Toolkit Items

2A is a short viral oligopeptide sequence that mediates a ribosome skipping effect during translation, causing co-translational cleavage of polyproteins. It is used in heterologous co-expression systems to separate proteins of biotechnological interest from a single coding sequence.

The 5-deazaFMN-based Avena sativa LOV2 photoswitch is an AsLOV2 protein domain in which the native FMN chromophore is replaced by the flavin analogue 5-deazaFMN. Upon illumination, this cofactor-exchanged construct forms a thermodynamically stable adduct, and recovery to the dark-adapted state can be induced by light, enabling a repeatable photoswitching cycle.

The A. sativa LOV2 domain is a light-responsive protein domain used as a regulatory module in engineered optogenetic switches. In a DHFR/LOV2 fusion, photoactivation thermally destabilized the fusion and lowered the catalytic transition free energy of the lit state relative to the dark state.

The A'α-helix is an N-terminal upstream element of the Arabidopsis thaliana phototropin1 LOV2 photosensory module that interacts with the Jα-helix and contributes to blue-light signal transmission to the downstream serine/threonine kinase. Truncation of this region or Ala substitution of conserved A'α/Aβ-gap residues Glu474 and Lys475 impairs blue-light-induced kinase activation in phot1 LOV2-STK polypeptides.

The A'α-LOV2-Jα photosensory module is a light-responsive domain from Arabidopsis phototropin 1 that primarily controls light-induced activation of the C-terminal kinase domain and subsequent receptor autophosphorylation. Available evidence links LOV2-dependent photosensory input to regulation of phot1 kinase activity.

The A'α/Aβ gap is a structurally defined region N-terminal to the LOV2 core of Arabidopsis thaliana phototropin1. In LOV2-serine/threonine kinase polypeptides, this region contributes to blue-light signal transmission from LOV2 to kinase activation, and conserved residues Glu474 and Lys475 are required for efficient light-induced kinase activation.

AcrIIA4 is an anti-CRISPR protein characterized in Nicotiana benthamiana as an inhibitor of CRISPR/Cas9 function. In plant assays, it blocks Cas9-mediated site-directed mutagenesis and represses CRISPR/dCas-based transcriptional activation, including when delivered by Tobacco etch virus.

AcrIIC3 is an anti-CRISPR protein that inhibits Neisseria meningitidis Cas9 (NmeCas9). Engineered AcrIIC3-Avena sativa LOV2 hybrids function as blue-light-switchable NmeCas9 inhibitors, blocking genome editing in the dark and permitting robust editing under blue light.

AcrVA1 is an anti-CRISPR protein functionally characterized in Nicotiana benthamiana as an inhibitor of Cas12a-dependent activities. In the cited plant study, transient co-expression of AcrVA1 suppressed both CRISPR/Cas12a-mediated genome editing and CRISPR/dCas-based transcriptional activation reporter output.

The active phytochrome binding (APB) domain is a protein interaction module present in most phytochrome-interacting factors (PIFs) that mediates binding to light-activated phytochrome B (phyB). In Arabidopsis PIF4 and PIF5, this domain is required for phyB-associated, phosphorylation-preceded, proteasome-sensitive degradation in a light-regulated shade-avoidance pathway.

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.

ALovD-1 is an archaeal LOV protein domain functionally characterized as a blue-light-responsive photoreceptor. In heterologous expression, it retained conserved dark- and light-adapted state photophysics, exhibited slow photocycle recovery, and remained active at 0.5 M monovalent salt.

AM1_1557 is a typical red/green cyanobacteriochrome domain from Acaryochloris marina that can bind biliverdin at a level almost comparable to phycocyanobilin. In its biliverdin-bound form, the Pfr state is reported to fluoresce at room temperature with an emission maximum at 730 nm.

Am1_c0023g2 is a cyanobacteriochrome photosensory domain from Acaryochloris marina that covalently binds either phycocyanobilin or biliverdin with high binding efficiency. It has been used as the light-responsive target for engineered, state-selective binders that enable green-, orange-, red-, and far-red-controlled protein-protein interactions and transcriptional regulation in yeast.

AM1_C0023g2 Ser334Gly mutant is a cyanobacteriochrome-derived protein domain variant in which Ser334 is replaced by Gly. It retains the AM1_C0023g2 scaffold’s covalent bilin-binding and light-dependent photoconversion properties, and the mutation was reported to significantly improve the yield of the biliverdin-binding holoprotein, supporting its use as a platform for future optogenetic switch development.

Anion channelrhodopsins (ACRs) are natural light-gated anion-conducting microbial rhodopsins from cryptophyte algae used as optogenetic actuators. In cultured neonatal rat ventricular cardiomyocytes, their expression enables light-evoked inhibitory currents, suppression of electrical activity, and shortening of action potential duration when illumination is applied during repolarization.

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.

Arabidopsis cryptochrome 2 (AtCRY2) is a blue-light-responsive plant photoreceptor domain that has been heterologously expressed in mammalian cells. In that context, blue light induces AtCRY2 photobody formation and also triggers AtCRY2 degradation, providing a light-controlled module linked to protein clustering and turnover.

The Arabidopsis CRY2 photosensory domain is a light-responsive protein domain from plant cryptochrome-2 whose active-state crystal structure was determined in a tetrameric form. Structural analysis indicates that this domain undergoes photo-induced oligomerization and contains specific structural elements and residues that participate in activation.

Arabidopsis phototropins phot1 and phot2 are blue-light receptor proteins from Arabidopsis thaliana that optimize photosynthetic efficiency. Targeted mutagenesis of these photoreceptors can tune photocycle lifetime and thereby alter the duration of receptor activation in planta.

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.

Archaerhodopsin-3 (Arch) is a light-sensitive microbial rhodopsin proton pump used as an optogenetic inhibitory tool. The supplied evidence identifies Arch as a previously available optogenetic tool and specifically as an ion-pumping rhodopsin.

The artificial intelligence-guided designed LOV domain is a computationally designed light-oxygen-voltage protein domain that remains photoreactive despite being sequence-divergent from its maternal template. It preserves core LOV photocycle behavior while displaying distinct biophysical properties, indicating access to a new region of LOV-domain functional space.

AsLOV2 is the light-oxygen-voltage 2 photosensory domain from Avena sativa phototropin 1 used as a blue-light-responsive actuator in engineered fusion proteins. Blue-light activation drives allosteric conformational extension involving sequential unfolding of the N-terminal A'α helix and the C-terminal Jα helix, enabling conformational uncaging and related optogenetic control.

AsLOV2 T418C is a cysteine-substituted variant of the Avena sativa LOV2 domain evaluated as a light-induced dissociable FMN photosensitizer carrier. In the reported comparison, it showed higher irradiation-induced FMN dissociation efficiency and effective singlet oxygen production than wild-type AsLOV2 and the V416C variant, but lower performance than the V416C/T418C double variant.

AsLOV2 V416C is a single-amino-acid variant of the Avena sativa LOV2 photosensory domain evaluated for light-induced flavin mononucleotide (FMN) dissociation and singlet oxygen photosensitization. In the reported comparison, V416C outperformed wild-type AsLOV2 for both irradiation-induced FMN dissociation and effective singlet oxygen production, but was weaker than T418C and the V416C/T418C double variant.

AsLOV2 V416C/T418C is a double-cysteine variant of the Avena sativa LOV2 domain reported as part of a mutant series designed to alter flavin mononucleotide handling under irradiation. In the reported comparison with WT, V416C, and T418C, it showed the highest irradiation-induced FMN dissociation efficiency and the highest effective singlet oxygen production.

AsLOV2-Jα is the light-oxygen-voltage-2/Jα photoswitch domain from Avena sativa phototropin1. In the reported LOV-TAP fusion, ligation of AsLOV2-Jα to TrpR enables light-dependent control of DNA binding through photoinduced structural and electrostatic changes.

The AsLOV2-Jα photosensor is the Avena sativa LOV2-Jα light-sensing domain used in an artificial fusion with Rac1 GTPase. In the reported AsLOV2-Jα-Rac1 construct, light initiates LOV-domain structural changes that relieve steric inhibition of Rac1 and permit effector binding.

AsLOV2-V416L is a point-mutated Avena sativa LOV2 photosensory domain variant with strongly decelerated dark-state recovery after photoactivation. In the reported screen, it exhibited a thermal reversion time constant of 4.3 × 10^3 s, corresponding to a 78-fold slower recovery than wild-type AsLOV2.

AsLOV2-V416T is a point-mutated Avena sativa LOV2 photosensory domain variant identified in a mutagenesis and fluorescence imaging-based screen for altered recovery kinetics. It exhibits markedly accelerated thermal reversion from the light-activated state, with a reported time constant of 2.6 s, 21-fold faster than wild-type AsLOV2.

The AUREO1 LOV-only construct is an isolated LOV photosensory domain derived from aureochrome-1. In the cited study, blue light induced a secondary-structure shift from increased alpha-helical to increased beta-sheet character in this LOV-only construct without a detectable change in hydrodynamic radius.

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.

Aureochrome-1 (AUREO1) is a blue-light receptor from Vaucheria frigida with an N-terminal bZIP DNA-binding domain and a C-terminal LOV photosensory domain. Full-length AUREO1 binds DNA in a sequence-specific manner, and light signaling is transmitted from the LOV core via the hydrophobic region of the LOV β-sheet surface.

The Aureochrome1a LOV domain from Phaeodactylum tricornutum is a flavin-binding blue-light sensory protein domain used as the basis for designed LOV-domain flavoproteins. In the cited 2020 Scientific Reports study, tailored LOV-domain flavoproteins produced nuclear hyperpolarization upon illumination, functioning as light-driven spin machines.

The Avena sativa LOV2 domain is a light-sensing LOV photoreceptor domain whose dark-state recovery kinetics can be altered by homologous mutations in a conserved hydrophobic pocket. The available evidence supports its use as a tunable photosensory module in LOV-based and optogenetic tool design.

Avena sativa LOV2 domain variants are engineered insertion modules used to build thermosensitive allosteric chimeric proteins. In Escherichia coli, insertion of optimized LOV2 variants into diverse, structurally and functionally unrelated proteins produced potent thermoswitchable variants operating within a narrow 37-41 °C range.

The Avena sativa phototropin LOV2 domain is a recombinant blue-light-sensing protein domain that binds flavin mononucleotide (FMN) and undergoes a reversible light-triggered conformational change. Blue light induces formation of a cysteinyl-FMN adduct, and the adduct spontaneously reverses in the dark, enabling optomechanical signal transduction.

The Avena sativa phototropin-1 LOV2 domain is a blue-light-sensing flavin-binding photosensory domain used as a module for light-controlled conformational uncaging. Available evidence shows that its dark-state recovery follows a base-catalyzed mechanism and that its light responsiveness is influenced by the flavin redox state.

Bacterial phytochromes (BphPs) are phytochrome protein domains that utilize the heme-derived tetrapyrrole biliverdin as a chromophore. They are distinguished by strongly near-infrared-shifted spectra that fall within the tissue transparency window.

Bacteriophytochrome (BphP) photoreceptors are biliverdin-binding protein photoreceptors that detect red and far-red light. Upon illumination, they photoconvert between spectroscopically, structurally, and functionally distinct Pr and Pfr states.

The bacteriophytochrome sensor unit is a light-sensing protein domain discussed in photoreceptor histidine kinases. A 2019 review places it among receptor sensor units that use recurring signaling strategies for light-driven signal transduction.

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.

The CpbHLH gene family is the set of basic helix-loop-helix transcription factor genes identified in Chimonanthus praecox. A genome-wide study reported 131 CpbHLH genes distributed across 11 chromosomes and characterized their expression across tissues and flower developmental stages.

BcLOV4 is a blue-light-responsive photoreceptor domain that undergoes both clustering and plasma membrane translocation. These coupled light-induced behaviors have been harnessed as a single-component optogenetic module to control protein localization and downstream signaling.

BcLOVclust is a cytoplasmic BcLOV4-derived protein domain engineered for light-controlled intracellular clustering. It enables optogenetic clustering in mammalian cells and has been applied to control signaling proteins and stress granules.

BEE2 (brassinosteroid enhanced expression2) is an Arabidopsis HBI1-related basic helix-loop-helix transcription factor considered here as an overexpressed protein domain tool. Source evidence indicates that BEE2 overexpression partially inhibits immunity and that BEE2 may function redundantly with HBI1-related growth–immunity regulatory activities.

Beggiatoa photoactivated adenylyl cyclase (bPAC) is a blue light-activated optogenetic adenylyl cyclase used to generate cyclic AMP in cells. The cited studies used it to drive cAMP-dependent signaling, including PKA activation, to increase endogenous cortisol in a blue light-dependent manner, and to localize cAMP production to defined subcellular compartments such as the cilium.

Beggiatoa sp. IS2 PAC (biPAC) is a blue light-responsive photoactivated adenylyl cyclase protein domain used in transfected macrophages. In the cited study, light activation of biPAC suppressed macrophage expression and production of the pro-inflammatory cytokines IL-1 and TNF-β1.

The bilin-binding GAF domain is the photosensory domain shared by cyanobacteriochromes and phytochromes. In cyanobacteriochromes, this domain binds a bilin chromophore and supports light sensing across colors extending beyond the red/far-red range.