Toolkit Items

As a tool component, CIB1 is most directly supported as the cryptochrome-interacting bHLH partner used with CRY2 to create blue-light-controlled protein association systems. In these systems, CIB1 is typically fused to localization, transcriptional, or enzymatic modules so that blue light drives CRY2–CIB1 binding and light withdrawal reverses the interaction.

Cry2 is a blue-light photoreceptor cryptochrome from Arabidopsis used as a light-responsive multi-component optogenetic switch. The supplied evidence supports blue-light-dependent photoactivation linked to regulation of transcription factor control and to CRY2 degradation.

CRY2/CIB1 is a blue-light-inducible multi-component interaction switch composed of the photoreceptor CRY2 and its interacting partner CIB1. It is used for acute light-dependent protein recruitment, including plasma-membrane recruitment and clustering, to control protein localization and downstream signaling with high spatial and temporal resolution.

EL222 is a blue light-activated LOV-HTH transcription factor from the marine bacterium Erythrobacter litoralis HTCC2594 that functions as a light-dependent DNA-binding protein for optical control of transcription. Its flavin mononucleotide chromophore photodynamics have been characterized in free solution and when embedded in EL222 variants.

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.

SspB is the binding partner used in the iLID blue-light-inducible dimerization system. Upon blue-light activation of iLID, the exposed SsrA peptide binds SspB, enabling light-controlled recruitment and localization of SspB-fused cargo proteins.

The Light-Oxygen-Voltage (LOV) domain is a small blue-light-sensing protein domain used as an optogenetic input module. It binds flavin nucleotides and undergoes blue-light-induced structural rearrangements that can regulate linked effector domains, including in phototropins where LOV1 and LOV2 are coupled to a C-terminal serine/threonine kinase.

nano is the wild-type SspB protein used as the binding partner for iLID in a blue-light-responsive dimerization system. In the cited work, the iLID–nano pair is used to control protein interactions and localization with light.

PpSB1-LOV is a bacterial short LOV photosensory domain from Pseudomonas putida KT2440 with a light-induced flavin-cysteinyl photo-adduct and exceptionally slow dark recovery. It has been characterized as a compact LOV building block whose photocycle kinetics can be tuned by conserved hydrophobic-pocket mutation, including the I48T variant that accelerates adduct rupture while remaining structurally and mechanistically benign.

YtvA is a blue-light-sensing LOV-STAS photoreceptor from Bacillus subtilis whose LOV domain has been structurally analyzed for LOV-LOV dimerization and interdomain interactions. Homologous mutations in a conserved LOV hydrophobic pocket alter activation-state kinetics, supporting YtvA as a tunable LOV sensor domain relevant to optogenetic design.

PhyB/PIF is a genetically encoded red/far-red light-inducible dimerization system built from phytochrome B and phytochrome-interacting factor. It enables reversible light-controlled protein association and dissociation on the second time scale and has been applied to gene regulation, protein transport, and subcellular recruitment.

split-TurboID is a split proximity-labeling enzyme used in the Light Activated BioID (LAB) system, where its two halves are fused to the photodimeric proteins CRY2 and CIB1. Blue light induces CRY2–CIB1 association, reconstitutes split-TurboID, and triggers proximity-dependent biotinylation.

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.

The Avena sativa LOV2 domain is a blue-light-sensing photosensory domain used as a photoswitchable scaffold for engineered control of protein interactions. In the iLID design, the bacterial SsrA peptide is embedded in the LOV2 C-terminal helix so that blue light triggers helix undocking and enables binding to SspB.

The Arabidopsis thaliana phototropin 1 LOV2 domain is a blue-light-sensing protein domain from phototropin 1 whose dark-adapted crystal structure has been determined. In this state, the domain is dimeric and contains an N-terminal A'α helix and a C-terminal Jα helix that contribute to coiled-coil-mediated dimerization.

PpSB2-LOV is a compact "short" light, oxygen, voltage (LOV) photosensory protein from Pseudomonas putida KT2440. It forms a light-induced LOV photoadduct and exhibits rapid dark-state thermal recovery, with a reported recovery time of 3.5 min at 20 °C, making it a candidate building block for genetically encoded photoswitches.

OptoRAF1 is a blue light-responsive optogenetic RAF1 system built on the CRY2/CIB1 dimerizer pair. It reversibly activates the RAF/MEK/ERK pathway by recruiting RAF1 to the plasma membrane.

Magnets are engineered pairs of distinct light-responsive protein modules derived from the Neurospora crassa photoreceptor Vivid. They act as a multi-component optogenetic switch by converting a native Vivid homodimerization interface into complementary light-dependent heterodimers for protein interaction and recruitment in subcellular volumes.

The split Cas9 logic gate is a synthetic multi-component circuit that uses split Cas9 halves to sense biological events through conditional reconstitution of Cas9 activity. In the reported 2023 implementation, self-assembling inteins reconstituted split Cas9 and enabled reporter activation only when specified transcriptional or cell-state inputs were present.

TAEL is an engineered optogenetic transcription factor optimized for zebrafish in which blue light induces TAEL dimerization, binding to the C120 promoter element, and activation of downstream transcription. TAEL 2.0 is an improved transgenic implementation that enables inducible expression at late embryonic and larval stages and produces faster, higher reporter expression than the original system.

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.

Cryptochromes are blue/ultraviolet-A light-responsive photoreceptor protein domains, including Arabidopsis thaliana cry1 and cry2 variants, that were incorporated into a yeast optogenetic toolkit. In this toolkit context, cryptochrome variants were used as light-sensitive modules in split transcription factors to optically control transcription.

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.

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 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.

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 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.

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).

GntR is a gluconate-responsive transcriptional repressor from Escherichia coli that has been repurposed as a protein domain for synthetic gene-control switches. Reported designs use GntR to construct gluconate-regulated transcriptional systems in mammalian cells, including rewired OFF/ON transcriptional architectures and a split transcriptional activator.

The heme PAS domain of Escherichia coli direct oxygen sensor (Ec DOS) is a bacterial heme-binding sensor domain structurally characterized in inactive Fe(3+) and active Fe(2+) states. It acts as a redox-responsive molecular switch in which changes in heme coordination are coupled to conformational rearrangements within the PAS domain.

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 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.

Q-PAS1 is an engineered single-domain binding partner for the bacterial phytochrome BphP1 that enables near-infrared-light-inducible protein interactions. It was developed as a smaller, non-oligomerizing alternative to the natural BphP1 partner PpsR2 and has been applied to transcription regulation, chromatin state modification, and spectral multiplexing.

Reverse cross-saturation NMR methodology is an NMR assay approach that maps the binding interface on a larger binding partner by applying selective radio-frequency irradiation to a smaller binding partner. In the cited study, irradiation of the αIIb peptide enabled detection of the interaction surface on Ca2+-bound CIB1.

The RhoPDE C-terminal phosphodiesterase catalytic domain is the isolated catalytic region of the rhodopsin/phosphodiesterase fusion protein RhoPDE from the choanoflagellate Salpingoeca rosetta. It has been expressed, purified, and structurally characterized by crystallography, while the parent full-length protein was reported to function as a cGMP-selective phosphodiesterase.

The SMN tudor domain is a globular protein domain from SMN that is sufficient for dimerization-induced condensation in vivo. Its condensate-forming activity requires binding to dimethylarginine, supporting its use as a chemical-input interaction module for specifying membraneless organelle assembly.

Thioflavine T (ThT) associates rapidly with aggregated fibrils ... giving rise to a new excitation maximum at 450 nm and enhanced emission at 482 nm ... This fluorometric technique should allow the kinetic elucidation of the amyloid fibril assembly process as well as the testing of agents that might modulate their assembly or disassembly.

The TRIM21 RING domain is a catalytic protein domain whose ubiquitination activity is activated by substrate-induced clustering that promotes intermolecular RING dimerization. In the cited 2020 study, this activation mechanism underlies TRIM21-dependent antiviral responses and Trim-Away-mediated protein degradation.

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 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.

LOVpep/ePDZb is a blue-light-inducible heterodimerization system examined as one of three optogenetic dimer variants in a comparative cellular optogenetics study. It mediates light-dependent protein association that was used to control cellular localization and activity in assays including transcription, intracellular localization, and GTPase signaling.

OptoBAX is an optimized light-activated Cry2-BAX multi-component optogenetic system developed for one-click initiation of the BAX-mediated apoptotic cascade. It is used to trigger outer mitochondrial membrane permeabilization and induce early apoptotic events with light.

YF1 is an engineered light-oxygen-voltage (LOV) histidine kinase that acts as a blue-light-regulated signaling switch. Available evidence indicates that blue-light input is transmitted through structural transitions in the photosensor and linker regions that control its signaling state.

CRISPR-dCas9 was used in an optogenetic LITE configuration to control endogenous PIM1 transcription in U87 glioblastoma cells in vitro. In this study, the system mediated light-inducible, reversible transcriptional induction or repression rather than genome editing.

The basic helix-loop-helix (bHLH) domain is a highly conserved eukaryotic protein motif present in transcription factors. It contains a basic DNA-binding region and a helix-loop-helix region, supporting transcriptional regulatory functions across diverse physiological contexts.

Using the TBK1 inhibitor, BX795, we discovered that HBsAg-enhanced TBK1 dimerization, promoting sequestosome-1 (p62) phosphorylation, was necessary for HBV-induced autophagy and HBV replication.

The light-switchable condensate system is a genetically encoded, multi-component platform for blue light-controlled organization of functional cargoes in Escherichia coli. It couples a condensation-enabling scaffold to cargo proteins through the iLID/SspB light-responsive interaction pair to dynamically regulate cargo localization.

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.

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.

EL346 is a full-length blue light-activated histidine kinase from Erythrobacter litoralis HTCC2594 that contains a LOV photosensor domain. Structural evidence indicates that the LOV domain regulates kinase state by controlling intramolecular domain interactions, maintaining an inhibited dark-state conformation, and releasing that inhibition upon photoactivation.