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.
12 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 1-12 of 12
CRY2-BIC1 is a multi-component blue-light-dependent interacting protein pair derived from Arabidopsis thaliana cryptochrome 2 (CRY2) and Blue-light Inhibitor of Cryptochromes 1 (BIC1). It functions as a light-input protein interaction switch, and phage-assisted continuous evolution was applied to increase the dynamic range of the blue-light-dependent CRY2-BIC1 interaction.
Cryptochromes are evolutionarily conserved flavoprotein photoreceptors that sense blue light in multiple organisms. As a protein-domain class, they are used as light-responsive modules in optogenetic systems, while native cryptochromes regulate plant photoresponses and circadian-associated transcriptional programs.
Directed evolution is an engineering method that improves biological tool performance by iteratively selecting functional protein variants. In the cited split fluorescent protein study, it was demonstrated as one of two approaches used to improve split fluorescent proteins, contributing to brighter split sfCherry3 variants.
The gene-pyramiding approach is an insect resistance management strategy used in the U.S. to combat the evolution of insect resistance to Bt crops. The supplied evidence identifies it as one of the two main IRM strategies alongside the high dose/refuge approach, but does not provide further mechanistic detail.
The high dose/refuge approach is an insect resistance management strategy used with Bt crops to combat the evolution of insect resistance. In the supplied evidence, it is identified as one of the two main IRM strategies used in the U.S.
The nMag/pMag photodimerization system, also called Magnets photosensors, is a light-controlled protein-domain pair that mediates heterodimerization. Reported engineering work altered its light sensitivity and tuned its light-activity dose-response behavior through directed evolution and high-throughput screening.
PACE (Phage Assisted Continuous Evolution) is an engineering method used in this study to evolve cryptochrome properties. In the cited work, it was applied to increase the dynamic range of the blue-light-dependent interaction between Arabidopsis thaliana CRY2 and BIC1.
PAR3/INSC/LGN is an evolutionarily conserved multi-protein complex that forms a polarity-associated machinery required for asymmetric cell division in the developing brain. Human genetic evidence further links this machinery to function in the adult peripheral nervous system, where its dysfunction is associated with tubulin aggregation and necrotic neurodegeneration.
Split APEX peroxidase (sAPEX) is an engineered two-fragment version of APEX generated by directed evolution. It consists of a 200-amino acid N-terminal fragment (AP) and a 50-amino acid C-terminal fragment (EX) that can reconstitute peroxidase activity in mammalian cells.
Split sfCherry3 variants are engineered split red fluorescent proteins derived from sfCherry through directed evolution. They were reported to show substantially enhanced overall brightness and to support visualization of endogenous proteins and neuronal synapses.
SpyTag/SpyCatcher interaction is a protein-domain interaction used as an assistance strategy to improve split fluorescent proteins. In the cited 2019 Communications Biology study, it was demonstrated alongside directed evolution as an approach for improving split sfCherry-based reporters.
Time-resolved vibrational spectroscopy coupled with isotope labeling is an assay method used to resolve light-triggered structural dynamics in the Avena sativa LOV2 (AsLOV2) photosensory domain. In the cited study, it mapped structural evolution from 100 fs to 1 ms after optical excitation and supported a sequential allosteric model linking the flavin pocket to Jα-helix unfolding.