.

The UV light had only excited NeoR367. It couldn't directly excite NeoR690, which absorbs far-red light. Yet NeoR690's excited state appeared anyway, building up on a timescale of about 93 picoseconds.

Energy was transferring from one retinal to the other.

Measuring the Unmeasurable

To quantify this process, the team conducted a series of experiments with varying background illumination. Red light converts NeoR690 to NeoR367. UV light does the reverse. By controlling the ratio, they could tune the population of mixed dimers—those containing one chromophore in each state.

They built a sophisticated kinetic model incorporating the different dimer types: UV-UV pairs, Red-Red pairs, and UV-Red pairs. Only the UV-Red configuration permits the observed energy transfer. Through simultaneous analysis of multiple datasets with different dimer ratios, they extracted an energy transfer rate constant of (200 picoseconds)^-1.

This means that when the UV chromophore reaches its excited S1 state, it has about a 200-picosecond window to hand off its energy to a neighboring near-IR chromophore before other decay pathways dominate. The transfer competes with photoproduct formation. High concentrations of UV-Red dimers show more energy transfer and less photoproduct. High concentrations of UV-UV dimers show the opposite.

The precision of this measurement required accounting for direct excitation of residual NeoR690 (which absorbs weakly at 360 nm), spectral overlap between different molecular states, and the coherent artifacts that appear near time zero in ultrafast experiments. The researchers separately recorded and subtracted buffer signals and carefully sampled the data around the critical early timepoints.

The Mechanism Behind the Relay

Energy transfer between molecules happens through several possible mechanisms. The best known is Förster resonance energy transfer, or FRET, which involves dipole-dipole coupling. But FRET calculations typically assume a point-dipole approximation—treating molecules as infinitesimal points. At 19 angstroms edge-to-edge separation, this approximation strains.

More sophisticated methods account for the actual charge distributions in both donor and acceptor molecules. The researchers performed structure-based calculations using the fluorescence properties of unprotonated retinal Schiff base in organic solvent as a reference. These calculations predicted an energy transfer rate about five times slower than observed.

The discrepancy points to something enhancing the process.

One clue comes from the NeoR367 S1 excited state itself. Although this state is nominally optically forbidden, the data reveal weak stimulated emission around 700 nanometers. This shouldn't exist if the state were purely forbidden. The emission suggests the S1 state has acquired some transition dipole moment—some capacity to interact with light.

How? Likely through mixing with an intramolecular charge-transfer state. The electronegativity of the nitrogen atom in the unprotonated Schiff base, combined with the polar protein environment around the chromophore, could stabilize a charge-separated configuration. This charge-transfer state, when mixed with the S1 state, partially lifts the optical forbiddenness.

That same mixing could enhance energy transfer. With increased transition dipole moment and good spectral overlap with the NeoR690 absorption, the donor chromophore becomes more efficient at coupling to its neighbor.

Similar phenomena occur in photosynthetic light harvesting. Carotenoids—pigments with electronic structures resembling retinal—often have optically forbidden lowest excited states. Yet they transfer energy to chlorophylls in plant and bacterial antenna complexes. Structural distortions and mixing with charge-transfer states enable these processes despite the formal optical selection rules.

Implications Beyond the Bench

Why does any of this matter?

Microbial rhodopsins have become indispensable tools in neuroscience. Optogenetics uses light-activated rhodopsins to control neurons with millisecond precision, enabling researchers to probe brain circuits by turning specific cells on or off with pulses of light. Engineered rhodopsins also serve as optical voltage sensors, reporting neural activity through fluorescence changes.

NeoR's strongly fluorescent near-infrared absorption makes it promising for deep-tissue imaging. Near-infrared light penetrates biological tissue far better than visible light. A rhodopsin that absorbs in this window could enable visualization of neural activity in intact brains with reduced scattering and absorption.

But NeoR doesn't work alone in nature. It functions as part of a heterodimeric complex—two different rhodopsin units working together. The homodimers studied here represent a simplified system for understanding the fundamental biophysics. Yet the energy transfer process they reveal may play broader roles.

Microbial rhodopsins show remarkable diversity. Some form homodimeric channelrhodopsins. Others belong to families of homodimeric heliorhodopsins, recently discovered proteins widely distributed across microbial genomes. In these native oligomeric structures, retinal chromophores position themselves at distances comparable to those in NeoR dimers.

Bistability isn't required. Even long-lived intermediate states that accumulate during photocycles could absorb photons under moderate to high light conditions. Energy transfer might modulate rhodopsin function, redistributing excitation energy across oligomeric assemblies in ways that evolution has tuned for specific purposes.

The number of known microbial rhodopsins increases rapidly as genomic databases expand. Many remain functionally uncharacterized. Some may exploit energy transfer in ways not yet imagined.

The Forbidden Made Possible

There's an elegant physics at work here. The unprotonated retinal Schiff base in NeoR367 exists in an unusual excited-state manifold. The bright state that initially absorbs the UV photon lies above the dark state that ultimately donates energy. A 39-femtosecond plunge bridges them. The dark state shouldn't couple efficiently to anything. Yet through subtle quantum mechanical mixing—a charge-transfer state lending its transition moment—it becomes a competent energy donor.

The researchers found no evidence for population of a theoretically predicted nπ* state, an excited configuration involving the lone electron pair on nitrogen. Femtosecond stimulated Raman spectroscopy saw only the hallmarks of the optically forbidden state, with its characteristic upshifted vibrations. The electronic structure calculations and experimental spectroscopy tell a consistent story, even as they reveal how much remains to be understood about these UV-absorbing rhodopsins.

Light-driven proton pumps. Ion channels. Photosensors. Molecular switches spanning the spectrum from ultraviolet to near-infrared. Now: nanoscale energy relays.

The rhodopsin family continues to expand its repertoire. Each new capability reframes what's possible when proteins harvest light.

Credit & Disclaimer: This article is a popular science summary written to make peer-reviewed research accessible to a broad audience. All scientific facts, findings, and conclusions presented here are drawn directly and accurately from the original research paper. Readers are strongly encouraged to consult the full research article for complete data, methodologies, and scientific detail. The article can be accessed through https://doi.org/10.1021/jacs.5c01276

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