Source 1primary paperPMC
Toolkit/AlphaFold2
AlphaFold2
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The paper explicitly names AlphaFold2 multimer modeling as part of the study workflow for AtaApore trimer prediction.
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Construction and characterization of a nanopore derived from the transmembrane domain of a trimeric autotransporter adhesin
Objective: Engineer and characterize an open nanopore from the transmembrane β-barrel of the trimeric autotransporter adhesin AtaA.
Why it works: The workflow combines experimental pore characterization with computational structural analysis so that the engineered AtaA-derived pore can be evaluated both functionally and structurally against the parent transmembrane-domain reference.
β-barrel trimer pore formation from a trimeric autotransporter adhesin transmembrane domaincell-free expressionplanar lipid bilayer electrophysiologyAlphaFold2 multimer modelingmolecular dynamics simulation
Stages
- 1.Construct and express AtaA-derived nanopore(library_build)
The engineered AtaA-derived pore must be produced before functional characterization can be performed.
- 2.Electrophysiology characterization in planar lipid bilayers(functional_characterization)
This stage tests whether the engineered AtaA-derived construct functions as a nanopore.
Selection: nanopore behavior measured by planar lipid bilayer electrophysiology
- 3.Computational structural comparison(secondary_characterization)
This stage provides structural interpretation of the engineered pore after functional characterization.
Selection: agreement of predicted and simulated AtaApore structure with the AtaA transmembrane-domain reference structure
Steps
- 1.Generate the AtaA transmembrane-domain-derived nanopore constructengineered nanopore construct
Create the AtaApore design from the AtaA transmembrane β-barrel.
The engineered pore design is required before expression and characterization.
- 2.Express AtaApore using a cell-free systemengineered nanopore being produced
Produce the engineered pore for downstream functional testing.
Expression must occur before planar lipid bilayer electrophysiology can be performed.
- 3.Measure AtaApore by planar lipid bilayer electrophysiologyengineered nanopore being characterized
Test whether the engineered AtaA-derived construct behaves as a nanopore.
Functional electrophysiology follows production of the pore and provides direct evidence of nanopore behavior.
- 4.Predict the AtaApore trimer structure with AlphaFold2engineered nanopore and structure-prediction method
Generate a structural model of the engineered pore.
Structure prediction supports interpretation of the engineered pore after or alongside functional characterization.
- 5.Compare predicted AtaApore structure to the AtaA transmembrane-domain reference using molecular dynamics analysisengineered nanopore being structurally interpreted
Assess how the engineered pore relates structurally to the parent AtaA transmembrane-domain reference structure.
This analysis refines mechanistic interpretation after a structural model is available.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
OligomerizationTechniques
Computational DesignTarget processes
No target processes tagged yet.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The study used AlphaFold2 and molecular dynamics to compare the engineered AtaApore structure against the AtaA transmembrane-domain reference structure PDB 9VNJ.
AtaApore was characterized by planar lipid bilayer electrophysiology.
The study constructed an engineered nanopore named AtaApore from the transmembrane domain of the trimeric autotransporter adhesin AtaA.
Approval Evidence
1 source1 linked approval claimfirst-pass slug alphafold2
The paper explicitly names AlphaFold2 multimer modeling as part of the study workflow for AtaApore trimer prediction.
Source:
structural analysissupports
The study used AlphaFold2 and molecular dynamics to compare the engineered AtaApore structure against the AtaA transmembrane-domain reference structure PDB 9VNJ.
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.