Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy

Schubert, Luiz; Langner, Pit; Ehrenberg, D.; Lórenz-Fonfrı́a, Vı́ctor A.; Heberle, Joachim

doi:10.1063/5.0088526

Cited by 12 publications

(9 citation statements)

References 29 publications

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“…Thermal back-isomerization of the chromophore occurs during the N–O transition, and deprotonation of the Asp sidechain completes the catalytic cycle . Most transient IR studies have been performed with “slower” spectroscopic techniques, such as step-scan FTIR spectroscopy ,,,,, or more recently with the help of quantum cascade lasers − while the fs–ps timescale has been addressed separately. , …”

Section: Resultsmentioning

confidence: 99%

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy

Helbing

Hamm

2023

J. Phys. Chem. A

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Several ways to electronically synchronize different types of amplified femtosecond laser systems are presented based on a single freely programmable electronics hardware: arbitrary-detuning asynchronous optical sampling (ADASOPS), as well as actively locking two femtosecond laser oscillators, albeit not necessarily to the same round-trip frequency. They allow us to rapidly probe a very wide range of timescales, from picoseconds to potentially seconds, in a single transient absorption experiment without the need to move any delay stage. Experiments become possible that address a largely unexplored aspect of many photochemical reactions, in particular in the context of photo-catalysis as well as photoactive proteins, where an initial femtosecond trigger very often initiates a long-lasting cascade of follow-up processes. The approach is very versatile and allows us to synchronize very different lasers, such as a Ti:Sa amplifier and a 100 kHz Yb-laser system. The jitter of the synchronization, and therewith the time-resolution in the transient experiment, lies in the range from 1 to 3 ps, depending on the method. For illustration, transient IR measurements of the excited state solvation and decay of a metal carbonyl complex as well as the full reaction cycle of bacteriorhodopsin are shown. The pros and cons of the various methods are discussed, with regard to the scientific question one might want to address, and also with regard to the laser systems that might be already existent in a laser lab.

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Section: Resultsmentioning

confidence: 99%

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy

Helbing

Hamm

2023

J. Phys. Chem. A

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“…An emerging transient absorption technique using quantum cascade laser (QCL) has been employed in the spectral and kinetic investigations of reactive species in gaseous phase, summarized by Chung and Lee [132]. QCL-based transient absorption has also been employed in probing the photocycle of bacteriorhodopsin in condensed phase [133,134]. An absorbance difference as low as 1 Â 10 À4 is achievable in single-shot QCL experiments at t > 1 μs [133].…”

Section: Discussionmentioning

confidence: 99%

Applications of time‐resolved step‐scan Fourier‐transform infrared spectroscopy in revealing the light‐initiated reactions in condensed phases

Chu

2023

J Chinese Chemical Soc

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Step‐scan Fourier‐transform infrared spectroscopy (ssFTIR) simultaneously provides the spectroscopic and kinetic information of a given reaction. ssFTIR has been extensively employed to acquire the transient absorption and emission spectra in gas phase for identifying unstable species, for example, various Criegee intermediates, and elucidating the dynamics and kinetics of the reaction, such as the molecular elimination dynamics of haloalkenes and the bimolecular reactions involving chlorine atoms and singlet oxygen atoms. In addition to gaseous studies, ssFTIR has been also utilized to record the time‐resolved difference spectra of the photochemical reactions in condensed phases, such as the photolysis of metal–ligand complexes, photocycles of the retinal proteins, coordination capability of solvents to unstable transient species, chemical reactions of atmosphere‐related molecules in aqua, and the exciplex dynamics of organic light emitting materials. Moreover, my group has pioneered the recording of the transient thermal infrared emission of gold nanostructures upon photoexcitation. The experimental setups and the working principles for probing the time‐resolved infrared absorption and emission in condensed phases will be revealed and a number of studies on chemical, biological, and materials systems will be described. These reported results demonstrate that ssFTIR is a versatile tool for exploring the properties of novel materials and photoreactions in condensed phases.

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“…It can be countered that the [Ser/Thr] K+1 –Asp WB pair does not interact directly with W cat . However, direct tracing of intra-protein displacements of protons in energy converting enzymes and chemical models (see [ 181 , 182 , 197 , 198 , 199 , 200 , 201 , 202 , 203 , 204 , 205 , 206 , 207 , 208 , 209 ] for reviews) showed that fast proton transfer over a distance of up to 20 Å can be mediated by water bridges, provided that the distance between the groups involved is ≤3.0 Å, in accordance with Eigen [ 182 ]. Thereby it does not matter that water molecules are equally poor proton acceptors (with pK b of 0.0) and proton donors (with pK a of 14.0) because protons pass water by the so-called von Grotthuss mechanism [ 210 , 211 , 212 ].…”

Section: Discussionmentioning

confidence: 99%

Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases—United in Diversity

et al. 2022

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To clarify the obscure hydrolysis mechanism of ubiquitous P-loop-fold nucleoside triphosphatases (Walker NTPases), we analysed the structures of 3136 catalytic sites with bound Mg-NTP complexes or their analogues. Our results are presented in two articles; here, in the second of them, we elucidated whether the Walker A and Walker B sequence motifs—common to all P-loop NTPases—could be directly involved in catalysis. We found that the hydrogen bonds (H-bonds) between the strictly conserved, Mg-coordinating Ser/Thr of the Walker A motif ([Ser/Thr]WA) and aspartate of the Walker B motif (AspWB) are particularly short (even as short as 2.4 ångströms) in the structures with bound transition state (TS) analogues. Given that a short H-bond implies parity in the pKa values of the H-bond partners, we suggest that, in response to the interactions of a P-loop NTPase with its cognate activating partner (which are analysed in the first article, reference, Biomolecules-1832854), a proton relocates from [Ser/Thr]WA to AspWB. The resulting anionic [Ser/Thr]WA alkoxide withdraws a proton from the catalytic water molecule, and the nascent hydroxyl attacks the gamma phosphate of NTP. When the gamma-phosphate breaks away, the trapped proton at AspWB passes by the Grotthuss relay via [Ser/Thr]WA to beta-phosphate and compensates for its developing negative charge that is thought to be responsible for the activation barrier of hydrolysis.

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Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy

Cited by 12 publications

References 29 publications

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy

Versatile Femtosecond Laser Synchronization for Multiple-Timescale Transient Infrared Spectroscopy

Applications of time‐resolved step‐scan Fourier‐transform infrared spectroscopy in revealing the light‐initiated reactions in condensed phases

Common Mechanism of Activated Catalysis in P-loop Fold Nucleoside Triphosphatases—United in Diversity

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