Substrate Induced Structural and Dynamics Changes in Human Phosphomevalonate Iinase and Implications for Mechanism

Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK using NMR-based dynamics and chemical shift perturbation measurements. Mg-ADP and M5P Kd\u27s were 6–60 μM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (τc = 13.5 nsec), whereas subsequent binding of Mg-ADP opens the structure up (τc = 15.6 nsec). The overall complex seems to stay very rigid on the psec-nsec timescale with an average NMR order parameter of S2 ∼0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the “Walker-A” catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; however, these observations do not indicate an obvious role for γ-phosphate binding interactions. Indeed, the role of γ-phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, because the conservative O to NH substitution in the β-γ bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first nine residues of the N-terminus are highly disordered, suggesting that they may be part of a cleavable signal or regulatory peptide sequence. Proteins 2009. © 2008 Wiley-Liss, Inc

Thermal conductivity of crystalline AlN and the influence of atomic-scale defects

Aluminum nitride (AlN) plays a key role in modern power electronics and deep-ultraviolet photonics, where an understanding of its thermal properties is essential. Here we measure the thermal conductivity of crystalline AlN by the 3${\omega}$ method, finding it ranges from 674 ${\pm}$ 56 W/m/K at 100 K to 186 ${\pm}$ 7 W/m/K at 400 K, with a value of 237 ${\pm}$ 6 W/m/K at room temperature. We compare these data with analytical models and first principles calculations, taking into account atomic-scale defects (O, Si, C impurities, and Al vacancies). We find Al vacancies play the greatest role in reducing thermal conductivity because of the largest mass-difference scattering. Modeling also reveals that 10% of heat conduction is contributed by phonons with long mean free paths, over ~7 ${\mu}$m at room temperature, and 50% by phonons with MFPs over ~0.3 ${\mu}$m. Consequently, the effective thermal conductivity of AlN is strongly reduced in sub-micron thin films or devices due to phonon-boundary scattering

Unique prospects of graphene-based THz modulators

The modulation depth of 2-D electron gas (2DEG) based THz modulators using AlGaAs/GaAs heterostructures with metal gates is inherently limited to < 30%. The metal gate not only attenuates the THz signal (> 90%) but also severely degrades the modulation depth. The metal losses can be significantly reduced with an alternative material with tunable conductivity. Graphene presents a unique solution to this problem due to its symmetric band structure and extraordinarily high mobility of holes that is comparable to electron mobility in conventional semiconductors. The hole conductivity in graphene can be electrostatically tuned in the graphene-2DEG parallel capacitor configuration, thus more efficiently tuning the THz transmission. In this work, we show that it is possible to achieve a modulation depth of > 90% while simultaneously minimizing signal attenuation to < 5% by tuning the Fermi level at the Dirac point in graphene.Comment: 15 pages, 3 figures, 1 tabl

The structure of the BfrB-Bfd complex reveals protein-protein interactions enabling iron release from bacterioferritin

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ja305180n.Ferritin-like molecules are unique to cellular iron homeostasis because they can store iron at concentrations much higher than those dictated by the solubility of Fe3+. Very little is known about the protein interactions that deliver iron for storage, or promote the mobilization of stored iron from ferritin-like molecules. Here, we report the X-ray crystal structure of Pseudomonas aeruginosa bacterioferritin (Pa-BfrB) in complex with bacterioferritin-associated ferredoxin (Pa-Bfd) at 2.0 Å resolution. As the first example of a ferritin-like molecule in complex with a cognate partner, the structure provides unprecedented insight into the complementary interface that enables the [2Fe-2S] cluster of Pa-Bfd to promote heme-mediated electron transfer through the BfrB protein dielectric (~18 Å), a process that is necessary to reduce the core ferric mineral and facilitate mobilization of Fe2+. The Pa-BfrB-Bfd complex also revealed the first structure of a Bfd, thus providing a first view to what appears to be a versatile metal binding domain ubiquitous to the large Fer2_BFD family of proteins and enzymes with diverse functions. Residues at the Pa-BfrB-Bfd interface are highly conserved in Bfr and Bfd sequences from a number of pathogenic bacteria, suggesting that the specific recognition between Pa-BfrB and Pa-Bfd is of widespread significance to the understanding of bacterial iron homeostasis

Pseudomonas aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity

We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe2+ utilizing H2O2 (not O2) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H2O2-mediated oxidative stress. In agreement, a P. aeruginosa Δdps mutant is significantly more susceptible to H2O2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H2O2 or O2 but requires divalent cations and 12-mer Pa Dps

GASZ promotes germ cell derivation from embryonic stem cells

AbstractPrimordial germ cells (PGCs) are the first germ-line population that forms from the proximal epiblast of the developing embryo. Despite their biological importance, the regulatory networks whereby PGCs arise, migrate, and differentiate into gametes during embryonic development remains elusive, largely due to the limited number of germ cells in the early embryo. To elucidate the molecular mechanisms that govern early germ cell development, we utilized an in vitro differentiation model of embryonic stem cells (ESCs) and screened a series of candidate genes with specific expression in the adult reproductive organs. We discovered that gain of function of Gasz, a gene previously reported to participate in meiosis of postnatal spermatocytes, led to the most robust upregulation of PGC formation from both human and murine ESCs. In contrast, Gasz deficiency resulted in pronounced reduction of germ cells during ESC differentiation and decreased expression of MVH and DAZL in genital ridges during early embryonic development. Further analyses demonstrated that GASZ interacted with DAZL, a key germ cell regulator, to synergistically promote germ cell derivation from ESCs. Thus, our data reveal a potential role of GASZ during embryonic germ cell development and provide a powerful in vitro system for dissecting the molecular pathways in early germ cell formation during embryogenesis

Observation of oscillatory relaxation in the Sn-terminated surface of epitaxial rock-salt SnSe {111}\{111\} topological crystalline insulator

Topological crystalline insulators have been recently predicted and observed in rock-salt structure SnSe $\{111\}$ thin films. Previous studies have suggested that the Se-terminated surface of this thin film with hydrogen passivation, has a reduced surface energy and is thus a preferred configuration. In this paper, synchrotron-based angle-resolved photoemission spectroscopy, along with density functional theory calculations, are used to demonstrate conclusively that a rock-salt SnSe $\{111\}$ thin film epitaxially-grown on \ce{Bi2Se3} has a stable Sn-terminated surface. These observations are supported by low energy electron diffraction (LEED) intensity-voltage measurements and dynamical LEED calculations, which further show that the Sn-terminated SnSe $\{111\}$ thin film has undergone a surface structural relaxation of the interlayer spacing between the Sn and Se atomic planes. In sharp contrast to the Se-terminated counterpart, the observed Dirac surface state in the Sn-terminated SnSe $\{111\}$ thin film is shown to yield a high Fermi velocity, $0.50\times10^6$m/s, which suggests a potential mechanism of engineering the Dirac surface state of topological materials by tuning the surface configuration.Comment: 12 pages, 13 figures, supplementary materials include