Motion of the Zinc Ions in Catalysis by a Dizinc Metallo-β-Lactamase

We report rapid-freeze-quench X-ray absorption spectroscopy of a dizinc metallo-β-lactamase (MβL) reaction intermediate. The Zn(II) ions in the dinuclear active site of the S. maltophilia Class B3 MβL move away from each other, by ∼0.3 Å after 10 ms of reaction with nitrocefin, from 3.4 to 3.7 Å. Together with our previous characterization of the resting enzyme and its nitrocefin product complex, where the Zn(II) ion separation relaxes to 3.6 Å, these data indicate a scissoring motion of the active site that accompanies the ring-opening step. The average Zn(II) coordination number of 4.5 in the resting enzyme appears to be maintained throughout the reaction with nitrocefin. This is the first direct structural information available on early stage dizinc metallo-β-lactamase catalysis

A Five-coordinate Metal Center in Co(II)-substituted VanX

In an effort to structurally probe the metal binding site in VanX, electronic absorption, EPR, and extended x-ray absorption fine structure (EXAFS) spectroscopic studies were conducted on Co(II)-substituted VanX. Electronic spectroscopy revealed the presence of Co(II) ligand field transitions that had molar absorptivities of ∼100 m–1 cm–1, which suggests that Co(II) is five-coordinate in Co(II)-substituted VanX. Low temperature EPR spectra of Co(II)-substituted VanX were simulated using spin Hamiltonian parameters of M = |±½〉, E/D = 0.14, greal(x,y) = 2.37, and grealS(z) = 2.03. These parameters lead to the prediction that Co(II) in the enzyme is five-coordinate and that there may be at least one solvent-derived ligand. Single scattering fits of EXAFS data indicate that the metal ions in both native Zn(II)-containing and Co(II)-substituted VanX have the same coordination number and that the metal ions are coordinated by 5 nitrogen/oxygen ligands at ∼ 2.0 Å. These data demonstrate that Co(II) (and Zn(II) from EXAFS studies) is five-coordinate in VanX in contrast to previous crystallographic studies (Bussiere, D. E., Pratt, S. D., Katz, L., Severin, J. M., Holzman, T., and Park, C. H. (1998) Mol. Cell 2, 75–84). These spectroscopic studies also demonstrate that the metal ion in Co(II)-substituted VanX when complexed with a phosphinate analog of substrate d-Ala-d-Ala is also five-coordinate

Walking with wapiti: measuring late Holocene climatic variability through Cervus elaphus abundance and stable isotope analysis in the Gulf of Georgia Region

Native hunters of the Northwest Coast valued the local wapiti subspecies (Cervus elaphus roosevelti) greater than any other land animals as a source of both food and raw materials for tools. Wapiti population size depends on the quantity and quality of their preferred foods: easily digestible, high protein plants that occur most abundantly in meadows and thickets, particularly after spring and summer rains. Changing climate regimes affected the productivity of these foods but there is disagreement about whether climate periods with long dry summers helped or hindered wapiti populations on the Northwest Coast. Lepofsky et al. (2005) suggests wapiti abundance increased in periods with persistent summer drought due to increased fire frequency destroying forests and expanding meadows, and increasing the productivity of their preferred foods. While Broughton et al. (2008) suggests wapiti abundance decreased in periods with low spring-summer precipitation due to reductions in the duration and forage quality of the growing season. The goal of this thesis is to eliminate one of these hypotheses with a systematic analysis of wapiti remains from six sites in western Whatcom County representing 300 to 5300 cal yr BP. Stable isotope analysis of nitrogen and carbon in wapiti bone collagen from contexts closely associated with radiocarbon dates. Mammal remains from levels closely associated to these radiocarbon dates were separated and counted to determine mammal NISP, and wapiti remains were identified to determine wapiti NISP. The relative abundance of wapiti was determined by dividing wapiti NISP by mammal NISP and converting to a percentage for each radiocarbon date, and for each climate period. Relative wapiti abundance was found to be dependent on climate period, with significantly lower wapiti abundance relative to other mammals during hot, dry climate periods. The δ13C values are low compared to other regions worldwide and remain stable through time suggesting that closed canopied temperate rainforests were the dominant terrestrial environment over the last 5300 calendar years. During the Medieval Warm period δ15N values are significantly higher suggesting that the hottest driest conditions of the late Holocene occurred at that time. During the warm dry climate periods such as the Medieval Warm Period, increased seasonality would lead to reduced hunting return and plant forage rates for people

Ultraviolet-visible diode-array spectrophotometer as a detector for gas chromatography

An ultraviolet-visible diode-array spectrophotometer is used as a detector for gas chromatography. This detector can provide a full u.v.-visible spectrum of each compound as it elutes from the column, thus enhancing discrimination between incompletely separated components. A discrimination of ca. 1:5000 could be achieved for a mixture of toluene and benzene. The detection limit is comparable to that of the thermal conductivity detector, i.e., about 0.5 [mu]g for the various components. The detector is particularly useful when gases other than helium are used because the sensitivity does not depend on the gas used.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25682/1/0000236.pd

Differential Binding of Co(II) and Zn(II) to Metallo-β-Lactamase Bla2 from \u3cem\u3eBacillus anthracis\u3c/em\u3e

In an effort to probe the structure, mechanism, and biochemical properties of metallo-β-lactamase Bla2 from Bacillus anthracis, the enzyme was overexpressed, purified, and characterized. Metal analyses demonstrated that recombinant Bla2 tightly binds 1 equiv of Zn(II). Steady-state kinetic studies showed that mono-Zn(II) Bla2 (1Zn-Bla2) is active, while di-Zn(II) Bla2 (ZnZn-Bla2) was unstable. Catalytically, 1Zn-Bla2 behaves like the related enzymes CcrA and L1. In contrast, di-Co(II) Bla2 (CoCo-Bla2) is substantially more active than the mono-Co(II) analogue. Rapid kinetics and UV−vis, 1H NMR, EPR, and EXAFS spectroscopic studies show that Co(II) binding to Bla2 is distributed, while EXAFS shows that Zn(II) binding is sequential. To our knowledge, this is the first documented example of a Zn enzyme that binds Co(II) and Zn(II) via distinct mechanisms, underscoring the need to demonstrate transferability when extrapolating results on Co(II)-substituted proteins to the native Zn(II)-containing forms

Structure and Metal Binding Properties of ZnuA, a Periplasmic Zinc Transporter from \u3cem\u3eEscherichia coli\u3c/em\u3e

ZnuA is the periplasmic Zn2+-binding protein associated with the high-affinity ATP-binding cassette ZnuABC transporter from Escherichia coli. Although several structures of ZnuA and its homologs have been determined, details regarding metal ion stoichiometry, affinity, and specificity as well as the mechanism of metal uptake and transfer remain unclear. The crystal structures of E. coli ZnuA (Eco-ZnuA) in the apo, Zn2+-bound, and Co2+-bound forms have been determined. ZnZnuA binds at least two metal ions. The first, observed previously in other structures, is coordinated tetrahedrally by Glu59, His60, His143, and His207. Replacement of Zn2+ with Co2+ results in almost identical coordination geometry at this site. The second metal binding site involves His224 and several yet to be identified residues from the His-rich loop that is unique to Zn2+ periplasmic metal binding receptors. Electron paramagnetic resonance and X-ray absorption spectroscopic data on CoZnuA provide additional insight into possible residues involved in this second site. The second site is also detected by metal analysis and circular dichroism (CD) titrations. Eco-ZnuA binds Zn2+ (estimated K d \u3c 20 nM), Co2+, Ni2+, Cu2+, Cu+, and Cd2+, but not Mn2+. Finally, conformational changes upon metal binding observed in the crystal structures together with fluorescence and CD data indicate that only Zn2+ substantially stabilizes ZnuA and might facilitate recognition of ZnuB and subsequent metal transfer

Sequential Binding of Cobalt(II) to Metallo-β-lactamase CcrA

In an effort to probe Co(II) binding to metallo-β-lactamase CcrA, EPR, EXAFS, and 1H NMR studies were conducted on CcrA containing 1 equiv (1-Co(II)-CcrA) and 2 equiv (Co(II)Co(II)-CcrA) of Co(II). The EPR spectra of 1-Co(II)-CcrA and Co(II)Co(II)-CcrA are distinct and indicate 5/6-coordinate Co(II) ions. The EPR spectra also reveal the absence of significant spin-exchange coupling between the Co(II) ions in Co(II)Co(II)-CcrA. EXAFS spectra of 1-Co(II)-CcrA suggest 5/6-coordinate Co(II) with two or more histidine ligands. EXAFS spectra of Co(II)Co(II)-CcrA also indicate 5/6 ligands at a similar average distance to 1-Co(II)-CcrA, including an average of about two histidines per Co(II). 1H NMR spectra for 1-Co(II)-CcrA revealed seven paramagnetically shifted resonances, three of which were solvent-exchangeable, while the NMR spectra for Co(II)Co(II)-CcrA showed at least 16 shifted resonances, including an additional solvent-exchangeable resonance and a resonance at 208 ppm. The data indicate sequential binding of Co(II) to CcrA and that the first Co(II) binds to the consensus Zn1 site in the enzyme

Anomalies in low-energy Gamma-Ray Burst spectra with the Fermi Gamma-Ray Burst Monitor

A Band function has become the standard spectral function used to describe the prompt emission spectra of gamma-ray bursts (GRBs). However, deviations from this function have previously been observed in GRBs detected by BATSE and in individual GRBs from the \textit{Fermi} era. We present a systematic and rigorous search for spectral deviations from a Band function at low energies in a sample of the first two years of high fluence, long bursts detected by the \textit{Fermi} Gamma-Ray Burst Monitor (GBM). The sample contains 45 bursts with a fluence greater than 2$\times10^{-5}$ erg / cm$^{2}$ (10 - 1000 keV). An extrapolated fit method is used to search for low-energy spectral anomalies, whereby a Band function is fit above a variable low-energy threshold and then the best fit function is extrapolated to lower energy data. Deviations are quantified by examining residuals derived from the extrapolated function and the data and their significance is determined via comprehensive simulations which account for the instrument response. This method was employed for both time-integrated burst spectra and time-resolved bins defined by a signal to noise ratio of 25 $\sigma$ and 50 $\sigma$. Significant deviations are evident in 3 bursts (GRB\,081215A, GRB\,090424 and GRB\,090902B) in the time-integrated sample ($\sim$ 7%) and 5 bursts (GRB\,090323, GRB\,090424, GRB\,090820, GRB\,090902B and GRB\,090926A) in the time-resolved sample ($\sim$ 11%).} The advantage of the systematic, blind search analysis is that it can demonstrate the requirement for an additional spectral component without any prior knowledge of the nature of that extra component. Deviations are found in a large fraction of high fluence GRBs; fainter GRBs may not have sufficient statistics for deviations to be found using this method

Nanometer To Millimeter Scale Peptide-porphyrin Materials

AQ-Pal14 is a 30-residue polypeptide that was designed to form an alpha-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal 14)(2) species that creates two coiled-coil oligomerization domains Coordinated to opposite laces of the porphyrin ring. It is found that this species undergoes a buffer-dependent Self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like materials were prepared when the reaction was performed in phosphate buffer (20 mM, pH 7). It is suggested that assembly of the globular material is dictated by the conformational properties of the coiled-coil forming AQ-Pal14 peptide, whereas that a the rod-like material involves interactions between Co-PPIX and phosphate ion