Toolkit Items

Allosteric Cre regulation with NS3 ligands is a chemical multi-component recombination switch in which an NS3-based ligand-responsive system is used to allosterically regulate Cre recombinase. It was reported as an orthogonal recombination control strategy in eukaryotic cells and as a way to control prokaryotic recombinase activity across divergent organisms.

The alpha-helical domain linker is a construct pattern in which a rigid alpha-helical segment is placed between fused protein domains to couple their functions. In the cited design context, it is proposed to act as a helical allosteric lever arm that transmits conformational information between domains.

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.

The atomic force sensing technique is an assay method for dynamically probing protein conformational changes with microsecond time resolution. In the cited 1997 study, it was applied to light-induced conformational changes in bacteriorhodopsin.

The AUREO1 bZIP-LOV truncated construct (ZL) is an N-terminally truncated aureochrome-1 derivative that retains the bZIP DNA-binding region and the LOV photosensory domain. It binds DNA in a sequence-specific manner and undergoes a blue-light-induced conformational response measurable as an approximately 5% increase in hydrodynamic radius without a detectable change in secondary structure.

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.

Bacteriophage-derived peptides are peptide inhibitors reported to allosterically inhibit CRISPR-Cas9. Based on the supplied evidence, they act as anti-CRISPR-like modulators of Cas9 activity in genome editing contexts.

Caging/uncaging events are optogenetic control strategies in which light is used to regulate the functional state of signaling proteins. In the cited review, they are presented as one of two broad routes, alongside light-regulated protein-protein interactions, for steering signal transduction.

Catalytically inactive NS3 protease is a protein domain repurposed as a high-affinity binder for genetically encoded antiviral peptides. In the reported system, peptide-bound NS3 complexes are displaced by FDA-approved NS3-targeting drugs to chemically control transcription, cell signaling, split-protein complementation, and allosteric Cre recombinase regulation.

A chemoreceptor domain was incorporated as an alternative thermosensing module in modular thermoresponsive allosteric proteins. In this context, the domain is used to confer temperature-responsive control, supporting receptor domains as interchangeable thermosensory elements.

A chemoreceptor domain was reported as an alternative thermosensing module in a modular thermo-responsive allosteric protein engineering framework. The available evidence indicates that this domain can be incorporated into engineered proteins to confer temperature-dependent control.

Co-opting natural allosteric coupling is a protein engineering method that converts proteins into conformational switches by leveraging pre-existing allosteric relationships. The cited literature describes its use to generate proteins that respond to signaling events and thereby enable biosensing or regulated biological function.

This computational design strategy combines in silico design with biophysical experiments to improve the response kinetics of protein conformational switches. In the cited 2018 Nature Communications study, it was applied to an engineered protein-based Ca2+ sensor and rationally accelerated its response into the range of fast physiological Ca2+ fluctuations.

Conventional replica exchange molecular dynamics (REMD) is a molecular simulation method used for statistical sampling of biomolecular conformational ensembles. In the cited evidence, it functions as the benchmark comparator against two coarse kMC-based replica exchange methods.

The DHFR/LOV2 fusion is an engineered photoswitch in which the LOV2 light-sensing module was used to create a light-regulated dihydrofolate reductase (DHFR) enzyme. Source evidence indicates that light activation modulates DHFR catalysis through allosteric effects associated with local disorder and altered transition-state thermodynamics.

The Diaphanous Autoregulatory Domain from mDia1, in this tool context, is an optogenetic fusion between the Avena sativa Phototropin1 LOV2 domain and an isolated mDia1 DAD. Blue light uncages the DAD, enabling rapid activation of endogenous diaphanous-related formins and acute actin cytoskeletal remodeling.

Domain insertion permissibility is an experimental engineering paradigm established in the human inward rectifier K+ channel Kir2.1 to identify engineerable allosteric sites. In this framework, sites permissive to insertion of regulatory domains can be converted into functional control points, including light-sensitive regulation when light-switchable domains are inserted.

EF-IV is the C-terminal EF-hand IV region of calcium- and integrin-binding protein 1 (CIB1), represented here with the F173W variant. Available evidence indicates that this region is partially unfolded and dynamic in apo CIB1, and becomes more ordered in Mg2+-bound CIB1 while retaining some conformational heterogeneity.

The engineered focal adhesion kinase (FAK) is a single-protein, two-input logic OR gate that integrates chemogenetic and optogenetic control within the native FAK domain architecture. It places a rapamycin-inducible uniRapR module in the kinase domain and a light-inducible LOV2 module in the FERM domain to allosterically regulate FAK activity.

This tool is an engineered protein-based Ca2+ sensor that switches through mutually exclusive folding of two alternate frames. Computational design and biophysical experiments were used to improve its conformational switching kinetics, producing Ca2+-responsive behavior on the timescale of fast physiological Ca2+ fluctuations.

FtsZ is a prokaryotic filamentous cell-division protein that was adapted as a light-responsive protein domain by site-specific incorporation of a photocaged tyrosine. In this engineered form, UV-mediated uncaging at tyrosine 222 was used to control FtsZ self-organization, GTPase regulation, and treadmilling-related dynamics.

Glass nanopipette-based single-cell extraction is an ex situ single-cell sampling method that removes material from individual cells for downstream analysis. In the cited Chemical Science study, it was coupled to SiNx solid-state nanopores to identify LOV2 and monitor its conformational changes from single-cell extracts.

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.

Human inward rectifier K+ channel Kir2.1 was used as a protein scaffold to identify engineerable allosteric sites through domain insertion permissibility mapping. Insertion of light-switchable domains into existing or latent allosteric sites, but not other positions, rendered Kir2.1 activity sensitive to light.

Hybrid phototropin LOV2 domains were engineered to incorporate the BID Bcl homology region 3 (BH3), creating a light-dependent optogenetic switch. Illumination induces LOV2 conformational changes that expose the BH3 element and modulate binding to the anti-apoptotic Bcl-2 family protein Bcl-xL.

Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) is an assay method used to complement structural characterization of light-activated photoreceptors. It reports on protein conformational dynamics in solution and can probe multiple functionally relevant states.

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.

"Joining proteins in creative ways" is a protein engineering construct pattern in which protein domains are fused or otherwise combined to create stimulus-coupled conformational switching in proteins that previously lacked such behavior. The cited literature presents this strategy as a route to generate switchable proteins for biosensing and regulated biological function.

LANS is a light-activated nuclear shuttle, or LOV/NLS switch, that uses blue light to control nuclear localization by uncaging a nuclear localization signal. It has been used to regulate transcription in yeast and to manipulate nuclear localization and cell fate in the C. elegans embryo, including light-dependent control of the native transcription factor LIN-1.

The LHCII N-terminal domain is the region of the light-harvesting complex II chlorophyll-protein substrate that contains the phosphothreonine site. In thylakoid studies, illumination induces a reversible conformational change that increases exposure of this N-terminal region, enabling access by endogenous thylakoid protein kinase(s) and increasing susceptibility to tryptic cleavage.

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.

Light-regulated protein-protein interaction is a construct pattern in optogenetics that controls signaling protein function by coupling light input to regulated protein-protein interactions or to caging/uncaging events. It is presented as a general strategy for the spatiotemporal control of signal transduction pathways.

Likelihood maximization analysis is a computational method for selecting reaction coordinate models for individual substeps of a conformational transition and inferring tentative transition states. In the cited application, it was applied to transition path sampling data from explicit-solvent molecular dynamics of the millisecond partial unfolding transition in the photoactive yellow protein photocycle.

LOV-LexA is a light-gated LexA-based expression system for Drosophila that fuses the bacterial LexA transcription factor to a plant-derived LOV photosensitive domain and a fluorescent protein. Blue light uncages a nuclear localization signal, drives nuclear translocation, and initiates LexAop transgene expression with spatial and temporal control.

LOV-TAP is an artificial light-activable allosteric protein constructed by ligating the AsLOV2-Jα photoswitch to the tryptophan repressor TrpR. It is designed to regulate protein-DNA association by coupling light-triggered changes in the LOV module to structural and electrostatic changes in the interdomain region that alter DNA binding.

The LOV2 domain C450A variant is a mutant form of the LOV2 photosensory domain that has been examined for its conformational properties across a broad pH range. The available evidence supports biophysical characterization of this variant rather than a demonstrated engineered application.

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 LOV2 module is a light-inducible protein domain incorporated into the FERM domain of an engineered focal adhesion kinase (FAK). In the reported 2021 Nature Communications system, it provides optogenetic input to an allosterically regulated single-protein two-input OR gate while preserving overall FAK domain architecture.

LOV2-based photoswitches are optogenetic switches engineered from the LOV2 photoreceptor domain to control biological activities with light. They repurpose endogenous light-induced conformational changes in LOV2 to generate new cellular outputs and have been developed on the basis of detailed biophysical characterization of the isolated domain.

The LOV2/Jα domain from Avena sativa phototropin 1 is a light-responsive protein domain examined for conformational heterogeneity and propagation of structural changes. The supplied evidence specifically supports its structural characterization by temperature-dependent FTIR spectroscopy.

Markov State Modeling (MSM) is a computational method applied with molecular dynamics simulations to resolve conformational dynamics in the AsLOV2 photosensory domain. In the cited 2023 study, MSM was used to explain blue-light-induced stepwise unfolding of the C-terminal Jα-helix and to identify seven structurally distinguishable unfolding states spanning initiation and post-initiation phases.

Molecular dynamics simulations combined with Markov state modeling were used to characterize blue-light-induced conformational switching in the Avena sativa LOV2 (AsLOV2) domain. This computation method resolved C-terminal Jα-helix unfolding into seven structurally distinguishable steps spanning initiation and post-initiation phases.

Molecular dynamics simulation is a computational method for modeling atomistic conformational dynamics of proteins and analyzing residue fluctuations and vibrational behavior. In the cited studies, it was used as a noninvasive approach to validate dynamic behavior and to compare PAS-domain dynamics across functional groups.

NC80 is an 80-residue motif from Arabidopsis CRY2 that is sufficient to confer CRY2 physiological function. Source evidence indicates that blue light activates CRY2 by a phosphorylation-associated conformational change that derepresses the NC80 motif.

New switching mechanisms are a protein engineering approach that introduces stimulus-responsive conformational switching into proteins that previously lacked such behavior. In the cited review, these engineered switches are described as enabling reagent-free biosensing and regulated biological function.

OptoORAI1 is a photoswitchable CRAC channel engineered from ORAI1 by insertion of a LOV2 photosensory domain into an ORAI1 loop region. In this design, LOV2 functions as an allosteric light-responsive switch that opens the channel, enabling optical control of calcium signaling.

PA-Rac1 is an AsLOV2-Jα-regulated photoactivable Rac1 GTPase in which light-driven conformational changes in the LOV2 module relieve inhibition at the Rac1 switch II activation site. This release permits effector-protein binding and activates Rac1-associated signaling.

Phosphorothioate-caged antisense oligonucleotides are mixed-backbone antisense oligonucleotides in which phosphorothioate linkages are modified with 2-nitroveratryl photocages. In the caged state, these modifications suppress target RNA duplex formation and RNase H activity, and UV uncaging restores antisense function to enable light-controlled knockdown of cell-free protein synthesis.