Source 1review2015Frontiers in Molecular Biosciences
Toolkit/time-resolved infrared spectroscopy
time-resolved infrared spectroscopy
Also known as: infrared spectroscopy, time-resolved IR spectroscopy, transient infrared spectroscopy
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Time-resolved infrared spectroscopy, also termed transient infrared spectroscopy, is a light-triggered functional assay that monitors vibrational and structural dynamics of LOV photoreceptors on picosecond-to-microsecond timescales. In the cited studies, it resolved FMN triplet-state progression to cysteinyl-FMN adduct formation and subsequent protein conformational changes, including Jα helix unfolding.
Usefulness & Problems
Why this is useful
This assay is useful for dissecting ultrafast and early-time photocycles in LOV domains by directly tracking vibrational signatures of chromophore and protein structural states after photoexcitation. The cited work shows that it can compare conserved versus divergent activation steps across AsLOV2, YtvA, EL222, and LovK.
Problem solved
It addresses the problem of measuring how light absorption in LOV photoreceptors is converted into specific chemical intermediates and protein structural responses over picosecond-to-microsecond intervals. The method specifically enables observation of the pathway from the FMN triplet state to cysteinyl adduct formation and the divergence of post-adduct dynamics linked to output function.
Problem links
enables investigation of poorly understood photocycle and gating mechanisms
LiteratureIt helps address limited mechanistic understanding of channelrhodopsin photocycles, ion channel gating, and conductance. The method provides molecular-level information that complements functional use of these optogenetic tools.
Source:
It helps address limited mechanistic understanding of channelrhodopsin photocycles, ion channel gating, and conductance. The method provides molecular-level information that complements functional use of these optogenetic tools.
provides a molecular-level readout of channelrhodopsin function in near-native environment
LiteratureIt helps address limited mechanistic understanding of channelrhodopsin photocycles, ion channel gating, and conductance. The method provides molecular-level information that complements functional use of these optogenetic tools.
Source:
It helps address limited mechanistic understanding of channelrhodopsin photocycles, ion channel gating, and conductance. The method provides molecular-level information that complements functional use of these optogenetic tools.
Published Workflows
Objective: Use time-resolved infrared spectroscopic approaches to investigate channelrhodopsin photocycle, ion channel gating, and conductance across the full kinetic range of the light response.
Why it works: The review states that channelrhodopsin dynamics span femtoseconds to minutes, so different IR approaches are needed to observe distinct mechanistic phases over that full range.
retinal isomerizationformation of conductive statesreturn to dark-adapted statetime-resolved infrared spectroscopymultiple spectroscopical approaches matched to kinetic regime
Stages
- 1.Ultrafast photochemical observation(functional_characterization)
The review states that retinal isomerization occurs within femtoseconds, requiring an approach suitable for the ultrafast regime.
Selection: Capture earliest light-induced molecular events immediately after photon absorption.
- 2.Conductive-state characterization(functional_characterization)
The review identifies the microsecond regime as the timescale on which conductive states are reached.
Selection: Measure molecular changes associated with formation of conductive states on the microsecond timescale.
- 3.Dark-state recovery characterization(secondary_characterization)
The review states that return into the fully dark-adapted state may take more than minutes, so slower measurements are needed.
Selection: Track return to the fully dark-adapted state over slow timescales.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
conformational change monitoringcovalent cysteinyl-fmn adduct formation monitoringmonitoring of covalent cysteinyl-fmn adduct formationmonitoring of protein conformational changetime-resolved detection of photoinduced state transitionsvibrational spectroscopyTechniques
Functional AssayTarget 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: sensor
The assay is light-triggered and was applied to LOV photoreceptors containing FMN, with measurements spanning picoseconds to microseconds. The cited examples include AsLOV2, YtvA, EL222, and LovK, but the supplied evidence does not specify instrument configuration or sample preparation details.
The supplied evidence is limited to LOV photoreceptors and does not establish performance outside this protein family. The evidence also does not provide practical details on spectral resolution, sample requirements, throughput, or compatibility with in vivo measurements.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2016The Journal of Physical Chemistry Letters
Source 3primary paper2017Biochemistry
Ranked Claims
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
time to complete Jα helix unfolding 500 μs
In D2O buffer, covalent cysteinyl-FMN adduct formation in Avena sativa LOV2 occurs in 10 μs.
formation of the covalent cysteinyl-FMN adduct in 10 μcs
cysteinyl-FMN adduct formation time 10 μs
In D2O buffer, FMN singlet-to-triplet conversion in Avena sativa LOV2 occurs in 2 ns.
In D2O buffer, FMN singlet-to-triplet conversion occurs in 2 ns
FMN singlet-to-triplet conversion time 2 ns
Jα helix unfolding in Avena sativa LOV2 proceeds in two steps, with a first phase at 10 μs concomitant with Cys-FMN adduct formation and a second phase at approximately 240 μs.
We observe a two-step unfolding of the Jα helix: The first phase occurs concomitantly with Cys-FMN covalent adduct formation in 10 μcs ... The second phase occurs in approximately 240 μcs.
first Jα helix unfolding phase time 10 μssecond Jα helix unfolding phase time 240 μs
The Avena sativa LOV2 domain binds a C-terminal Jα helix docked on a β-sheet, and the Jα helix unfolds upon light absorption by the FMN chromophore.
The light, oxygen, and voltage 2 (LOV2) sensing domain of plant phototropin binds a C-terminal Jα helix that is docked on a β-sheet and unfolds upon light absorption by the flavin mononucleotide (FMN) chromophore.
The first phase of Jα helix unfolding is accompanied by rupture of the hydrogen bond between FMN C4=O and Gln-513, motion of the β-sheet, and an additional helical element.
The first phase occurs concomitantly with Cys-FMN covalent adduct formation in 10 μcs, along with hydrogen-bond rupture of the FMN C4═O with Gln-513, motion of the β-sheet, and an additional helical element.
A range of different spectroscopical approaches is necessary to cover the full set of channelrhodopsin time regimes from ultrafast photochemistry to slow dark-state recovery.
Infrared spectroscopy is a preferred method for studying channelrhodopsins because it allows observation of proteins and their function at a molecular level and in near-native environment.
Approval Evidence
3 sources3 linked approval claimsfirst-pass slug time-resolved-infrared-spectroscopy
Time-Resolved Infrared Spectroscopy
Source:
investigated using time-resolved infrared spectroscopy from picoseconds to microseconds
Source:
One of the preferred methods for these studies is infrared spectroscopy since it allows observation of proteins and their function at a molecular level and in near-native environment. This mini-review focuses on time-resolved applications of the infrared technique to study channelrhodopsins and other light triggered proteins.
Source:
measurementsupports
By 500 μs, the final time-resolved spectrum is essentially identical to the steady-state light-minus-dark FTIR spectrum, indicating that Jα helix unfolding is complete on that time scale.
The final spectrum at 500 μcs is essentially identical to the steady-state light-minus-dark Fourier transform infrared spectrum, indicating that Jα helix unfolding is complete on that time scale.
Source:
method requirementsupports
A range of different spectroscopical approaches is necessary to cover the full set of channelrhodopsin time regimes from ultrafast photochemistry to slow dark-state recovery.
Source:
method suitabilitysupports
Infrared spectroscopy is a preferred method for studying channelrhodopsins because it allows observation of proteins and their function at a molecular level and in near-native environment.
Source:
Comparisons
Source-stated alternatives
The abstract does not name non-IR alternatives. It contrasts different time-resolved IR approaches as complementary rather than interchangeable.
Source:
The abstract does not name non-IR alternatives. It contrasts different time-resolved IR approaches as complementary rather than interchangeable.
Source-backed strengths
The cited studies indicate that the method captures mechanistic conservation across multiple LOV proteins, showing a highly conserved pathway leading to cysteine adduct formation from the FMN triplet state. It also resolves function-linked divergence after adduct formation and quantified that adduct formation rates varied by only 3.6-fold among the studied proteins.
Compared with CLARITY technology
time-resolved infrared spectroscopy and CLARITY technology address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Strengths here: appears more independently replicated; looks easier to implement in practice.
Compared with Langendorff perfused heart electrical recordings
time-resolved infrared spectroscopy and Langendorff perfused heart electrical recordings address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Strengths here: appears more independently replicated; looks easier to implement in practice.
Compared with native green gel system
time-resolved infrared spectroscopy and native green gel system address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Strengths here: appears more independently replicated; looks easier to implement in practice.
Ranked Citations
- 1.
- 2.
- 3.