NRVS for Fe in Biology: Experiment and Basic Interpretation

Gee, Leland B.; Wang, Hongxin; Cramer, Stephen P.

doi:10.1016/bs.mie.2017.11.002

Cited by 14 publications

(8 citation statements)

References 43 publications

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“…In turn, it presents some distinct advantages in comparison with traditional vibrational spectroscopies such as FTIR [8], resonant Raman spectroscopy [8], and laser-induced fluorescence spectroscopy [11][12][13][14]. Most extraordinarily, NRVS is isotope-specific (site-specific) and is, therefore, an excellent tool to study, for example, Fe-S/P/Cl/O, Fe-CO/CN/NO, and Fe-H/D vibrations [15][16][17][18], etc., inside complicated systems in physics, earth sciences, materials sciences, coordination chemistry, and bioinorganic chemistry [10,[16][17][18][19][20][21][22][23][24][25][26]. In particular, when a specific site can be selectively labeled with 57 Fe while all the other sites are not labeled [8,27,28], NRVS becomes a pinpoint tool to target the site interested in complicated systems.…”

Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

“…Due to the nature of nuclear events, which have much longer decaying times (in the order of ns) than electronic scattering (in the order of fs), and due to the fact that nuclear backscattering has a narrow transition bandwidth, NRVS does not use a diffraction spectrometer and thus has a much better photon in and photon out efficiency [6,8,10,20,22]. Due to the same nature, NRVS also has an almost zero background (after filtering out the electronic scattering background), which leads to the observation of some extremely weak signals, such as the 0.1 cts/s Ni−H−Fe [10,22] or X−Fe−H [27,28,31] features inside various hydrogenase samples.…”

Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

“…For example, it is water transparent in comparison with far IR spectroscopy, and thus well suited for investigating biological samples in their natural aqueous environment; it is free of fluorescence problems in comparison with resonance Raman spectroscopy, and thus suitable for evaluating photosensitive states; it distinguishes well among O, N, and C in comparison with extended X-ray absorption fine structure (EXAFS) or crystallography [32,33]. Due to these advantages, its user community, as well as the research results, grow exponentially [10,[16][17][18][19][20][21][22][23][24][25]27,28,31,34]. For example, in the last decade, it has become the third modern X-ray spectroscopy to become popular among biochemical researchers, following crystallography and EXAFS [8,33].…”

Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

“…where E real , E obs , E* stand for the calibrated real energy, the uncalibrated observed energy, the correction for the zero energy position, respectively, and α is the energy axis scaling factor which needs to measure a standard calibration spectrum [5,6,20] to calculate. All the calibrations discussed in this publication are practical calibrations.…”

Section: Energy Calibration In Nrvsmentioning

confidence: 99%

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The True Nature of the Energy Calibration for Nuclear Resonant Vibrational Spectroscopy: A Time-Based Conversion

2022

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Nuclear resonant vibrational spectroscopy (NRVS) is an excellent synchrotron-based vibrational spectroscopy. Its isotope specificity and other advantages are particularly good to study, for example, iron center(s) inside complicated molecules such as enzymes. In order to investigate some small energy shifts, the energy scale variation from scan to scan must be corrected via an in-situ measurement or with other internal reference peak(s) inside the spectra to be calibrated. On the other hand, the energy re-distribution within each scan also needs attention for a sectional scan which has a different scanning time per point in different sections and is often used to measure weak NRVS signals. In this publication, we: (1) evaluated the point-to-point energy re-distribution within each NRVS scan or within an averaged scan with a time-scaled (not energy-scaled) function; (2) discussed the errorbar contributed from the improper “distribution” of Ei or the averaged E within one scan (Eerr1) vs. that due to the different Ei from different scans (Eerr2). It is well illustrated that the former (Eerr1) is as important as, or sometimes even more important than, the latter (Eerr2); and (3) provided a procedure to re-calibrate the published NRVS-derived PVDOS spectra in case of need. This article establishes the concept that, at least for sectional NRVS scans, the energy positions should be corrected according to the time scanned rather than be scaled with a universal constant, as in a conventional calibration procedure.

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Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

Section: Nuclear Resonant Vibrational Spectroscopymentioning

confidence: 99%

Section: Energy Calibration In Nrvsmentioning

confidence: 99%

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The True Nature of the Energy Calibration for Nuclear Resonant Vibrational Spectroscopy: A Time-Based Conversion

2022

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“…Raw NRVS data were converted to single-phonon 57 Fe partial vibrational densities of states (PVDOS) using the PHOENIX software package (https://www.spectra.tools/). 68,69 The energy scales were calibrated with a [NEt4][ 57 FeCl4] sample characterized by two prominent peaks at 378 cm -1 (asymmetric Fe-Cl stretching mode), and 139 cm -1 (Fe-Cl bending mode) (Fig. S14).…”

mentioning

confidence: 99%

Active site assembly of [NiFe]-hydrogenase scrutinized on the basis of purified maturation intermediates

Caserta

Hartmann

Stappen

et al. 2022

Preprint

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[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H2 into 2 e– and 2 H+ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)2(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN– molecules. Herein, we investigated the sequential assembly of the [NiFe]-cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O2-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)2(CO) fragment, a precursor that contained all cofactor components but remained redox-inactive, and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption, and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.

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Structure–Function Relationships of the NsrR and RsrR Transcription Regulators

Volbeda¹,

Crack²,

Brun³

2020

Encyclopedia of Inorganic and Bioinorganic Chemistry

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Protein‐coordinated iron–sulfur clusters play multiple crucial functions in biological processes. One of these functions is the response to effectors that regulate gene expression. This response can be very variable. Several members of the Rrf2 family of bacterial transcriptional regulators contain [FeS] clusters that perform a variety of sensing roles, including those involved in controlling cellular iron levels (RirA), controlling [FeS] cluster synthesis (IscR), responding to nitrosative stress (NsrR), and monitoring and possibly regulating the redox status of the cell (RsrR). Cluster ligation and composition varies significantly, and, with the exception of RsrR, DNA binding is regulated by effector‐dependent either partial or total cluster disassembly. Our own recent work has concentrated on the structure–function relationships of NsrR and RsrR, which coordinate [4Fe4S] and [2Fe2S] clusters, respectively. The reaction of nitric oxide with the NsrR [4Fe4S] cluster is progressive and modulates NsrR binding to different promotors. One consequence of cluster disassembly is the disruption of a key salt bridge that, in turn, causes a conformational change in the helix‐turn‐helix DNA‐binding domain of NsrR. The case of RsrR is especially interesting because its DNA binding depends on a one‐electron cluster redox change. This reduction causes the protonation of a neighboring His residue, which is followed by the generation of a protein cavity and the rotation of a tryptophan residue into it. Like in the case of NsrR, this rotation provokes a conformational change in the helix‐turn‐helix DNA‐binding domain of the protein.

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NRVS for Fe in Biology: Experiment and Basic Interpretation

Cited by 14 publications

References 43 publications

The True Nature of the Energy Calibration for Nuclear Resonant Vibrational Spectroscopy: A Time-Based Conversion

The True Nature of the Energy Calibration for Nuclear Resonant Vibrational Spectroscopy: A Time-Based Conversion

Active site assembly of [NiFe]-hydrogenase scrutinized on the basis of purified maturation intermediates

Structure–Function Relationships of the NsrR and RsrR Transcription Regulators

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