Source 1primary paper2020Nature
Toolkit/serial crystallography at pump-probe delays
serial crystallography at pump-probe delays
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Serial crystallography at pump-probe delays is a time-resolved structural characterization method that collects crystallographic data at defined times after light excitation. In the cited KR2 study, it was used to follow the light-driven sodium pump photocycle across ten delays spanning femtoseconds to milliseconds and capture structural intermediates over time.
Usefulness & Problems
Why this is useful
This method is useful for observing light-triggered structural changes as they evolve over time rather than inferring mechanism from resting-state crystal structures alone. In the cited work, it enabled time-resolved tracking of the KR2 photocycle after photoactivation.
Source:
This method collects serial crystallographic data at defined pump-probe delays to capture structural intermediates over time. In this paper it was used to follow the KR2 photocycle from femtoseconds to milliseconds.
Source:
capturing time-resolved structural snapshots
Source:
resolving photocycle intermediates across femtosecond-to-millisecond timescales
Problem solved
It addresses the problem of resolving transient structural intermediates in a light-activated protein photocycle. Specifically, it provides structural snapshots at defined pump-probe delays from femtoseconds to milliseconds after excitation.
Source:
It addresses the need to observe structural alterations over time rather than only resting-state structures. This enables direct observation of photocycle-linked conformational changes.
Source:
provides structural snapshots over time during the KR2 photocycle
Problem links
provides structural snapshots over time during the KR2 photocycle
LiteratureIt addresses the need to observe structural alterations over time rather than only resting-state structures. This enables direct observation of photocycle-linked conformational changes.
Source:
It addresses the need to observe structural alterations over time rather than only resting-state structures. This enables direct observation of photocycle-linked conformational changes.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Target 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: sensor
The method requires light excitation to initiate the photocycle and crystallographic data collection at defined pump-probe delays. The extraction notes state that the cited work used the Swiss X-ray Free Electron Laser and ten pump-probe delays, indicating dependence on specialized serial crystallography infrastructure.
The supplied evidence supports structural capture after light excitation, but does not establish that serial crystallography alone resolves all mechanistic details. In the cited study, conclusions about transient sodium binding near retinal within one millisecond were supported by structural and spectroscopic data combined with quantum chemical calculations.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
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
Approval Evidence
1 source1 linked approval claimfirst-pass slug serial-crystallography-at-pump-probe-delays
we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds
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:
Comparisons
Source-stated alternatives
The abstract contrasts these time-resolved data with previously solved resting state structures of KR2.
Source:
The abstract contrasts these time-resolved data with previously solved resting state structures of KR2.
Source-backed strengths
The cited study reports serial crystallographic data collected at ten pump-probe delays from femtoseconds to milliseconds, providing broad temporal coverage of the KR2 photocycle. The method directly captures time-dependent structural intermediates in a light-driven sodium pump.
Source:
captures high-resolution structural snapshots across multiple time delays
Compared with CLARITY technology
serial crystallography at pump-probe delays and CLARITY technology address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: looks easier to implement in practice; may avoid an exogenous cofactor requirement.
Compared with Langendorff perfused heart electrical recordings
serial crystallography at pump-probe delays and Langendorff perfused heart electrical recordings address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: looks easier to implement in practice; may avoid an exogenous cofactor requirement.
Compared with native green gel system
serial crystallography at pump-probe delays and native green gel system address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: looks easier to implement in practice; may avoid an exogenous cofactor requirement.
Ranked Citations
- 1.