Exploring the 2D-IR repertoire of the –SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin

Schmidt-Engler, Julian M.; Zangl, René; Guldan, Patrick; Morgner, Nina; Bredenbeck, Jens

doi:10.1039/c9cp06808b

Cited by 27 publications

(39 citation statements)

References 63 publications

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“…In the present study, real-time measurement of Ca 2+ flux showed that Ca 2+ influxes in the Low OA group were the highest, followed by those of the control group, and Ca 2+ influxes in the High OA group were the lowest among these three groups. Greater Ca 2+ uptake in the control group and the Low OA group is associated with higher concentrations of intracellular Ca 2+ ; thus, more Ca 2+ interacts with calmodulin, which serves as the dynamic Ca 2+ protein sensor in eukaryotes ubiquitously and transmits calcium signals downstream 33 . Therefore, intracellular H 2 O 2 and Ca 2+ increased in the Low OA group but decreased in the High OA group compared to the control group.…”

Section: Discussionmentioning

confidence: 98%

Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid

Xing

et al. 2021

Sci Rep

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Polyporus umbellatus is a precious medicinal fungus. Oxalic acid was observed to affect sclerotial formation and sclerotia possessed more medicinal compounds than mycelia. In this study, the transcriptome of P. umbellatus was analysed after the fungus was exposed to various concentrations of oxalic acid. The differentially expressed genes (DEGs) encoding a series of oxidases were upregulated, and reductases were downregulated, in the low-oxalic-acid (Low OA) group compared to the control (No OA) group, while the opposite phenomenon was observed in the high-oxalic-acid (High OA) group. The detection of reactive oxygen species (ROS) in P. umbellatus mycelia was performed visually, and Ca2+ and H2O2 fluxes were measured using non-invasive micro-test technology (NMT). The sclerotial biomass in the Low OA group increased by 66%, however, no sclerotia formed in the High OA group. The ROS fluorescence intensity increased significantly in the Low OA group but decreased considerably in the High OA group. Ca2+ and H2O2 influx significantly increased in the Low OA group, while H2O2 exhibited efflux in the High OA group. A higher level of oxidative stress formed in the Low OA group. Different concentrations of oxalic acid were determined to affect P. umbellatus sclerotial formation in different ways.

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Section: Discussionmentioning

confidence: 98%

Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid

Xing

et al. 2021

Sci Rep

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“…Important properties of chemical systems, from water to polymers, are determined by their molecular level dynamics. , Ultrafast time-resolved IR spectroscopy is particularly well-suited for investigating the relationships among dynamics, interactions, and structures because it can measure properties such as orientational relaxation − and spectral diffusion − of a vibrational probe molecule. Such measurements can be used to investigate dynamics and how they are influenced by local and mesoscopic environments. ,,,,− A successful experiment requires the detection of a spectrally resolved vibrational signal, ideally from a vibration with a lifetime at least as long as the dynamics of interest. , However, the native structures of many chemical systems suffer from overlapping signals and short vibrational lifetimes, , which are frequently not sufficient to fully capture the time range of the dynamic processes of interest.…”

Section: Introductionmentioning

confidence: 99%

“…These challenges have been circumvented by using vibrational probes. Vibrational probes are molecules that absorb infrared (IR) light, typically in the mid-IR region. ,− Their use became common practice in pump–probe and 2D IR spectroscopy, as it is possible to find probes with a spectrally resolved resonance that offers a sufficiently long vibrational lifetime. An additional desirable characteristic of vibrational probes is sensitivity to local environments, which makes it possible to investigate structural dynamics .…”

Section: Introductionmentioning

confidence: 99%

Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis

et al. 2021

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Ultrafast infrared vibrational spectroscopy is widely used for the investigation of dynamics in systems from water to model membranes. Because the experimental observation window is limited to a few times the probe's vibrational lifetime, a frequent obstacle for the measurement of a broad time range is short molecular vibrational lifetimes (typically a few to tens of picoseconds). Five new longlifetime aromatic selenocyanate vibrational probes have been synthesized and their vibrational properties characterized. These probes are compared to commercial phenyl selenocyanate. The vibrational lifetimes range between ∼400 and 500 ps in complex solvents, which are some of the longest room-temperature vibrational lifetimes reported to date. In contrast to vibrations that are long-lived in simple solvents such as CCl 4 , but become much shorter in complex solvents, the probes discussed here have ∼400 ps lifetimes in complex solvents and even longer in simple solvents. One of them has a remarkable lifetime of 1235 ps in CCl 4 . These probes have a range of molecular sizes and geometries that can make them useful for placement into different complex materials due to steric reasons, and some of them have functionalities that enable their synthetic incorporation into larger molecules, such as industrial polymers. We investigated the effect of a range of electron-donating and electron-withdrawing para-substituents on the vibrational properties of the CN stretch. The probes have a solvent-independent linear relationship to the Hammett substituent parameter when evaluated with respect to the CN vibrational frequency and the ipso 13 C NMR chemical shift.

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“…Simulation parameters are representative of a cyanylated cysteine residue in the calmodulin protein. 17 The second Kubo component is treated as static on the time scale of the waiting-time measurements by holding τ 2 constant at 1 ns. The transient absorption spectrum in panel (A) and the 2D IR spectrum in panel (B) at T W = 0 ps illustrates just how modest the quality of the raw data is at 10:1 SNR.…”

Section: Resultsmentioning

confidence: 99%

Least-Squares Fitting of Multidimensional Spectra to Kubo Line-Shape Models

Robben

Cheatum

2021

J. Phys. Chem. B

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We report a comprehensive study of the efficacy of least-squares fitting of multidimensional spectra to generalized Kubo line-shape models and introduce a novel least-squares fitting metric, termed the scale invariant gradient norm (SIGN), that enables a highly reliable and versatile algorithm. The precision of dephasing parameters is between 8× and 50× better for nonlinear model fitting compared to that for the centerline-slope (CLS) method, which effectively increases data acquisition efficiency by 1–2 orders of magnitude. Whereas the CLS method requires sequential fitting of both the nonlinear and linear spectra, our model fitting algorithm only requires nonlinear spectra but accurately predicts the linear spectrum. We show an experimental example in which the CLS time constants differ by 60% for independent measurements of the same system, while the Kubo time constants differ by only 10% for model fitting. This suggests that model fitting is a far more robust method of measuring spectral diffusion than the CLS method, which is more susceptible to structured residual signals that are not removable by pure solvent subtraction. Statistical analysis of the CLS method reveals a fundamental oversight in accounting for the propagation of uncertainty by Kubo time constants in the process of fitting to the linear absorption spectrum. A standalone desktop app and source code for the least-squares fitting algorithm are freely available, with example line-shape models and data. We have written the MATLAB source code in a generic framework where users may supply custom line-shape models. Using this application, a standard desktop fits a 12-parameter generalized Kubo model to a 106 data-point spectrum in a few minutes.

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Exploring the 2D-IR repertoire of the –SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin

Abstract: 2D-IR spectroscopy of site-specifically incorporated –SCN labels in the calcium sensor protein calmodulin reveals local dynamics and solvation as they change upon calcium uptake and protein–ligand interaction.

Cited by 27 publications

References 63 publications

Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid

Use of transcriptomic profiling to identify candidate genes involved in Polyporus umbellatus sclerotial formation affected by oxalic acid

Long Vibrational Lifetime R-Selenocyanate Probes for Ultrafast Infrared Spectroscopy: Properties and Synthesis

Least-Squares Fitting of Multidimensional Spectra to Kubo Line-Shape Models

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