Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface

The active site of cytochrome c (Cyt c) consists of a heme covalently linked to a pentapeptide segment (Cys-X-X-Cys-His), which provides a link between the heme and the protein surface, where the redox partners of Cyt c bind. To elucidate the vibrational properties of heme c, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c 552, including 13C8-heme-, 13C 515N-Met-, and 13C15N-polypeptide (pp)-labeled samples, revealing heme-based vibrational modes in the 200- to 450-cm-1 spectral region. Simulations of the NRVS spectra of H. thermophilus cytochrome c552 allowed for a complete assignment of the Fe vibrational spectrum of the protein-bound heme, as well as the quantitative determination of the amount of mixing between local heme vibrations and pp modes from the Cys-X-XCys-His motif. These results provide the basis to propose that heme-pp vibrational dynamic couplings play a role in electron transfer (ET) by coupling vibrations of the heme directly to vibrations of the pp at the protein - protein interface. This could allow for the direct transduction of the thermal (vibrational) energy from the protein surface to the heme that is released on protein/protein complex formation, or it could modulate the heme vibrations in the protein/protein complex to minimize reorganization energy. Both mechanisms lower energy barriers for ET. Notably, the conformation of the distal Met side chain is fine-tuned in the protein to localize heme-pp mixed vibrations within the 250-to 400-cm-1 spectral region. These findings point to a particular orientation of the distal Met that maximizes ET

Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes

The reaction of protein-bound iron–sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2(NO)4(Cys)2]) and Roussin's Black Salt (RBS, [Fe4(NO)7S3]. In the latter case, the absence of 32S/34S shifts in the Fe−S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates

Measuring velocity of sound with nuclear resonant inelastic x-ray scattering

Nuclear resonant inelastic x-ray scattering is used to measure the projected partial phonon density of states of materials. A relationship is derived between the low-energy part of this frequency distribution function and the sound velocity of materials. Our derivation is valid for harmonic solids with Debye-like low-frequency dynamics. This method of sound velocity determination is applied to elemental, composite, and impurity samples which are representative of a wide variety of both crystalline and noncrystalline materials. Advantages and limitations of this method are elucidated

Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates

Nuclear Inelastic X-Ray Scattering of FeO to 48 GPa

The partial density of vibrational states has been measured for Fe in compressed FeO (w\"ustite) using nuclear resonant inelastic x-ray scattering. Substantial changes have been observed in the overall shape of the density of states close to the magnetic transiton around 20 GPa from the paramagnetic (low pressure) to the antiferromagnetic (high pressure) state. Our data indicate a substantial softening of the aggregate sound velocities far below the transition, starting between 5 and 10 GPa. This is consistent with recent radial x-ray diffraction measurements of the elastic constants in FeO. The results indicate that strong magnetoelastic coupling in FeO is the driving force behind the changes in the phonon spectrum of FeO.Comment: 4 pages, 4 figure

Mechanism of selective benzene hydroxylation catalyzed by iron-containing zeolites

A direct, catalytic conversion of benzene to phenol would have wide-reaching economic impacts. Fe zeolites exhibit a remarkable combination of high activity and selectivity in this conversion, leading to their past implementation at the pilot plant level. There were, however, issues related to catalyst deactivation for this process. Mechanistic insight could resolve these issues, and also provide a blueprint for achieving high performance in selective oxidation catalysis. Recently, we demonstrated that the active site of selective hydrocarbon oxidation in Fe zeolites, named α-O, is an unusually reactive Fe(IV)=O species. Here, we apply advanced spectroscopic techniques to determine that the reaction of this Fe(IV)=O intermediate with benzene in fact regenerates the reduced Fe(II) active site, enabling catalytic turnover. At the same time, a small fraction of Fe(III)-phenolate poisoned active sites form, defining a mechanism for catalyst deactivation. Density-functional theory calculations provide further insight into the experimentally defined mechanism. The extreme reactivity of α-O significantly tunes down (eliminates) the rate-limiting barrier for aromatic hydroxylation, leading to a diffusion-limited reaction coordinate. This favors hydroxylation of the rapidly diffusing benzene substrate over the slowly diffusing (but more reactive) oxygenated product, thereby enhancing selectivity. This defines a mechanism to simultaneously attain high activity (conversion) and selectivity, enabling the efficient oxidative upgrading of inert hydrocarbon substrates

The Relationship between Source Memory and Linguistic Encoding of Source: A Study of 3-6 year-olds

This study aimed to explore whether the development of source memory is related to the use of linguistic markers of evidentiality. Eighty-seven 3-, 4-, 5-, and 6-year-old Turkish-speaking monolingual children participated in two source memory tasks: (1) Mode of Knowledge Acquisition Task and (2) Source Identification Task, and three language tasks (1) Direct Experience Task, (2) Inference Task and (3) Reportative Task. Results of the source memory tasks revealed lower performance for 3-year-old children compared to older children. On the Direct Experience Task, children of all ages could use the -DI inflection correctly, but in the other two language tasks younger children displayed lower performance than older children in using the correct evidentiality markers. Children's performance in using (I)mIs on the Reportative Task was found to predict their performance on the Source Identification Task. Moreover, children's performance on this source memory task was compared to English-speaking children's performance on the same task in Drummey and Newcombe's (2002) study. This comparison indicated that Turkish-speaking children show correct source identification performance at an earlier age compared to English-speaking children. The findings are discussed in terms of the development of source memory and the relation between language and cognition

Magma redox and structural controls on iron isotope variations in Earth's mantle and crust

International audienceThe heavy iron isotopic composition of Earth's crust relative to chondrites has been explained by vaporization during the Moon-forming impact, equilibrium partitioning between metal and silicate at core–mantle-boundary conditions, or partial melting and magma differentiation. The latter view is supported by the observed difference in the iron isotopic compositions of MORBS and peridotites. However, the precise controls on iron isotope variations in igneous rocks remain unknown. Here, we show that equilibrium iron isotope fractionation is mainly controlled by redox (Fe3+/Fetot ratio) and structural (e.g. , polymerization) conditions in magmas. We measured, for the first time, the mean force constants of iron bonds in silicate glasses by synchrotron Nuclear Resonant Inelastic X-ray Scattering (NRIXS, also known as Nuclear Resonance Vibrational Spectroscopy – NRVS, or Nuclear Inelastic Scattering – NIS). The same samples were studied by conventional Mössbauer and X-ray Absorption Near Edge Structure (XANES) spectroscopy. The NRIXS results reveal a +0.2 to +0.4‰+0.4‰ equilibrium fractionation on 56Fe/54Fe ratio between Fe2+ and Fe3+ end-members in basalt, andesite, and dacite glasses at magmatic temperatures. These first measurements can already explain ∼1/3∼1/3 of the iron isotopic shift measured in MORBs relative to their source. Further work will be required to investigate how pressure, temperature, and structural differences between melts and glasses affect equilibrium fractionation factors. In addition, large fractionation is also found between rhyolitic glass and commonly occurring oxide and silicate minerals. This fractionation reflects mainly changes in the coordination environment of Fe2+ in rhyolites relative to less silicic magmas and mantle minerals, as also seen by XANES. We provide a new calibration of XANES features vs. Fe3+/Fetot ratio determinations by Mössbauer to estimate Fe3+/Fetot ratio in situ in glasses of basaltic, andesitic, dacitic, and rhyolitic compositions. Modeling of magma differentiation using rhyolite-MELTS shows that iron structural changes in silicic magmas can explain the heavy iron isotopic compositions of granitoids and rhyolites. This study demonstrates that iron stable isotopes can help reveal planetary redox conditions and igneous processes. Other heterovalent elements such as Ti, V, Eu, Cr, Ce, or U may show similar isotopic variations in bulk rocks and individual minerals, which could be used to establish past and present redox condition in the mantles of Earth and other planets

Effects of Protein Structure on Iron–Polypeptide Vibrational Dynamic Coupling in Cytochrome <i>c</i>

Cytochrome <i>c</i> (Cyt <i>c</i>) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein–protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on ⁵⁷Fe-labeled ferric <i>Hydrogenobacter thermophilus</i> cytochrome <i>c</i>-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150–325 cm^–1 region is dominated by N_His–Fe–S_Met axial ligand and polypeptide motions, while the 325–400 cm^–1 region shows dominant contributions from ν­(Fe–N_Pyr) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe–His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe–N_His interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe–N_His bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Implications of these results for Cyt <i>c</i> biogenesis and electron transfer are also discussed