Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.
20 items matching 1 filter
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Showing 1-20 of 20
The modular degron library is a protein-domain toolkit presented for synthetic circuits in mammalian cells. Based on the available evidence, it comprises degron modules intended to regulate protein stability in mammalian synthetic biology applications.
First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses.
Bacterial degraders are a proposed construct pattern for targeted protein degradation in bacteria. They are discussed as tools to interrogate protein function and as potential antimicrobial modalities.
Between 2020 and 2025, major progress has been achieved across five modalities: proteolysis-targeting chimeras (PROTACs), molecular glues... Each exploits endogenous degradation or regulatory pathways using chemically engineered bifunctional or monofunctional small molecules.
Orthogonal degrons are bacterial construct patterns used in tunable degradation systems to direct targeted proteolysis of proteins of interest. The cited literature places them among recent advances that enable large screens and functional interrogation through regulated protein degradation.
The development of proteolysis targeting chimeras (PROTACs) that trigger degradation of the target proteins provides a conceptually novel approach to address drug targets that remained previously elusive.
This entry refers broadly to imaging-oriented tools and sensors associated with bacterial degron and degrader concepts. The supplied evidence only states that bacterial degrons can be used to interrogate and control protein function and mentions “tools and sensors for imaging,” without defining a specific construct, sensor architecture, or imaging readout.
These heterobifunctional molecules are comprised of three units: a ligand for the protein of interest (POI), a ligand for an E3 ubiquitin ligase, and a linker that tethers the two motifs together. Von Hippel-Lindau (VHL) is one of the most widely employed E3 ligases in PROTACs development.
Nanobody-mediated proteolysis-targeting chimeras are a degradation-based engineering method used in an optogenetically coordinated platform to regulate the intracellular factor Survivin in cancer cells. In the cited study context, they are combined with split-Cas9-based targeted gene editing for multi-level control of cancer cell fate.
opto-PROTAC is a light-inducible PROTAC design in which a photolabile caging group is installed on pomalidomide-based degraders to block activity in the dark and permit target protein degradation after ultraviolet A irradiation. It was demonstrated using caged pomalidomide and the PROTACs dBET1 and dALK to achieve spatiotemporal control of protein destruction.
pc-PROTAC1 is a photocaged PROTAC construct designed for light-dependent targeted protein degradation in live cells. In the cited study, it exhibited potent degradation activity only after light irradiation, establishing a light-activated degradation strategy.
pc-PROTAC3 is a photocaged PROTAC constructed against Bruton's tyrosine kinase (BTK) within a light-inducible protein degradation strategy. The available evidence states that this approach was successfully applied to generate pc-PROTAC3 and that photocaged PROTACs can activate degradation activity upon light exposure.
Photo-caged PROTACs (pc-PROTACs) are light-activated proteolysis-targeting chimeras designed to trigger targeted protein degradation only after irradiation. The reported study presented pc-PROTACs as a general strategy for inducing degradation activity with light and showed that pc-PROTAC1 was potently active in live cells only after light exposure.
TRIM21-nanobody chimeras are engineered Trim-Away constructs that fuse TRIM21 activity to nanobody-based target recognition. In the cited 2020 work, these chimeras were described as highly active and were further adapted for optogenetic control of targeted protein degradation.
Flash-Away is an intrabody-directed optogenetic protein degradation system that enables blue-light-triggered, targeted degradation of selected proteins. It has been reported to act on actin, MLKL, and ALFA-tagged proteins.
The supplied web research summary identifies Azo-PROTAC as an explicitly supported related item candidate and as a major photoswitchable degrader design emphasized by the anchor review.
This Logic-gated AdPROM deploying SrtA-mediated Element Recombination (LASER) platform allows us to expand the possible protein degradation outcomes in mammalian cells using Boolean logic operations depending on the input combinations.
we developed the molecular glue and ternary binding (MGTbind) database, providing comprehensive resources about ternary structures and experimental data for the coverage of MG-engaged interactome
Nanoparticle-assisted targeted protein degraders (NanoTACs) offer a compelling solution by coupling the catalytic efficiency of TPD with the spatial precision and tunability of nanotechnology.
The supplied web research summary identifies PHOTACs as a photoswitchable PROTAC class directly central to the anchor review and as an explicitly supported related component/tool name in sources discussed by the review.