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Cloning, heterologous expression, and characterization of recombinant class II cytochromes c from Rhodopseudomonas palustris - McGuirl, Michele A.; Lee, Jennifer C.; Lyubovitsky, Julia G.; Thanyakoop, Chalita; Richards, John H.; Gray, Harry B.; Winkler, Jay R.
The cytochrome (cyt) c′, cyt c_(556), and cyt c_2 genes from Rhodopseudomonas palustris have been cloned; recombinant cyt c′ and cyt c_(556) have been expressed, purified, and characterized. Unlike mitochondrial cyt c, these two proteins are structurally similar to cyt b_(562), in which the heme is embedded in a four-helix bundle. The hemes in both recombinant proteins form covalent thioether links to two Cys residues. UV/vis spectra of the Fe^(II) and Fe^(III) states of the recombinant cyts are identical with those of the corresponding native proteins. Equilibrium unfolding measurements in guanidine hydrochloride solutions confirm that native Fe^(II)-cyt c_(556) is more...
Mimicking protein-protein electron transfer: voltammetry of Pseudomonas aeruginosa azurin and the Thermus thermophilus Cu_A domain at ω-derivatized self-assembled-monolayer gold electrodes - Fujita, Kyoko; Nakamura, Nobufumi; Ohno, Hiroyuki; Leigh, Brian S.; Niki, Katsumi; Gray, Harry B.; Richards, John H.
Well-defined voltammetric responses of redox proteins with acidic-to-neutral pI values have been obtained on pure alkanethiol as well as on mixed self-assembled-monolayer (SAM) ω-derivatized alkanethiol/gold bead electrodes. Both azurin (P. aeruginosa) (pI = 5.6) and subunit II (CuA domain) of ba_3-type cytochrome c oxidase (T. thermophilus) (pI = 6.0) exhibit optimal voltammetric responses on 1:1 mixtures of [H_3C(CH_2)_nSH + HO(CH_2)_nSH] SAMs. The electron transfer (ET) rate vs distance behavior of azurin and CuA is independent of the ω-derivatized alkanethiol SAM headgroups. Strikingly, only wild-type azurin and mutants containing Trp48 give voltammetric responses: based on modeling, we suggest that electronic coupling...
Probing folded and unfolded states of outer membrane protein a with steady-state and time-resolved tryptophan fluorescence - Kim, Judy E.; Arjara, Gitrada; Richards, John H.; Gray, Harry B.; Winkler, Jay R.
Steady-state and time-resolved fluorescence measurements on each of five native tryptophan residues in full-length and truncated variants of E. coli outer-membrane protein A (OmpA) have been made in folded and denatured states. Tryptophan singlet excited-state lifetimes are multiexponential and vary among the residues. In addition, substantial increases in excited-state lifetimes accompany OmpA folding, with longer lifetimes in micelles than in phospholipid bilayers. This finding suggests that the Trp environments of OmpA folded in micelles and phospholipid bilayers are different. Measurements of Trp fluorescence decay kinetics with full-length OmpA folded in brominated lipid vesicles reveal that W102 is the most distant...
Th/U Microdistribution in Enstatite Meteorites - Murrell, M. T.; Burnett, D. S.
We report here our results to date for the mineralogical distribution of Th and U in the enstatite chondrites. By investigating the behavior of Th and U under the reducing conditions for which the enstatite meteorites formed, we hope to evaluate the suitability of these objectives for ^(244)Pu(_(1/2) = 82 m.y .) chronology, as well as gain insight into the origin of the E-chondrites. Induced fission tracks from a double irradiation have been used to map the distribution of Th and U in polished sections. The preliminary results are shown in Table I. The values are the mean contents of...
Electron Tunneling through Pseudomonas aeruginosa Azurins on SAM Gold Electrodes - Yokoyama, Keiko; Leigh, Brian S.; Sheng, Yuling; Niki, Katsumi; Nakamura, Nobuhumi; Ohno, Hiroyuki; Winkler, Jay R.; Gray, Harry B.; Richards, John H.
Robust voltammetric responses were obtained for wild-type and Y72F/H83Q/Q107H/Y108F azurins adsorbed on CH_3(CH_2)_nSH:HO(CH_2)_mSH (n=m=4,6,8,11; n=13,15 m=11) self-assembled monolayer (SAM) gold electrodes in acidic solution (pH 4.6) at high ionic strengths. Electron-transfer (ET) rates do not vary substantially with ionic strength, suggesting that the SAM methyl headgroup binds to azurin by hydrophobic interactions. The voltammetric responses for both proteins at higher pH values (>4.6 to 11) also were strong. A binding model in which the SAM hydroxyl headgroup interacts with the Asn47 carboxamide accounts for the relatively strong coupling to the copper center that can be inferred from the ET rates....
Excited-State Dynamics of Structurally Characterized [Re^I(CO)_3(phen)(HisX)]^+ (X = 83, 109) Pseudomonas aeruginosa Azurins in Aqueous Solution - Blanco-Rodríguez, Ana María; Busby, Michael; Grădinaru, Cristian; Crane, Brian R.; Di Bilio, Angel J.; Matousek, Pavel; Towrie, Michael; Leigh, Brian S.; Richards, John H.; Vlček, Antonín, Jr.; Gray, Harry B.
The triplet metal-to-ligand charge transfer (^3MLCT) dynamics of two structurally characterized Re^I(CO)_3(phen)(HisX)-modified (phen = 1,10-phenanthroline; X = 83, 109) Pseudomonas aeruginosa azurins have been investigated by picosecond time-resolved infrared (TRIR) spectroscopy in aqueous (D_2O) solution. The ^3MLCT relaxation dynamics exhibited by the two Re^I−azurins are very different from those of the sensitizer [Re^I(CO)_3(phen)(im)]+ (im = imidazole). Whereas the Re^I(CO)_3 intramolecular vibrational relaxation in Re^I(CO)_3(phen)(HisX)Az (4 ps) is similar to that of [ReI(CO)3(phen)(im)]+ (2 ps), the medium relaxation is much slower (∼250 vs 9.5 ps); the 250-ps relaxation is attributable to reorientation of D_2O molecules as well as structural reorganization of...
Submillimetre observations of WISE/radio-selected AGN and their environments - Jones, Suzy F.; Blain, Andrew W.; Lonsdale, Carol; Condon, James; Farrah, Duncan; Stern, Daniel; Tsai, Chao-Wei; Assef, Roberto J.; Bridge, Carrie; Kimball, Amy; Lacy, Mark; Eisenhardt, Peter; Wu, Jingwen; Jarrett, Tom
We present JCMT SCUBA-2 850 μm submillimetre (submm) observations of 30 mid-infrared (mid-IR) luminous active galactic nuclei (AGNs), detected jointly by the Wide-field Infrared Survey Explorer (WISE) all-sky IR survey and the NVSS/FIRST radio survey. These rare sources are selected by their extremely red mid-IR spectral energy distributions (SEDs) and compact radio counterparts. Further investigations show that they are highly obscured, have abundant warm AGN-heated dust and are thought to be experiencing intense AGN feedback. These galaxies appear to be consistent with a later AGN-dominated phase of merging galaxies, while hot, dust-obscured galaxies are an earlier starburst-dominated phase. When comparing...
Silica-bearing chondrules and clasts in ordinary chondrites - Brigham, C. A.; Yabuki, H.; Ouyang, Z.; Murrell, M. T.; El Goresy, A.; Burnett, D. S.
Unusual silica-bearing chondrules and clasts have been observed in several unequilibrated ordinary chondrites. There appear to be two distinct types: (I) silica, low-Ca pyroxene assemblages, and (II) silica, fayalite intergrowths coexisting with low-Ca pyroxene. Only the former types are chondrules. The bulk compositions of most of these objects can be expressed in terms of three components—MgO, FeO, and SiO_2—since Ca, Al, and Na are essentially trace elements. Secondary alteration has probably perturbed the Fe/Mg ratios in most objects and produced Ca-rich pyroxenes in some type II clasts, but the silica, low-Ca pyroxene and fayalite are hard to understand as other...
The behavior of actinides, phosphorus, and rare earth elements during chondrite metamorphism - Murrell, M. T.; Burnett, D. S.
New data on the U, Pu, and P distributions in less metamorphosed H-chondrites (type 3–5), coupled with literature results, permit a provisional picture to be assembled of the chemistry of these elements and for the rare earth elements in ordinary chondrites and the changes brought about by chondritic metamorphism. Preferential associations of phosphates with metals and/or sulndes in all chondrites strongly indicate an “initially” siderophile or conceivably chalcophile character for P in ordinary chondrite precursor materials with phosphate subsequently formed by oxidation. This oxidation occurred prior to or during chondritic metal-silicate fractionation. Uranium is initially concentrated in chondrule glass at...
Actinide chemistry in Allende Ca-Al-rich inclusions - Murrell, M. T.; Burnett, D. S.
The microscale distribution of U and Th has been studied by fission track radiography in a set of Ca-Al-rich inclusions from the Allende meteorite. In the Type B inclusions, generally believed to have been melted, the major phases melilite and fassaite are important actinide host phases with similar Th/U and roughly three times higher concentrations in melilite than fassaite. Significant enrichments are also found on grain boundaries and in some regions of alteration. The distribution is not completely understood in terms of igneous partitioning and may also reflect incomplete assimilation of relict materials during melting. On the rims of Type...
Actinide microdistributions in the enstatite meteorites - Murrell, M. T.; Burnett, D. S.
Oldhamite is a major Th and U bearing phase in the enstatite meteorites. Oldhamite from E-6 chondrites has mean Th and U abundances of 1550 ± 80 ppb Th and 410 ± 20 ppb U, with Th/U = 3.8 ± .2. With the exception of ferroan alabandite which contains 25 ± 1 ppb U, no other Th or U enriched phases were located in the E-6 chondrites, and nearly all of the total rock Th and U can be accounted for by oldhamite. In Khairpur (E6), excess fossil fission tracks were observed in enstatite grains in contact with oldhamite which...
Locating the Most Energetic Electrons in Cassiopeia A - Grefenstette, Brian W.; Reynolds, Stephen P.; Harrison, Fiona A.; Humensky, T. Brian; Boggs, Steven E.; Fryer, Chris L.; Delaney, Tracey; Madsen, Kristin K.; Miyasaka, Hiromasa; Wik, Daniel R.; Zoglauer, Andreas; Foster, Karl; Kitaguchi, Takao; Lopez, Laura; Nynka, Melania; Christensen, Finn E.; Craig, William W.; Hailey, Charles J.; Stern, Daniel; Zhang, William W.
We present deep (>2.4 Ms) observations of the Cassiopeia A supernova remnant with NuSTAR, which operates in the 3–79 keV bandpass and is the first instrument capable of spatially resolving the remnant above 15 keV. We find that the emission is not entirely dominated by the forward shock nor by a smooth "bright ring" at the reverse shock. Instead we find that the >15 keV emission is dominated by knots near the center of the remnant and dimmer filaments near the remnant's outer rim. These regions are fit with unbroken power laws in the 15–50 keV bandpass, though the central...
Additive extensions of a Barsotti-Tate group - Mantovan, Elena
In this paper we classify up to isomorphism the additive extensions of a Barsotti-Tate group, in positive characteristic p over a perfect field k and in characteristic 0 over W(k) the ring of Witt vectors with coefficients in k. The extensions arise as group functors associated to suitable submodules of the Dieudonné module. In particular we give an explicit description of the universal additive extension in both cases.
On the cohomology of certain PEL-type Shimura varieties - Mantovan, Elena
In this article we study the local geometry at a prime p of PEL-type Shimura varieties for which there is a hyperspecial level subgroup. We consider the Newton polygon stratification of the special fiber at p of Shimura varieties and show that each Newton polygon stratum can be described in terms of the products of the reduced fibers of the corresponding PEL-type Rapoport-Zink spaces with certain smooth varieties (which we call Igusa varieties) and of the action on them of a p-adic group that depends on the stratum. We then extend our construction to characteristic zero and, in the case...
Dense dislocation arrays embedded in grain boundaries for high-performance bulk thermoelectrics - Kim, Sang Il; Lee, Kyu Hyoung; Mun, Hyeon A.; Kim, Hyun Sik; Hwang, Sung Woo; Roh, Jong Wook; Yang, Dae Jin; Shin, Weon Ho; Li, Xiang Shu; Lee, Young Hee; Snyder, G. Jeffrey; Kim, Sung Wng
The widespread use of thermoelectric technology is constrained by a relatively low conversion efficiency of the bulk alloys, which is evaluated in terms of a dimensionless figure of merit (zT). The zT of bulk alloys can be improved by reducing lattice thermal conductivity through grain boundary and point-defect scattering, which target low- and high-frequency phonons. Dense dislocation arrays formed at low-energy grain boundaries by liquid-phase compaction in Bi_(0.5)Sb_(1.5)Te_3 (bismuth antimony telluride) effectively scatter midfrequency phonons, leading to a substantially lower lattice thermal conductivity. Full-spectrum phonon scattering with minimal charge-carrier scattering dramatically improved the zT to 1.86 ± 0.15 at 320...
A compactification of Igusa varieties - Mantovan, Elena
We investigate the notion of Igusa level structure for a one-dimensional Barsotti–Tate group over a scheme X of positive characteristic and compare it to Drinfeld’s notion of level structure. In particular, we show how the geometry of the Igusa covers of X is useful for studying the geometry of its Drinfeld covers (e.g. connected and smooth components, singularities). Our results apply in particular to the study of the Shimura varieties considered in Harris and Taylor (On the geometry and cohomology of some simple Shimura varieties. Princeton University Press, Princeton, 2001). In this context, they are higher dimensional analogues of the...
A Protocluster at z = 2.45 - Diener, C.; Lilly, S. J.; Ledoux, C.; Zamorani, G.; Bolzonella, M.; Murphy, D. N. A.; Capak, P.; Ilbert, O.; McCraken, H.
We present the spectroscopic confirmation of a z = 2.45 protocluster. Its member galaxies lie within a radius of 1.4 Mpc (physical) on the sky and within Δv ± 700 km^(-1) along the line of sight. We estimate an overdensity of 10, suggesting that the structure has made the turnaround but is not assembled yet. A comparison to the Millennium simulation suggests that analogous structures evolve into 10^(14)–10^(15) M_⊙h^(−1) type dark matter halos by z = 0, qualifying the notion of "protocluster." The search for the complete census of mock progenitor galaxies at z ~ 2.5 of these massive z...
Measurement of the branching fractions of the radiative leptonic τ decays τ→eγνν[bar] and τ→μγνν[bar] at BABAR - Lees, J. P.; Chao, Daniel S.; Cheng, Chih-Hsiang; Echenard, B.; Flood, K. T.; Hitlin, D. G.; Miyashita, Tomonari S.; Ongmongkolkul, P.; Porter, F. C.; Röhrken, M.
We perform a measurement of the τ→lγνν [bar] (l=e,μ) branching fractions for a minimum photon energy of 10 MeV in the τ rest frame, using 431 fb^(−1) of e^+ e^− collisions collected at the center-of-mass energy of the Υ(4S) resonance with the BABAR detector at the PEP-II storage rings. We find B(τ→μγνν [bar])=(3.69±0.03±0.10)×10^(−3) and B(τ→eγνν[bar]¯ )=(1.847±0.015±0.052)×10^(−2), where the first quoted error is statistical and the second is systematic. These results are substantially more precise than previous measurements.
Time-evolving a matrix product state with long-ranged interactions - Zaletel, Michael P.; Mong, Roger S. K.; Karrasch, Christoph; Moore, Joel E.; Pollmann, Frank
We introduce a numerical algorithm to simulate the time evolution of a matrix product state under a long-ranged Hamiltonian in moderately entangled systems. In the effectively one-dimensional representation of a system by matrix product states, long-ranged interactions are necessary to simulate not just many physical interactions but also higher-dimensional problems with short-ranged interactions. Since our method overcomes the restriction to short-ranged Hamiltonians of most existing methods, it proves particularly useful for studying the dynamics of both power-law interacting, one-dimensional systems, such as Coulombic and dipolar systems, and quasi-two-dimensional systems, such as strips or cylinders. First, we benchmark the method by...
Predicted Structures for Kappa Opioid G‑Protein Coupled Receptor Bound to Selective Agonists - Li, Quanjie; Kim, Soo-Kyung; Goddard, William A., III; Chen, Guangju; Tan, Hongwei
Human kappa opioid receptor (κ-OR), a G protein-coupled receptor (GPCR), has been identified as a drug target for treatment of such human disorders as pain perception, neuroendocrine physiology, affective behavior, and cognition. In order to find more selective and active agonists, one would like to do structure based drug design. Indeed, there is an X-ray structure for an antagonist bound to κ-OR, but structures for activated GPCRs are quite different from those for the inactive GPCRs. Here we predict the ensemble of 24 low-energy structures of human kappa opioid receptor (κ-OR), obtained by application of the GEnSeMBLE (GPCR Ensemble of...