Source 1primary paper2019Bulletin of the Chemical Society of Japan
Toolkit/bacteriorhodopsin
bacteriorhodopsin
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
the molecular mechanism of bacteriorhodopsin, a light-driven H+ pump and the best studied microbial rhodopsin, is described.
Usefulness & Problems
Why this is useful
Bacteriorhodopsin is described as a light-driven H+ pump. The review highlights it as the best studied microbial rhodopsin and discusses its molecular mechanism.; understanding microbial rhodopsin mechanism; informing functional design of optogenetics tools; Bacteriorhodopsin is described as an archaeal light-driven H+ pump within the microbial rhodopsin family. The review places it among the main optogenetic ion-pumping tools.; optogenetics; light-driven proton pumping
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Bacteriorhodopsin is described as a light-driven H+ pump. The review highlights it as the best studied microbial rhodopsin and discusses its molecular mechanism.
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understanding microbial rhodopsin mechanism
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informing functional design of optogenetics tools
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Bacteriorhodopsin is described as an archaeal light-driven H+ pump within the microbial rhodopsin family. The review places it among the main optogenetic ion-pumping tools.
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optogenetics
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light-driven proton pumping
Problem solved
It serves as a mechanistic reference point for understanding microbial rhodopsin photochemistry and function. The abstract links such understanding to future optogenetic tool design.; provides a mechanistically studied example of a light-driven proton pump; It provides a light-driven proton-pumping mechanism that can be used as an optogenetic actuator.; provides a light-driven ion-pumping actuator class for optogenetic control
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It serves as a mechanistic reference point for understanding microbial rhodopsin photochemistry and function. The abstract links such understanding to future optogenetic tool design.
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provides a mechanistically studied example of a light-driven proton pump
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It provides a light-driven proton-pumping mechanism that can be used as an optogenetic actuator.
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provides a light-driven ion-pumping actuator class for optogenetic control
Problem links
provides a light-driven ion-pumping actuator class for optogenetic control
LiteratureIt provides a light-driven proton-pumping mechanism that can be used as an optogenetic actuator.
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It provides a light-driven proton-pumping mechanism that can be used as an optogenetic actuator.
provides a mechanistically studied example of a light-driven proton pump
LiteratureIt serves as a mechanistic reference point for understanding microbial rhodopsin photochemistry and function. The abstract links such understanding to future optogenetic tool design.
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It serves as a mechanistic reference point for understanding microbial rhodopsin photochemistry and function. The abstract links such understanding to future optogenetic tool design.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Techniques
Computational DesignTarget 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
mechanistic interpretation centers on its light-driven H+ pump behavior; As a microbial rhodopsin, it uses a retinal chromophore and light to function. It is a seven-transmembrane photoactive protein.; requires light; requires retinal chromophore
The abstract does not state that bacteriorhodopsin itself is the main optogenetic channel tool or provide application benchmarks. Its role here is primarily mechanistic and historical.; the abstract emphasizes mechanistic understanding rather than direct optogenetic deployment details
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Understanding the molecular mechanism of microbial rhodopsins is a prerequisite for useful functional design of future optogenetics tools.
As history has proven, understanding the molecular mechanism of microbial rhodopsins is a prerequisite for useful functional design of optogenetics tools in future.
Several microbial rhodopsins transport ions passively or actively, and light-gated channels and light-driven pumps are the main optogenetic tools among them.
Unlike animal rhodopsins, several kinds of microbial rhodopsins are able to transport ions in a passive or an active manner, and light-gated channels or light-driven pumps, respectively, are the main tools in optogenetics.
Bacteriorhodopsin is a light-driven H+ pump and the best studied microbial rhodopsin.
bacteriorhodopsin, a light-driven H+ pump and the best studied microbial rhodopsin
Approval Evidence
4 sources9 linked approval claimsfirst-pass slug bacteriorhodopsin
the molecular mechanism of bacteriorhodopsin, a light-driven H+ pump and the best studied microbial rhodopsin, is described.
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Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) ... are the main tools in optogenetics.
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The method is applied to the light-induced changes in the membrane-bound proton pump bacteriorhodopsin (bR).
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Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium
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design principlesupports
Understanding the molecular mechanism of microbial rhodopsins is a prerequisite for useful functional design of future optogenetics tools.
As history has proven, understanding the molecular mechanism of microbial rhodopsins is a prerequisite for useful functional design of optogenetics tools in future.
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functional rolesupports
Several microbial rhodopsins transport ions passively or actively, and light-gated channels and light-driven pumps are the main optogenetic tools among them.
Unlike animal rhodopsins, several kinds of microbial rhodopsins are able to transport ions in a passive or an active manner, and light-gated channels or light-driven pumps, respectively, are the main tools in optogenetics.
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mechanistic descriptionsupports
Bacteriorhodopsin is a light-driven H+ pump and the best studied microbial rhodopsin.
bacteriorhodopsin, a light-driven H+ pump and the best studied microbial rhodopsin
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functional classificationsupports
Bacteriorhodopsin is an archaeal light-driven H+ pump.
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motif taxonomysupports
BR, HR, PR, FR, and KR2 are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins, respectively.
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applicationsupports
The atomic force sensing technique was applied to light-induced changes in bacteriorhodopsin.
The method is applied to the light-induced changes in the membrane-bound proton pump bacteriorhodopsin (bR).
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hypothesis challengecontradicts
The data question the hypothesis that all primary events in retinal proteins are attributable to an initial trans-cis isomerization.
our data question the current working hypothesis which attributes all primary events in retinal proteins to an initial trans<==>cis isomerization
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mechanistic inferencesupports
Protein conformational changes in bacteriorhodopsin can be initiated by light-triggered redistribution of electronic charge in the retinal chromophore even when isomerization cannot take place.
protein conformational changes in bR can be initiated as a result of a light-triggered redistribution of electronic charge in the retinal chromophore, even when isomerization cannot take place
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functional rolesupports
Bacteriorhodopsin is a light-driven proton pump in Halobacterium halobium.
Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium
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Comparisons
Source-stated alternatives
The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.; The abstract contrasts BR with other ion-pumping rhodopsins including halorhodopsin, proteorhodopsin, Fulvimarina pelagi rhodopsin, and KR2.
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The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
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The abstract contrasts BR with other ion-pumping rhodopsins including halorhodopsin, proteorhodopsin, Fulvimarina pelagi rhodopsin, and KR2.
Source-backed strengths
described as the best studied microbial rhodopsin; described as a main optogenetic tool; mechanism has been extensively studied
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described as the best studied microbial rhodopsin
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described as a main optogenetic tool
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mechanism has been extensively studied
Compared with Channelrhodopsin variants
The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Shared frame: source-stated alternative in extracted literature
Strengths here: described as the best studied microbial rhodopsin; described as a main optogenetic tool; mechanism has been extensively studied.
Relative tradeoffs: the abstract emphasizes mechanistic understanding rather than direct optogenetic deployment details.
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The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Compared with optogenetic functional interrogation
The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Shared frame: source-stated alternative in extracted literature
Strengths here: described as the best studied microbial rhodopsin; described as a main optogenetic tool; mechanism has been extensively studied.
Relative tradeoffs: the abstract emphasizes mechanistic understanding rather than direct optogenetic deployment details.
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The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Compared with optogenetic membrane potential perturbation
The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Shared frame: source-stated alternative in extracted literature
Strengths here: described as the best studied microbial rhodopsin; described as a main optogenetic tool; mechanism has been extensively studied.
Relative tradeoffs: the abstract emphasizes mechanistic understanding rather than direct optogenetic deployment details.
Source:
The abstract contrasts bacteriorhodopsin with channelrhodopsin variants, which are introduced as light-gated ion channels used in optogenetics.
Ranked Citations
- 1.