Toolkit Items

The Aer PAS domain is the FAD-binding sensory domain from the dimeric Escherichia coli aerotaxis receptor Aer. It monitors cellular respiration through a redox-sensitive flavin cofactor and is structurally characterized in the Aer-PAS-GVV variant at 2.4 Å resolution.

The antiGFP nanobody is used as a targeting domain in an iLID fusion to localize the light-inducible iLID module to GFP-tagged proteins. In this configuration, blue-light illumination induces iLID-SspB heterodimerization while recruitment remains efficient at the GFP-labeled target.

AQTrip is an engineered EL222 variant carrying V41I, L52I, A79Q, and V121I substitutions in the blue-light-responsive LOV–HTH transcription factor. It stabilizes the photoactivated state and, in the reported study, oligomerizes without DNA and forms an EL222 dimer–DNA complex in the presence of DNA substrates.

Arabidopsis thaliana cryptochrome 2 (CRY2) is a plant photoreceptor protein domain used as an optogenetic module. In the supplied evidence, CRY2 mediates blue light-dependent dimerization to activate C-RAF in mammalian cells.

The aureochrome 1 LOV-domain-based optical TrkB activation approach is an optogenetic TrkB activation strategy built around the light-oxygen-voltage domain of aureochrome 1 from Vaucheria frigida. It was presented as a demonstration that optical TrkB activation can be implemented with an optical homo-dimerizer other than CRY2.

Automated 96-well microplate illumination and measurement is an assay method for high-throughput optogenetic characterization of cultures under controlled light input. In the cited Saccharomyces cerevisiae workflow, it supported construction and characterization of split transcription factors containing cryptochrome and Enhanced Magnet light-sensitive dimerizers.

This Bayesian computational approach is a data-analysis method developed to improve prediction of split protein behavior by contextualizing errors inherent to experimental procedures. In the cited study, it was applied to pooled, sequencing-based screening data from split Cre recombinase constructs generated with optogenetic dimers, enabling comprehensive analysis of split sites across the protein.

BcLOV4-ARHGEF11 is a single-transgene optogenetic fusion in which the upstream RhoA activator ARHGEF11 is fused to BcLOV4. It enables light-inducible, spatiotemporally precise control of RhoA signaling through dynamic membrane localization without requiring a separate protein binding partner.

The BcLOV4-RhoA optogenetic fusion is a single-transgene light-responsive construct in which RhoA GTPase, or its upstream activator ARHGEF11, is fused to BcLOV4. It enables spatiotemporally precise optical control of RhoA signaling and associated cytoskeletal and mechanotransductive responses without requiring a separate protein binding partner for dynamic membrane localization.

BcWCL1 PASΔ is a PAS-domain-deleted variant of the Botrytis cinerea blue-light photoreceptor BcWCL1 that functions in yeast as a blue-light-activated transcription switch. The reported activity depends on the BcWCL1 N-terminal region, which supports light-stimulated self-dimerization and contains a functional 9aaTAD-family transcriptional activation domain.

Biofunctional nanodot arrays (bNDAs) are nanoscale surface-patterned delivery harnesses designed to spatially control dimerization and clustering of cell-surface receptors. In live cells, they were used to capture extracellularly GFP-tagged Lrp6 and drive assembly of active Wnt signalosomes at the plasma membrane.

The blue light-inducible cryptochrome-based dimerization system is a light-responsive multi-component switch that uses blue light to induce protein dimerization. The cited evidence supports its use for spatiotemporally precise control of signaling or cytoskeletal events.

The blue light-inducible LOV domain-based dimerization system is a light-responsive multi-component switch in which blue light induces dimerization to control intracellular signaling or cytoskeletal events. The cited literature describes this class of systems as providing spatiotemporally precise perturbation of cell behavior.

The C120 promoter is a TAEL-responsive regulatory element used in the zebrafish TAEL optogenetic transcription system. Blue light induces TAEL transcription factor dimerization, which activates transcription from the C120 promoter.

The CIB1 N-terminal CRY2-binding region is a protein domain derived from the N terminus of calcium and integrin-binding protein 1 (CIB1). It serves as the CIB1 partner in blue light-activated CRY2-CIB1 optogenetic dimerization systems.

Cry2-Cib is a light-responsive photodimerizing protein pair used as a multi-component optogenetic switch. In the cited application, light stimulation drives translocation of a low-constitutive-activity protein kinase A catalytic subunit to a subcellular region containing Cib, thereby restoring kinase activity.

The CRY2-CIB1 interaction system is a blue-light-responsive optogenetic multi-component switch built from the light-inducible CRY2-CIB1 interaction system in mammalian cells. Photoexcited CRY2 supports inducible CRY2-CIB1 heterodimerization and can also undergo concomitant CRY2-CRY2 homo-oligomerization, enabling light-controlled manipulation of signaling pathways and cellular processes with high spatiotemporal precision.

Cry2/CIB is a genetically encoded blue-light-activated protein dimerization module derived from Arabidopsis thaliana. It is used to optically induce protein-protein interactions and has been applied to control transcription, protein localization, protein secretion, and, when coupled to BAX, light-triggered apoptosis.

The CRY2/CIBN light-gated dimerizer system is an optogenetic multi-component switch used to control subcellular RhoA activation through light-dependent recruitment of a CRY2-fused RhoA activator. In the cited implementation, the ARHGEF11 DHPH catalytic domain is fused to CRY2-mCherry to drive light-gated relocalization and thereby modulate force-related cellular phenotypes.

The cryptochrome 2-mediated optogenetic C-RAF activation tool is a mammalian-cell optogenetic system in which Arabidopsis thaliana cryptochrome 2 drives blue light-dependent dimerization to activate the protein kinase C-RAF. It enables reversible optical control of C-RAF signaling outputs, including ERK1/2 phosphorylation and serum response factor-mediated gene expression.

Cyanobacteriochromes are photoswitchable protein domains from cyanobacteria that sense light across a broad spectral range from the UV to the near infra-red. In the cited 2022 work, they were engineered into light-inducible dimer pairs that support orthogonal control with red, green, and blue light.

De novo tripeptides composed of glycine, tyrosine, and lysine were reported to generate cyan fluorescence in vitro. The same study further indicates that amino acid identity and residue order modulate the fluorescent output, and that these peptides form robust dimer structures under moderate oxidizing conditions.

The dimerization/histidine phosphotransfer-like (DHpL) domain is a regulatory domain element within the blue-light-responsive histidine kinase EL346. Structural evidence indicates that, in the dark, interactions involving the LOV sensor domain and the DHpL domain stabilize an inhibited kinase conformation and suppress dimerization, while photoactivation weakens these contacts to promote activation.

The Drosophila PERIOD PAS domain fragment is a dPER protein segment comprising the PAS-A and PAS-B domains. Structural and functional analyses indicate that this fragment participates in PAS-mediated protein interactions, with the PAS-B beta-sheet surface mediating heterodimer formation with Drosophila TIMELESS (dTIM).

The Drosophila PERIOD PAS-B beta-sheet surface is a protein interaction interface within dPER that mediates binding to the clock protein TIMELESS (dTIM). Comparative analysis further indicates that this PAS-B beta-sheet surface is a reusable interaction site within PERIOD-family proteins, supporting dPER-dTIM heterodimer formation in Drosophila and mPER2 homodimerization in mammals.

Drug-inducible lentiviral and transposon vectors were used to deliver the PhyB-PIF light-inducible dimerization system together with the synPCB phycocyanobilin synthesis module. In the cited study, doxycycline treatment induced PCB synthesis and enabled PhyB-PIF light-inducible dimerization function.

Electron-transfer/higher-energy collision dissociation (EThcD) is a top-down mass spectrometry fragmentation method used in a combined workflow with 213 nm ultraviolet photodissociation (UVPD) to characterize covalent insulin dimers. In the cited study, this workflow identified cross-link chemical composition and, with MS3 analysis of informative MS2 fragments, enabled residue-level localization of interchain cross-link sites.

Enhanced Magnets (eMags) are Vivid-derived light-sensitive protein dimerization domains used in optogenetic split transcription factors and subcellular recruitment systems. In Saccharomyces cerevisiae, optimized eMag-based transcription factor designs improved light-sensitive gene expression, and eMags were also validated for rapid, reversible protein recruitment to subcellular organelles.

FerriTag is a genetically encoded, chemically inducible tag for correlative light-electron microscopy built as a fluorescent, electron-dense ferritin particle. It labels target proteins through induced heterodimerization and enables nanoscale localization in electron micrographs.

The FKF1/GIGANTEA light-inducible transcription system is an optogenetic multi-component switch for mammalian cells built from the Arabidopsis photoreceptor FKF1 and its binding partner GIGANTEA. In an optimized split FKF1/GI dimerized Gal4-VP16 configuration, light induces transcriptional activation by reconstituting a functional transcriptional regulator.

Galpha(15i3) is a G protein chimera reported in HEK293 cells as a pathway-linking component that couples the sweet taste receptor heterodimer TAS1R2/TAS1R3 to an InsP3-dependent Ca2+ release pathway. It is described together with Galpha(16gust44) in receptor signaling assays.

Galpha(16gust44) is a G protein chimera used in HEK293 cells as part of a multi-component signaling switch. It couples the sweet taste receptor heterodimer TAS1R2/TAS1R3 to an InsP3-dependent intracellular Ca2+ release pathway.

The genetically encodable, light activatable heterodimerizer system is an optogenetic multi-component switch that places a protein cargo within a genetically encoded, light-responsive heterodimerization framework. In the cited application, incorporation of cofilin enabled illumination-dependent remodeling of the F-actin network and consequent changes in cell motility.

The genetically encoded PhyB–PIF light-inducible dimerization system is an optogenetic multi-component switch that uses a PhyB-based light-induced dimerization interaction to control signal transduction. The cited chapter describes a genetically encoded implementation enabled by efficient phycocyanobilin synthesis in cultured mammalian cells and reports applications in cultured cells and animals.

Higher-energy collisional dissociation (HCD) is a top-down mass spectrometry fragmentation method referenced in a study characterizing covalent insulin dimers. The supplied evidence identifies HCD by name, but does not describe its specific analytical role, performance, or outcomes in that study.

The iLID N414L variant is a modified iLID light-inducible dimerization system in which an N414L point mutation in the LOV domain lengthens the reversion half-life. In combination with SspB binding partners, it supports blue-light-dependent control of protein colocalization and has been used in reengineered iLID-SspB systems for processes including transmembrane protein localization.

iLID-antiGFP-nanobody is a multi-component optogenetic recruitment system in which iLID is fused to an antiGFP nanobody to target existing GFP-tagged proteins. Under blue-light illumination, iLID heterodimerizes with SspB, enabling light-dependent recruitment to locations defined by GFP fusions.

iLID-nano is a multi-component optogenetic switch built from an improved light-induced dimerization pair comprising LOV2-SsrA and SspB. It has been used to control talin-mediated cell spreading and migration and has been physically characterized for force-coupled regulation in mechanotransduction contexts.

iLID-RTK is a blue-light-controlled, multi-component receptor tyrosine kinase switch built from the iLID and tdnano system. In darkness it is cytosolic, monomeric, and inactive, while blue light recruits two iLID-RTK molecules to tdnano to drive RTK dimerization and activation.

The iLID-SspB A58V variant is a blue-light-inducible heterodimerization system in which SspB carries a single A58V substitution. It was reengineered to tune iLID-SspB binding for improved light-controlled protein colocalization, including transmembrane protein localization in neurons.

iLID/SspB is a blue-light-inducible heterodimerization system built from an engineered iLID module and the SspB binding partner. It is used to reversibly recruit proteins in cells for control of localization and signaling, including membrane recruitment, neurotrophin receptor construction, microtubule plus-end targeting, and perturbation of small GTPase pathways.

The in vitro mutation approach is an engineering method used to analyze how amino acid identity and residue order affect cyan fluorescence in de novo tripeptides. In the cited ChemBioChem study, it was applied to glycine-, tyrosine-, and lysine-containing tripeptides reported to generate cyan fluorescence and to form robust dimers under moderate oxidizing conditions.

The integrin αIIb cytoplasmic domain is a platelet integrin tail segment that functions as a specific binding partner for the calcium- and integrin-binding protein CIB1. Solution structural analysis indicates that this interaction involves EF-hand III of CIB1 and is associated with a CIB1 conformational response distinct from that of related EF-hand proteins.

LADL (light-activated dynamic looping system) is a multi-component optogenetic genome-engineering platform that targets two genomic anchors with CRISPR guide RNAs and promotes their spatial co-localization through light-induced heterodimerization between CRY2 and dCas9-CIBN. In the cited 2018 study, this engineered looping altered endogenous gene expression, including increased nascent Zfp462 transcription and increased synchronous Sox2 expression.

Light Activated BioID (LAB) is an optically controlled proximity-labeling system in which the two halves of split-TurboID are fused to the photodimerizing proteins CRY2 and CIB1. Blue light induces CRY2–CIB1 association, reconstituting split-TurboID and enabling proximity-dependent biotinylation of nearby proteins.

Light inducible dimer pairs are multicomponent optogenetic switches derived from cyanobacteriochrome photoswitchable proteins. They enable light-dependent heterodimerization and were developed to support orthogonal control of biological processes with red, green, and blue light.

Light-activated neurotrophin receptors are engineered optogenetic multi-component receptor systems built using the improved light-induced dimerizer (iLID). The available evidence indicates that they use light-controlled iLID interactions to drive neurotrophin receptor assembly or activation.

Light-harvesting complex II (LHCII) is the major chlorophyll a/b-binding photosynthetic antenna complex of plants that has been studied in isolated native and recombinant forms. The cited literature indicates that light induces reversible conformational changes in LHCII that expose its N-terminal phosphorylation site and can also promote formation of dimeric LHCII states with distinct chlorophyll excitation-quenching properties.

Opto-RGS2 is an optogenetic multi-component switch that uses a light-induced heterodimerization system to recruit the RGS2 domain to the plasma membrane, where it interacts with its cognate G protein. It was developed to enable optical control of Gq-protein signaling and associated calcium oscillation dynamics.

LINTAD is a multi-component light-inducible nuclear translocation and dimerization system developed for gene regulation. In the cited study, it was used to control chimeric antigen receptor (CAR) T-cell activation, and pulsed light stimulation activated LINTAD-engineered CAR T cells to produce strong cytotoxicity against target cancer cells in vitro and in vivo.