Scientific Publications 2004
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2004. "Solution NMR Structure of the Iron-Sulfur Cluster Assembly Protein U (IscU) with Zinc Bound at the Active Site ." Journal of Molecular Biology 344(2):567-583. Abstract IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an - sandwich architecture with a three-stranded antiparallel -sheet and four -helices. A nascent helix is located N-terminal to the core structure. The zinc is ligated by three cysteines and one histidine that are located in and near conformationally dynamic loops at one end of the IscU structure. Removal of the zinc metal by chelation results in widespread loss of structure in the apo form. The zinc-bound IscU may be a good model for iron-loaded IscU and may demonstrate structural features found in the iron-sulfur cluster bound form. Structural and functional similarities, genomic context in operons containing other homologous genes, and distributions of conserved surface residues support the hypothesis that IscU protein domains are homologous (i.e. derived from a common ancestor) with the SufE / YgdK family of iron sulfur cluster assembly proteins.
2004. "Own N-layered Integrated Molecular Orbital and Molecular Mechanics Study of the Reaction of OH– with Polychlorinated Hydrocarbons CH(4–n)Cln (n=2–4)." Theoretical Chemistry Accounts 112(2):59-67. doi:10.1007/s00214-003-0554-z Abstract No abstract is available for this publication at this time.
2004. "Microbeam Developments and Applications: A Low Linear Energy Transfer Perspective." Cancer and Metastasis Reviews 23(3-4):323-331. Abstract In the last few years there has been a significant increase in the number of centers having, or developing, both high- and low-linear energy transfer (LET) microbeams for radioabiological investigations. In this review we weill disucss the various approaches developing low-LET single cell irradiation devices and consider the instrument designs and how the machines capabilities can be exploited to investigate targeted and non-targeted effects of low-LET irradiation.
2004. "Radiation-Induced Genomic Instability: A Role for Secreted Soluble Factors in Communicating the Radiation Response to Non-Irradiated Cells." Journal of Cellular Biochemistry 92(5):1013-1019. Abstract Radiation induced genomic instability can be described as the increased rate of genomic alterations occurring in the progeny of an irradiated cell. Its manifestations are the dynamic ongoing production of chrososomal rearrangements, mutations, gene amplifications, transformation, microsatellite instability and/or cell killing. In this prospectus, we present the hypothesis that cellular exposure to ionizing radiation can result in the secretion of soluble factors by irradiated cells and/or their progeny, and that these factors can elicit responses in other cells thereby initiating and perpetuating ongoing genomic instability.
2004. "The Inhibitor DBMIB Provides Insight into the Functional Architecture of the Qo Site in the Cytochrome b(6)f Complex ." Biochemistry 43(24):7707-7716. Abstract ABSTRACT: Previously, we showed that two equivalents of the quinone analog, 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB), could occupy the Qo site of the cytochrome (cyt) b6f complex simultaneously. In this work, study of electron paramagnetic resonance (EPR) spectra from oriented cyt b6f complex shows that the Rieske iron-sulfur protein (ISP) is in distinct orientations, depending on the stoichiometry of the inhibitor at the Qo site. With a single DBMIB at the Qo site, the ISP is oriented with the 2Fe2S cluster toward cyt f, which is similar to the orientation of the ISP in the x-ray crystal structure of the cyt b6f complex from thermophilic cyanobacteria, Mastigocladus laminosus, in the presence of DBMIB, as well as that of the chicken mitochondrial cyt bc1 complex in the presence of the class II inhibitor myxothiazol, which binds in the so-called ‘proximal niche,’ near the cyt bL heme. These data suggest that the high affinity DBMIB site is at the proximal niche Qo pocket. With 2 equivalents or more of DBMIB bound, the Rieske ISP is in a position that resembles the ISPB position of chicken mitochondrial cyt bc1 complex in the presence of stigmatellin and Chlamydamonas reinhardtii cyt b6f complex in the presence of tridecyl-stigmatellin (TDS), which suggests that the low affinity DBMIB site is at the distal niche. The close interaction of DBMIB bound at the distal niche with the ISP induced the well-known effects on the 2Fe2S EPR spectrum and redox potential. To further test the effects of DBMIB on the ISP, the extents of cyt f oxidation after flash excitation in the presence of photosystem II inhibitor DCMU were measured as a function of DBMIB concentration in thylakoids. Addition of DBMIB concentrations where single binding was expected, did not markedly affect the extent of cyt f oxidation, whereas higher concentrations, where double occupancy was expected, increased the extent of cyt f oxidation to levels similar to cyt f oxidation in the presence of saturating stigmatellin. Simulations of the EPR g-tensor orientations of the 2Fe2S cluster versus the physical orientations based on single crystal studies of the cyt bc1 complex suggest that the soluble ISP domain of spinach cyt b6f complex can rotate by at least 53o, which is consistent with long-range ISP domain movement. Implications of these results are discussed in the context of the x-ray crystal structures of the chicken mitochondrial cyt bc1 complex, and M. laminosus and C. reinhardtii cyt b6f complexes.
2004. "Reorganization Energy Associated with Small Polaron Mobility in Iron Oxide." Journal of Chemical Physics 120(15):7050-7054. Abstract The reorganization energy is an important quantity controlling electron transfer rates. The internal contribution arising from the energy to reorganize donor/acceptor bonds can be evaluated by the ‘direct’ and ‘4-point’ methods. We examine how spatial separation leading to the non-interacting character of the donor and acceptor affects the reorganization energy. We show that the direct method captures contributions from interaction of the donor and acceptor while the 4-point method does not, and the two methods converge at large separation. Comparing reorganization energies determined by the two methods yields a measure of the degree of interaction between the initial and final states. The analysis is illustrated in the characterization of small polarons in iron oxides.
2004. "Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions." Journal of Physical Chemistry A 108(24):5242-5248. Abstract Aspects of aqueous iron and manganese (II/III) self-exchange electron transfer reactions
2004. "Self-Exchange Electron Transfer Kinetics and Reduction Potentials for Anthraquinone Disulfonate." Journal of Physical Chemistry A 108(16):3292-3303. Abstract Self-exchange electron transfer kinetics and reduction potentials for anthraquinone disulfonate
2004. "Oxygen-exchange Pathways in Aluminum Polyoxocations." Geochimica et Cosmochimica Acta 68(14):3011-3017. doi:10.1016/j.gca.2003.12.021 Abstract Using molecular dynamics simulations and electronic structure methods, we postulate a mechanism to explain the complicated reactivity trends that are observed for oxygen isotope exchange reactions between sites in aluminum polyoxocations of the E-Keggin type and bulk solution. Experimentally, the molecules have four nonequivalent oxygens that differ considerably in reactivity both within a molecule, and between molecules in the series: Al13, GaAl12, and GeAl12 [MO4Al12(OH)24(H2O)12 n*(aq); with M=Al(III) for Al13, n=7; M=Ga(III) for GaAl12, n=7; M=Ge(IV) for GeAl12, n=8]. We find that a partly dissociated, metastable intermediate molecule of expanded volume is necessary for exchange of both sets of u2-OH and that the steady-state concentration of this intermediate reflects the bond strengths between the central metal and the u4-O. Thus the central metal exerts extraordinary control over reactions at hydroxyl bridges, although these are three bonds away. This mechanism not only explains the reactivity trends for oxygen isotope exchange in u2-OH and u-OH2 sites in the E-Keggin aluminum molecules, but also explains the observation that the reactivities of minerals tend to reflect the presence of highly coordinated oxygens, such as the u4-O in boehmite, a-, and y-Al2O3 and their Fe(III) analogs. The partial dissociation of these highly coordinated oxygens, coupled with simultaneous activation and displacement of neighboring metal centers, may be a fundamental process by which metals atoms undergo ligand exchanges at mineral surfaces.
2004. "Molecular Dynamics Investigation of Ferrous-Ferric Electron Transfer in a Hydrolyzing Aqueous Solution: Calculation of the pH Dependence of the Diabatic Transfer Barrier and the Potential of Mean Force." Journal of Chemical Physics 120(16):7607-7615. Abstract We present a molecular model for ferrous–ferric electron transfer in an aqueous solution that accounts for electronic polarizability and exhibits spontaneous cation hydrolysis. An extended Lagrangian technique is introduced for carrying out calculations of electron-transfer barriers in polarizable systems. The model predicts that the diabatic barrier to electron transfer increases with increasing pH, due to stabilization of the Fe31 by fluctuations in the number of hydroxide ions in its first coordination sphere, in much the same way as the barrier would increase with increasing dielectric constant in the Marcus theory. We have also calculated the effect of pH on the potential of mean force between two hydrolyzing ions in aqueous solution. As expected, increasing pH reduces the potential of mean force between the ferrous and ferric ions in the model system. The magnitudes of the predicted increase in diabatic transfer barrier and the predicted decrease in the potential of mean force nearly cancel each other at the canonical transfer distance of 0.55 nm. Even though hydrolysis is allowed in our calculations, the distribution of reorganization energies has only one maximum and is Gaussian to an excellent approximation, giving a harmonic free energy surface in the reorganization energy F(DE) with a single minimum. There is thus a surprising amount of overlap in electron-transfer reorganization energies for Fe21– Fe(H2O)6 31, Fe21– Fe(OH)(H2O)521, and Fe21– Fe(OH)2(H2O)1 couples, indicating that fluctuations in hydrolysis state can be viewed on a continuum with other solvent contributions to the reorganization energy. There appears to be little justification for thinking of the transfer rate as arising from the contributions of different hydrolysis states. Electronic structure calculations indicate that Fe(H2O)6 21– Fe(OH)n(H2O)62n (32n)1 complexes interacting through H3O2 2 bridges do not have large electronic couplings.
