Source 1primary paper2013Nature Communications
Toolkit/Krokinobacter eikastus rhodopsin 2
Krokinobacter eikastus rhodopsin 2
Also known as: KR2
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Krokinobacter eikastus rhodopsin 2 (KR2) is the prototypical light-driven sodium pump. Upon illumination, it actively transports small cations across cellular membranes and has been described as a useful optogenetic tool with applications in neuroscience.
Usefulness & Problems
Why this is useful
KR2 is useful because it converts light input into active cation transport across membranes, enabling optical control of membrane potential. The cited literature specifically places light-driven sodium pumps in the context of optogenetic applications in neuroscience.
Source:
KR2 is a light-driven sodium pump used by microorganisms to convert light into membrane potential. The abstract also states that such pumps have become useful optogenetic tools with applications in neuroscience.
Source:
optogenetic applications in neuroscience
Source:
light-driven sodium pumping
Problem solved
KR2 helps solve the problem of generating membrane potential changes using light-driven ion transport. The source also indicates that structural and spectroscopic analysis addressed a mechanistic problem by revealing transient sodium binding near the retinal during the transport cycle.
Source:
It provides a way to use light-driven ion transport to generate membrane potential changes. This underlies its usefulness as an optogenetic tool.
Source:
converts light into membrane potential
Problem links
converts light into membrane potential
LiteratureIt provides a way to use light-driven ion transport to generate membrane potential changes. This underlies its usefulness as an optogenetic tool.
Source:
It provides a way to use light-driven ion transport to generate membrane potential changes. This underlies its usefulness as an optogenetic tool.
introduces a sodium-pumping microbial rhodopsin class
LiteratureIt provides a sodium-pumping option within the ion-pumping rhodopsin toolkit space.
Source:
It provides a sodium-pumping option within the ion-pumping rhodopsin toolkit space.
provides a light-driven sodium-pumping rhodopsin distinct from proton-pumping rhodopsins
LiteratureIt introduces a new functional class of microbial rhodopsin that can generate ion transport using light with sodium as the transported ion.
Source:
It introduces a new functional class of microbial rhodopsin that can generate ion transport using light with sodium as the transported ion.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Mechanisms
ion-environment-dependent switching to proton pumpinglight-driven active cation transportlight-driven lithium ion pumpinglight-driven outward sodium ion pumpingtransient sodium ion binding near retinalTechniques
Structural CharacterizationTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
cofactor dependency: requires exogenous cofactorencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: actuator
The tool requires light as the input modality and functions across cellular membranes as an active cation pump. The provided evidence does not report construct design, cofactor requirements, expression host, or delivery format.
The supplied evidence does not specify expression systems, delivery strategies, photocurrent properties, ion selectivity beyond small cations, or performance metrics in cells or animals. Independent replication and breadth of validation are not established from the provided material alone.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2020Nature
Source 3review2015Frontiers in Molecular Biosciences
Ranked Claims
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
transient sodium binding time 1 millisecond
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
pump-probe delays 10 delays
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
last structural intermediate time 20 milliseconds
Halorhodopsin is an archaeal light-driven Cl- pump.
Krokinobacter eikastus rhodopsin 2 is a light-driven Na+ pump.
BR, HR, PR, FR, and KR2 are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins, respectively.
Spectroscopic analysis showed that KR2 binds sodium ions in its extracellular domain.
KR2 converts to a proton pump when presented with potassium chloride or salts of larger cations.
KR2 can also pump lithium ions.
KR1 is a prototypical proton pump.
KR2 pumps sodium ions outward.
KR2 is a compatible sodium ion-proton pump.
Approval Evidence
3 sources12 linked approval claimsfirst-pass slugs kr2, krokinobacter-eikastus-rhodopsin-2
the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2)
Source:
In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2).
Source:
the second, KR2, pumps sodium ions outward. Rhodopsin KR2 can also pump lithium ions, but converts to a proton pump when presented with potassium chloride or salts of larger cations.
Source:
functionsupports
Light-driven sodium pumps actively transport small cations across cellular membranes and are useful optogenetic tools with applications in neuroscience.
Light-driven sodium pumps actively transport small cations across cellular membranes. These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience.
Source:
ion binding mechanismsupports
Structural and spectroscopic data combined with quantum chemical calculations indicate that a sodium ion binds transiently close to the retinal within one millisecond in KR2.
Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond.
Source:
structural mechanismsupports
High-resolution structural snapshots throughout the KR2 photocycle show that retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds.
Source:
structural mechanismsupports
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds during the KR2 photocycle.
Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds.
Source:
structural observationsupports
At 20 milliseconds after activation, the last structural intermediate of KR2 contains a potential second sodium-binding site close to the extracellular exit.
In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit.
Source:
functional classificationsupports
Krokinobacter eikastus rhodopsin 2 is a light-driven Na+ pump.
Source:
motif taxonomysupports
BR, HR, PR, FR, and KR2 are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins, respectively.
Source:
binding observationsupports
Spectroscopic analysis showed that KR2 binds sodium ions in its extracellular domain.
Source:
condition dependent functionsupports
KR2 converts to a proton pump when presented with potassium chloride or salts of larger cations.
Source:
ion selectivitysupports
KR2 can also pump lithium ions.
Source:
ion transport activitysupports
KR2 pumps sodium ions outward.
Source:
mechanistic propertysupports
KR2 is a compatible sodium ion-proton pump.
Source:
Comparisons
Source-stated alternatives
The abstract does not name alternative optogenetic tools, but it frames KR2 as a prototypical member of light-driven sodium pumps.; The abstract contrasts KR2 with proton-pumping BR and PR and chloride-pumping HR and FR.; The same organism contains KR1, described as a prototypical proton pump, which contrasts with KR2's sodium-pumping behavior.
Source:
The abstract does not name alternative optogenetic tools, but it frames KR2 as a prototypical member of light-driven sodium pumps.
Source:
The abstract contrasts KR2 with proton-pumping BR and PR and chloride-pumping HR and FR.
Source:
The same organism contains KR1, described as a prototypical proton pump, which contrasts with KR2's sodium-pumping behavior.
Source-backed strengths
KR2 is described as the prototypical sodium pump among light-driven sodium pumps. Structural, spectroscopic, and quantum chemical evidence support a specific mechanistic feature in which a sodium ion binds transiently close to the retinal within one millisecond.
Source:
described as a prototypical light-driven sodium pump
Source:
useful optogenetic tool according to the abstract
Compared with optogenetic
The abstract does not name alternative optogenetic tools, but it frames KR2 as a prototypical member of light-driven sodium pumps.
Shared frame: source-stated alternative in extracted literature
Strengths here: described as a prototypical light-driven sodium pump; useful optogenetic tool according to the abstract; identified as a light-driven Na+ pump.
Relative tradeoffs: mechanism of sodium translocation was previously unclear; converts to a proton pump in potassium chloride or salts of larger cations.
Source:
The abstract does not name alternative optogenetic tools, but it frames KR2 as a prototypical member of light-driven sodium pumps.
Ranked Citations
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