Source 1primary paper2019PLoS Computational Biology
Toolkit/Vivid (VVD) LOV domain
Vivid (VVD) LOV domain
Also known as: light, oxygen, voltage (LOV) domain, Vivid, VVD
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The Vivid (VVD) LOV domain is a photosensitive allosteric light, oxygen, voltage domain from a fungal circadian clock photoreceptor. It responds to blue-light-driven covalent bond formation with a large N-terminal conformational change, and its atomistic allosteric mechanism has been analyzed computationally.
Usefulness & Problems
Why this is useful
VVD is useful as a model photosensory domain for studying how blue-light input is converted into allosteric structural change. The available evidence particularly supports its value for mechanistic dissection of LOV-domain signaling at atomistic resolution.
Problem solved
This tool helps address the problem of understanding how a photochemical event in a LOV domain propagates into global protein conformational change. The cited work specifically evaluates how blue-light-driven covalent bond formation contributes to VVD allostery and identifies structural elements linked to the conformational response.
Problem links
Need precise spatiotemporal control with light input
DerivedThe Vivid (VVD) LOV domain is a photosensitive allosteric light, oxygen, voltage domain from a fungal circadian clock photoreceptor. It undergoes a large N-terminal conformational change associated with blue-light-driven covalent bond formation and has been analyzed at atomistic resolution for its allosteric mechanism.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level protein part used inside a larger architecture that realizes a mechanism.
Mechanisms
allosteric switchingallosteric switchingblue-light-induced covalent bond formationblue-light-induced covalent bond formationconformational uncagingconformational uncagingConformational UncagingTechniques
No technique tags yet.
Target processes
No target processes tagged yet.
Input: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: actuatorswitch architecture: uncaging
The input modality is light, specifically blue light, and the mechanistic trigger is blue-light-driven covalent bond formation within the LOV domain. Beyond its identity as a fungal photoreceptor domain, the supplied evidence does not specify construct design, cofactors, expression systems, or delivery considerations.
The supplied evidence is limited to one mechanistic study and does not report quantitative performance metrics, kinetics, reversibility, or engineering benchmarks. Independent replication, application in heterologous systems, and direct evidence for tool deployment are not provided in the supplied material.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The proposed atomistic allosteric mechanism identifies A'α/Aβ and Eα/Fα loops as important contributors to the VVD conformational change.
leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change
The VVD LOV domain undergoes a large N-terminal conformational change.
Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change
An integrative computational platform combining Markov state models, machine learning, and community analysis was used to evaluate the contribution of blue-light driven covalent bond formation to VVD global conformational change and to propose an atomistic allosteric mechanism.
We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism
Approval Evidence
1 source3 linked approval claimsfirst-pass slug vivid-vvd-lov-domain
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain
Source:
mechanistic insightsupports
The proposed atomistic allosteric mechanism identifies A'α/Aβ and Eα/Fα loops as important contributors to the VVD conformational change.
leading to the discovery of the unexpected importance of A'α/Aβ and previously overlooked Eα/Fα loops in the conformational change
Source:
mechanistic propertysupports
The VVD LOV domain undergoes a large N-terminal conformational change.
Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change
Source:
method applicationsupports
An integrative computational platform combining Markov state models, machine learning, and community analysis was used to evaluate the contribution of blue-light driven covalent bond formation to VVD global conformational change and to propose an atomistic allosteric mechanism.
We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an atomistic allosteric mechanism
Source:
Comparisons
Source-backed strengths
The domain exhibits a large N-terminal conformational change, providing a clear structural output associated with light activation. Its proposed allosteric mechanism has been resolved using an integrative computational framework that identified the A'α/Aβ and Eα/Fα loops as important contributors.
Compared with CRY2 C-terminal tail
Vivid (VVD) LOV domain and CRY2 C-terminal tail address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: allosteric switching; same primary input modality: light
Compared with Light-Oxygen-Voltage domain
Vivid (VVD) LOV domain and Light-Oxygen-Voltage domain address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: conformational uncaging, conformational_uncaging; same primary input modality: light
Vivid (VVD) LOV domain and photoactivatable inhibitor for cyclic-AMP dependent kinase (PKA) address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: allosteric switching; same primary input modality: light
Ranked Citations
- 1.