• Journal of the Korean Magnetic Resonance Society
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• v.28 no.2
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• pp.6-9
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• 2024

HscA is a Hsp70-type chaperone protein that plays an essential role to mediate the iron-sulfur (Fe-S) cluster biogenesis mechanism in Escherichia coli. Like other Hsp70 chaperones, HscA is composed of two domains: the nucleotide binding domain (NBD), which can hydrolyze ATP and use its chemical energy to facilitate the Fe-S cluster transfer process, and the substrate binding domain (SBD), which directly interacts with the substrate, IscU, the scaffold protein of an Fe-S cluster. In the present work, we prepared the isolated SBD construct of HscA (HscA(SBD)) and conducted the solution-state nuclear magnetic resonance (NMR) experiments to have its backbone chemical shift assignment information. Due to low spectral quality of HscA(SBD), we obtained all the NMR data from the sample containing the peptide LPPVKIHC, the HscA-interaction motif of IscU, from which the chemical shift assignment could be done successfully. We expect that this information provides an important basis to execute detailed structural characterization of HscA and appreciate its interaction with IscU.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.1
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• pp.1-5
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• 2024

IscU, the iron-sulfur (Fe-S) cluster scaffold protein, is an essential protein for biogenesis of Fe-S clusters. Previous studies showed that IscU manifests a metamorphic structural feature; at least two structural states, namely the structured state (S-state) and the disordered state (D-state), interconverting in a physiological condition, was observed. Moreover, subsequent studies demonstrated that the metamorphic flexibility of IscU is important for its Fe-S cluster assembly activity as well as for an efficient interaction with various partner proteins. Although solution nuclear magnetic resonance (NMR) spectroscopy has been a useful tool to investigate this protein, the detailed molecular mechanism that sustains the structural heterogeneity of IscU is still unclear. To tackle this issue, we applied a high-pressure NMR (HP-NMR) technique to the IscU variant, IscU(I8K), which shows an increased population of the S-state. We found that the equilibrium between the S- and D-state was significantly perturbed by pressure application, and the specific regions of IscU exhibited more sensitivity to pressure than the other regions. Our results provide novel insights to appreciate the dynamic behaviors of IscU and the related versatile functionality.

• Applied Biological Chemistry
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• v.48 no.3
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• pp.189-200
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• 2005

Biological nitrogen fixation is an important process for academic and industrial aspects. This review will briefly compare industrial and biological nitrogen fixation and cover the characteristics of biological nitrogen fixation studied in Azotobacter vinelandii. Various organisms can carry out biological nitrogen fixation and recently the researches on the reaction mechanism were concentrated on the free-living microorganism, A. vinelandii. Nitrogen fixation, which transforms atmospheric $N_2$ into ammonia, is chemically a reduction reaction requiring electron donation. Nitrogenase, the biological nitrgen fixer, accepts electrons from biological electron donors, and transfers them to the active site, FeMo-cofactor, through $Fe_4S_4$ cluster in Fe protein and P-cluster in MoFe protein. The electron transport and the proton transport are very important processes in the nitrogenase catalysis to understand its reaction mechanism, and the interactions between FeMo-cofactor and nitrogen molecule are at the center of biological nitrogen fixation mechanism. Spectroscopic studies including protein X-ray crystallography, EPR and $M{\ddot{o}}ssbauer$, biochemical approaches including substrate and inhibitor interactions as well as site-directed mutation study, and chemical approach to synthesize the FeMo-cofactor model compounds were used for biological nitrogen fixation study. Recent research results from these area were presented, and finally, a new nitrogenase reaction mechanism will be proposed based on the various research results.

• Mycobiology
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• v.42 no.4
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• pp.427-431
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• 2014

Mitochondrial protein Nfu1 plays an important role in the assembly of mitochondrial Fe-S clusters and intracellular iron homeostasis in the model yeast Saccharomyces cerevisiae. In this study, we identified the Nfu1 ortholog in the human fungal pathogen Cryptococcus neoformans. Our data showed that C. neoformans Nfu1 localized in the mitochondria and influenced homeostasis of essential metals such as iron, copper and manganese. Marked growth defects were observed in the mutant lacking NFU1, which suggests a critical role of Nfu1 in Fe-S cluster biosynthesis and intracellular metal homeostasis in C. neoformans.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.135-136
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• 2012

Carbon atoms near the surface of W(110) induce reconstructions such as $R(15{\times}12)$ -C/W(110) which consists of two characteristic parts, one square shaped and bright protrusion and two smaller ones. In the atomic resolution STM image, the bigger protrusion shows the periodicities of clean W(110), indicating that it is almost carbon poor region. The smaller protrusion contains hexagonal carbide surface layer of ${\alpha}$-W2C on W(110). Employing this carburized W(110) as templates, we grow Co and Fe clusters of less than ten atoms. Due to the selectivity of bonding sites, growth of larger cluster is highly unfavorable for Co and the size of clusters is very uniform. Since Co atoms prefer to sit on the bigger protrusion rather than smaller one, Co cluster can be arranged one-dimensionally in $R(15{\times}12)$-C/W(110) with quite uniform size distribution. However, Fe clusters sit on both sites without favored site, but still with uniform size distribution. On the other hand, Fe clusters can be grown with quasi one-dimensional order in $R(15{\times}3)$-C/W(110), which consists of only smaller protrusions. We investigate the magnetic properties of the ordered nano-sized clusters. Experiments using XMCD reveals little magnetic moment of Co cluster on $R(15{\times}12)$-C/W(110). This observation is consistent with the predictions of our first principles calculations that small Co clusters can be nonmagnetic or antiferromagnetic with low mean magnetic moment per atom.

• Journal of Photoscience
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• v.9 no.2
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• pp.388-390
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• 2002

Two ferredoxin (Fd) fractions, namely, Fd-A and Fd-B were isolated from Heliobacillus mobilis cells, and purified by ammonium sulfate fractionation, DEAE, gel-permeation and Phenyl-Superose column chromatographies under anaerobic conditions. Their absorption spectra were typical of 2[4Fe-4S] cluster type Fds with peaks at about 385 and 280 nm and a shoulder at about 305 nm. Their N-terminal amino acid sequences were determined, which showed that both of them contain a [4Fe-4S] cluster binding motif. Fd-B was sensitive to oxygen, and itsA$_{385}$ value decreased by about 50% in 2 h at 4$^{\circ}C$ under aerobic conditions. In contrast, $A_{385}$ of Fd-A was essentially unchanged up to 24 h under the same conditions.

• Proceedings of the Materials Research Society of Korea Conference
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• 1994.11a
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• pp.1-1
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• 1994

;The electronic state calculations for various types of ceramic materials have beell performed by the use of $DV-X\;{\alpha}$ cluster method. The molecular orbital levels and wave functions for model clusters have been computed to study the electronic properties ami chemical bonding of the ceramics. For ${\beta}-sialon(Si_{6-z}Al_zO_zN_{8-z})$ which is a high temperature structural material based on ${\beta}-Si_3N_4$, we have made model cluster calculations to estimate the strength of chemical bonding between atoms by the Mulliken population analysis. It is found that the covalent bonding between Si and N atoms is very strong in pure ${\beta}-Si_3N_4$, but the covalency around solute atom is considerably weakened when Si atom is substituted by AI. This tendency is enhanced by an additional substitution of oxygen atom for N. The result calculated can well explain the experimental data of changes in mechanical properties such as the reductions of Young's modulus and Vickers hardness with increment of z-value in ${\beta}-sialon$. Various model clusters for transition metal oxides which show many interesting physical and chemical properties have also been calculated. High-valent perovskite-type iron oxides EMFe0_3E(M=Ca and Sr) possess very interesting magnetic and chemical properties. In these oxides, iron exists as $Fe^{4+}$ state, but the experimental measurement of Mossba~er effect suggests that disproportionation $2Fe^{4+}=Fe^{3+}+Fe^{5+}$ takes place for $CaFe0_3$ at low temperatures. The model cluster calculations for these compounds indicated the existence of considerably strong covalent bonding of Fe-O. The calculations of hyperfine interaction at iron neucleus show very good agreement with the experimental Mossbauer measurements. The result calculated also implies that the disproportionation reaction is strongly possible by assuming the quenching of breathing phonon mode at low temperatures.tures.

• Journal of Life Science
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• v.14 no.5
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• pp.752-760
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• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.66-68
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• 2006

SUF machinery in Echerichia coli, responsible for the biosynthesis of iron-sulfur clusters, is composed of six protein components (SufABCDSE), among which SufB, SufC, and SufD associate in a complex. We have determined the structures of SufA, SufC, and SufD by X-ray crystallography. SufA is a dimer, in which C-terminal segments containing essential cysteine residues (Cys-Gly-Cys) are positioned to allow coordination of an Fe-S cluster and/or an Fe atom. SufC has the overall structure similar to that of ABC-ATPase but takes an inactive form. SufD has a ${\beta}-helix$ flanked with a-helical domains. We also studied the functional roles of the residues in SufD by mutagenesis and determined the crystal structure of SufCD complex. Molecular mechanism of Fe-S cluster biosynthesis is discussed on the basis of the structural and functional evidence.

• Journal of The Korean Astronomical Society
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• v.39 no.4
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• pp.115-123
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• 2006

We present $JHK_S$ near-infrared CCD photometric study for the Galactic open clusters NGC 1641 and NGC 2394. These clusters have never been studied before, and we provide, for the first time the cluster parameters; reddening, distance, metallicity and age. NGC 1641 is an old open cluster with age $1.6{\pm}0.2$ Gyr, metallicity $[Fe/H]=0.0{\pm}0.2$ dex, distance modulus$(m-M)_0=10.4{\pm}0.3\;mag(d=1.2{\pm}02\;kpc)$, and reddening $E(B-V)=0.10{\pm}0.05$ mag. The parameters for the other old open cluster NGC 2394 are estimated to be $age=1.1{\pm}0.2$ Gyr, $[Fe/H]=0.0{\pm}0.2$ dex, $(m-M)_0=9.1{\pm}0.4\;mag(d=660{\pm}120\;pc)$, and $E(B-V)=0.05{\pm}0.10$ mag. The metallicities and distance values for these two old open clusters are consistent with the relation between the metallicities and the Galactocentric distances of other old open clusters. We find the metallicity gradient of 53 old open clusters including NGC 1641 and NGC 2394 to be ${\Delta}[Fe/H]/{\Delta}R_{gc}=-0.067{\pm}0.009\;dex\;kpc^{-1}$.