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.
11 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 1-11 of 11
Substituting loops of thermophilic AtCas9 with counterparts from mesophilic Nme1Cas9 generated the AtCas9-Z7 variant, which significantly improves nuclease and base editing efficiency.
Designed decoy peptides targeting CIB1 are in silico engineered variants of the reference peptide UNC10245092 generated by residue scan methodology to bind CIB1. In the reported computational study, top candidates were prioritized by predicted binding free energy, evaluated by AMBER molecular dynamics simulations, and were predicted to interfere with RAF–CIB1 binding; mutant 2 showed stronger predicted interactions with CIB1 than the reference peptide.
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.
RGEPO1, targeted to the extracellular membrane, and RGEPO2, localized in the cytoplasm, exhibited positive K+-specific fluorescence response with affinities of 2.4 and 43.3 mM in HEK293FT cells, respectively.
In this study, we developed two novel red genetically encoded potassium indicators (RGEPOs), RGEPO1 and RGEPO2.
The paper names the engineered pore AtaApore and describes it as an open nanopore derived from the transmembrane β-barrel of the Acinetobacter trimeric autotransporter adhesin AtaA.
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.
Transition path sampling is a computational method applied to explicit-solvent molecular dynamics trajectories to extract atomistic features of conformational reaction networks. In the cited study, it was used to analyze the millisecond partial unfolding transition in the light-driven photocycle of photoactive yellow protein and to predict reaction coordinate models and tentative transition states.
psd3 is a variant of the photosensitive degron built around an AsLOV2 photoreceptor module for light-dependent control of protein abundance. Available evidence indicates that its light sensitivity can be tuned by photocycle mutations and that it was developed in a system for optogenetic regulation of transcription-related processes.
The photosensitive transcription factor (psTF) is an AsLOV2-based optogenetic multi-component switch for light-regulated control of transcription. In the cited work, photocycle mutations in AsLOV2 were used to tune the light sensitivity of psTF photoreceptor components, and distinct AsLOV2 variants showed context-dependent behavior.
Here, we present loop engineering as a streamlined strategy to enhance Cas9 performance.