Physical Sciences and Mathematics Commons^™

Divalent Metal Binding Properties Of The Methionyl Aminopeptidase From Escherichia Coli, Ventris D'Souza, Brian Bennett, Alicja Copik, Richard Holz

Richard C. Holz

The metal-binding properties of the methionyl aminopeptidase from Escherichia coli (MetAP) were investigated. Measurements of catalytic activity as a function of added Co(II) and Fe(II) revealed that maximal enzymatic activity is observed after the addition of only 1 equiv of divalent metal ion. Based on these studies, metal binding constants for the first metal binding event were found to be 0.3 ± 0.2 μM and 0.2 ± 0.2 μM for Co(II)- and Fe(II)-substituted MetAP, respectively. Binding of excess metal ions (>50 equiv) resulted in the loss of ∼50% of the catalytic activity. Electronic absorption spectral titration of a 1 …

The Proteomics Of N-Terminal Methionine Cleavage, Frédéric Frottin, Aude Martinez, Philippe Peynot, Sanghamitra Mitra, Richard Holz, Carmela Giglione, Thierry Meinnel

Richard C. Holz

Methionine aminopeptidase (MAP) is a ubiquitous, essential enzyme involved in protein N-terminal methionine excision. According to the generally accepted cleavage rules for MAP, this enzyme cleaves all proteins with small side chains on the residue in the second position (P1′), but many exceptions are known. The substrate specificity of Escherichia coli MAP1 was studied in vitro with a large (>120) coherent array of peptides mimicking the natural substrates and kinetically analyzed in detail. Peptides with Val or Thr at P1′ were much less efficiently cleaved than those with Ala, Cys, Gly, Pro, or Ser in this position. Certain residues …

Unraveling The Catalytic Mechanism Of Nitrile Hydratases, Sanghamitra Mitra, Richard Holz

Richard C. Holz

To elucidate a detailed catalytic mechanism for nitrile hydratases (NHases), the pH and temperature dependence of the kinetic constants kcat and Km for the cobalt-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) were examined. PtNHase was found to exhibit a bell-shaped curve for plots of relative activity versus pH at pH 3.2–11 and was found to display maximal activity between pH 7.2 and 7.8. Fits of these data provided pKES1 and pKES2 values of 5.9 ± 0.1 and 9.2 ± 0.1 (kcat′ = 130 ± 1 s-1), respectively, and pKE1 and pKE2 values of 5.8 ± 0.1 and 9.1 ± …

Proton Nmr Investigation Of The [4fe-4s]1+ Cluster Environment Of Nitrogenase Iron Protein From Azotobacter Vinelandii: Defining Nucleotide-Induced Conformational Changes, William Lanzilotta, Richard Holz, Lance Seefeldt

Richard C. Holz

This work presents the complete assignment of the isotropically shifted 1H NMR resonances of Azotobacter vinelandii nitrogenase iron protein (Fe protein) to β-CH2 and α-CH protons of the [4Fe- 4S]1+ cluster cysteinyl ligands. Four resonances were observed for the reduced Fe protein with chemical shifts of 49, 23, 17, and 13 ppm. T1 measurements and analysis of relative peak areas coupled with one-dimensional nuclear Overhauser effect (NOE) difference spectra were used to assign the two most downfield-shifted resonances (49 and 23 ppm) to cysteinyl ligand β-CH2 protons and the 17 and 14 ppm resonances to cysteinyl ligand α-CH protons. Temperature …

Hydrolysis Of Thionopeptides By The Aminopeptidase From Aeromonas Proteolytica:  Insight Into Substrate Binding, David Bienvenue, Danuta Gilner, Richard Holz

Richard C. Holz

A series of l-leucine aniline analogues were synthesized that contained either a carbonyl or thiocarbonyl as a part of the amide bond. Additionally, the para-position on the phenyl ring of several substrates was altered with various electron-withdrawing or donating groups. The kinetic constants Km and kcat were determined for the hydrolysis of each of these compounds in the presence of the aminopeptidase from Aeromonas proteolytica (AAP) containing either Zn(II) or Cd(II). The dizinc(II) form of AAP ([ZnZn(AAP)]) was able to cleave both carbonyl and thiocarbonyl containing peptide substrates with similar efficiency. However, the dicadmium(II) form of AAP ([CdCd(AAP)]) was unable …

Electrochemical Attachment Of Motile Bacterial Cells To Gold, Sergey Rozhok, Richard Holz

Richard C. Holz

Selective attachment of Escherichia coli K-12 bacterial cells to charged gold surfaces was demonstrated. Electrostatic binding of E. coli K-12 bacterial cells to positively charged surfaces was observed starting at +750 mV. The binding of E. coli K-12 cells to positively charged gold surfaces is proposed to occur due to long-range electrostatic interactions between the negatively charged O-chain of lipopolysaccharide (LPS) molecules protruding the bacterial cell body and the electrode surface. Removing LPS alters the cellular surface charge and results in cellular attachment to negatively charged surfaces. Thus, applying an electrical potential allows for the direct, real time detection of …

Synthesis, Molecular Structure, And Reactivity Of Dinuclear Copper(Ii) Complexes With Carboxylate-Rich Coordination Environments, Richard Holz, John Bradshaw, Brian Bennett

Richard C. Holz

The dinucleating ligand N,N‘-(2-hydroxy-5-methyl-1,3-xylylene)bis(N-(carboxymethyl)glycine) (CH₃HXTA) has been used to synthesize the dinuclear Cu(II) bis(pyridine) complex Na[Cu₂(CH₃HXTA)(Py)₂]·1.5(1,4-dioxane) (Na(1)):  triclinic space group P1̄ (a = 12.550(3) Å, b = 13.413(3) Å, c = 13.540(4) Å, α = 117.12(2)°, β = 104.70 (2)°, and γ = 92.13(2)°). The structure shows two distinct distorted square pyramidal Cu(II) centers with each Cu(II) ion bound by two carboxylate oxygen atoms, one amine nitrogen atom, a phenolate oxygen atom, and one pyridine nitrogen atom. The Cu--Cu separation is 3.531 Å, …

Proton Nmr Spectroscopy As A Probe Of Dinuclear Copper(Ii) Centers, Richard Holz, Julie Brink

Richard C. Holz

No abstract provided.

Dinuclear Copper(Ii) Complexes With Carboxylate-Rich Coordination Environments. Models For Substituted Copper(Ii) Aminopeptidases, Richard Holz, Julie Brink, Feben Gobena, Charles O'Connor

Richard C. Holz

The dinucleating ligand N,N'-(2-hydroxy-5-methyl1-, 3-xylylene)bis(N-carboxymethylglycine) (CH₃HXTA) has been used to synthesize the dinuclear Cu(II) diaqua complex [Cu₂(CH₃HXTA) (H₂O)₂]H•4H₂O (1): monoclinic space group P2₁In (a = 15.092(3) Å, b = 10.842(3) Å, c = 15.219(4) Å, and β = 104.70(2)°). The structure shows two distinct square pyramidal Cu(II) centers with each Cu(II) ion bound to two carboxylate oxygen atoms, one amine nitrogen atom, the phenolate oxygen atom, and one water oxygen atom. The Cu- -Cu separation is 3.726 Å and Cu1-O1-Cu2 angle …

Structures And Properties Of Dibridged (Μ-Oxo)Diiron(Iii) Complexes. Effects Of The Fe-O-Fe Angle, Richard Norman, Richard Holz, Stephane Menage, Charles O'Connor, Jian Zhang, Lawrence Que

Richard C. Holz

A series of (μ-oxo)diiron(lll) complexes of tris(2-pyridylmethy1)amine (TPA), [Fe2(TPA)2O(L)] (CIO4)n, were synthesized and characterized where L represents the bridging ligands carbonate, hydrogen maleate, diphenyl phosphate, diphenylphosphinate, maleate, and phthalate. Together with the linear dichloride complex, this series of compounds provides a unique opportunity to systematically study the effects of the Fe-0-Fe angle (125-180°) on the electronic spectral and magnetic properties of the (μ-oxo)diiron(lll) core. [Fe2(TPA)2O(CO3)](CIO4)2.2CH3OH (1) crystallizes in the monoclinic space group P21/c with a = 11.282 (7) Å, b = 18.253 (9) Å, c = 20.390 (7) Å, and β= 95.02 (4)°. The structure was determined at -50°C from …

Attachment Of Motile Bacterial Cells To Prealigned Holed Microarrays, Sergey Rozhok, Zhifang Fan, Dorjderem Nyamjav, Chang Liu, Chad Mirkin, Richard Holz

Richard C. Holz

Construction of biomotors is an exciting area of scientific research that holds great promise for the development of new technologies with broad potential applications in areas such as the energy industry and medicine. Herein, we demonstrate the fabrication of prealigned microarrays of motile Escherichia coli bacterial cells on SiOx substrates. To prepare these arrays, holed surfaces with a gold layer on the bottom of the holes were utilized. The attachment of bacteria to the holes was achieved via nonspecific interactions using poly-l-lysine hydrobromide (PLL). Our data suggest that a single motile bacterial cell can be selectively attached to an individual …

Two-Dimensional 1H Nmr Studies On Octahedral Nickel(Ii) Complexes, Richard Holz, Evgenij Evdokimov, Feben Gobena

Richard C. Holz

The dinucleating ligand ethylene glycol−bis(β-aminoethyl ether) N,N,N‘,N‘-tetrakis[(2-(1-ethylbenzimidazoyl)] (EGTB-Et; 1) was used to synthesize the dinuclear Ni(II) tetraacetonitrile complex cation [Ni2(EGTB-Et)(CH3CN)4]2+ (2):  triclinic space group P1̄ (a = 12.273(5) Å, b = 12.358(7) Å, c = 12.561(6) Å, α = 90.43(4)°, β = 110.26(3)°, γ = 99.21 (4)°, and Z = 1). The structure shows two identical octahedral Ni(II) centers each bound to two benzimidazole ring nitrogen atoms, one amine nitrogen atom, an ether oxygen atom, and two acetonitrile nitrogen atoms. The Ni(II) ions are tethered together by a diethyl ether linkage with a crystallographic center of inversion between the methylene …

Proton Nuclear Magnetic Resonance Investigation Of The [2fe-2s]1--Containing “Rieske-Type” Protein From Xanthobacter Strain Py2, Richard Holz, Frederick Small, Scott Ensign

Richard C. Holz

Proton NMR spectra of the Rieske-type ferredoxin from Xanthobacter strain Py2 were recorded in both H2O and D2O buffered solutions at pH 7.2. Several well-resolved hyperfine-shifted 1H NMR signals were observed in the 90 to −20 ppm chemical shift range. Comparison of spectra recorded in H2O and D2O buffered solutions indicated that the signals at −11.4 (L) and −15.5 (M) ppm were solvent-exchangeable and thus were assigned to the two histidine Nε2H protons. The remaining observed signals were assigned based upon chemical shift, T1 values, and one-dimensional nuclear Overhauser effect (nOe) saturation transfer experiments to either CβH or CαH protons …

Spectroscopic Characterization Of Some Rare Earth Complexes Of Triethylenetetraaminehexaacetic Acid, Richard Holz, William Horrocks

Richard C. Holz

The Eu3+ complexes formed with triethylenetetraaminehexaacetic acid (TTHA) were characterized in solution by laser-induced Eu3+ luminescence spectroscopy. Both 2:1 and 1:1 metal:ligand complexes were detected at pH 6.0 depending on the metal- ligand stoichiometry. These two species exhibit distinct excited-state lifetimes of 260 and 1210 μs, respectively. The 2:1 complex coordinates three or four water molecules at each Eu3+ ion while the 1:1 complex has no coordinated water molecules. The 7F0→5D0 excitation spectra revealed multiple isomeric forms for both the 2:1 and 1:1 complexes. Spectra and excited-state lifetimes were taken as a function of pH for a 1:1 metal:ligand solution. …

Yttrium-89 Nmr Spectroscopy, A New Probe For Calcium-Binding Proteins, Richard Holz, William Horrocks

Richard C. Holz

No abstract provided.

Molecular Discrimination Of Type-I Over Type-Ii Methionyl Aminopeptidases, Krzysztof Swierczek, Alicja Copik, Sabina Swierczek, Richard Holz

Richard C. Holz

Two residues that are conserved in type-I methionyl aminopeptidases (MetAPs) but are absent in all type-II MetAPs are the cysteine residues (Escherichia coli MetAP-I:   C59 and C70) that reside at the back of the substrate recognition pocket. These Cys residues are 4.4 Å apart and do not form a disulfide bond. Since bacteria and fungi contain only type-I MetAPs while all human cells contain both type-I and type-II MetAPs, type-I MetAPs represent a novel antibiotic/antifungal target if type-I MetAPs can be specifically targeted over type-II. Based on reaction of the thiol-specific binding reagent 5,5‘-dithio-bis(2-nitrobenzoic acid) (DTNB) with the type-I MetAP …

Zinc Aminopeptidases, Aminopeptidase From Vibrio Proteolyticus (Aeromonas Proteolytica) As Prototypical Enzyme, Richard Holz, Anna Starus, Danuta Gillner

Richard C. Holz

No abstract provided.

Arsenic Mobilization In An Alluvial Aquifer Of The Terai Region, Nepal, Jasmine Diwakar, Scott Johnston, Edward Burton, Suresh Das Shrestha

Associate Professor Edward D Burton

Study Region

A shallow (<50 m) alluvial aquifer in the Terai region of Nepal.

Study Focus

We examine the hydrogeochemical characteristics of a shallow alluvial aquifer system in the Terai region (Nawalparasi district) to identify possible mechanisms and controls on geogenic As mobilization in groundwater. Groundwater and river water samples from a topo-gradient flow-path and floodplain of a minor river draining the Siwalik forehills were analyzed for physico-chemical parameters.

New Hydrological Insights for the Region

The aquifer is characterized by Ca-HCO₃ type water and is multi-contaminated, with the WHO guideline values exceeded for As, Mn and F in 80%, 70% and 40% of cases respectively. The middle portion …

A Revised Method For Determining Existing Acidity In Re-Flooded Acid Sulfate Soils, Scott Johnston, Edward Burton, Roslyn Hagan, Thor Aaso, Gerard Tuckerman

Associate Professor Edward D Burton

Titratable actual acidity (TAA) is a technique commonly used to estimate the existing pool of exchangeable H⁺ in acid sulfate soils (ASS). A widely adopted version of the TAA method involves titrating a 1M KCl suspension of oven-dry soil (1:40) with NaOH to a known pH endpoint. However, when ASS are subject to long term re-flooding during wetland remediation, former sulfuric horizons can develop substantial quantities of porewater Fe²⁺, non-sulfidic solid-phase Fe(II) and a variety of reduced inorganic sulfur (RIS) species (e.g. pyrite, mackinawite, greigite and elemental sulfur). For these sediments, an oven-drying approach may induce oxidation …

Enrichment And Heterogeneity Of Trace Elements At The Redox-Interface Of Fe-Rich Intertidal Sediments, Annabelle Keene, Scott Johnston, Richard Bush, Edward Burton, Leigh Sullivan, Matthew Dundoon, Angus Mcelnea, C Smith, Col Ahern, Bernard Powell

Associate Professor Edward D Burton

Redox-interfacial sediments can undergo radical geochemical changes with oscillating tides. In this study, we examine trace element enrichment and availability, at both landscape and pedon-scales, in the surface sediments of a remediating acidic tidal wetland. Fe-rich sediments at the surface-water interface (0–10 mm in depth) were collected across an elevation gradient spanning the supratidal to subtidal range. These sediments were analysed for solid phase Fe fractions and trace elements (As, Pb, Cr, Cu, Mn, Ni, Zn, V, B, Co, Mo, Ba and U) via dilute HCl-extractions and total digests. Their concentrations were compared with those of underlying (0.05–0.65 m in …

Landslide-Induced Iron Mobilisation Shapes Benthic Accumulation Of Nutrients, Trace Metals And Ree Fractionation In An Oligotrophic Alpine Stream, Scott Johnston, Andrew Rose, Edward Burton, Jenny Webster-Brown

Associate Professor Edward D Burton

Large alpine landslides that entrain substantial organic material below the water table and create suspended floodplains may have long-term consequences for the mobilisation of redox sensitive elements, such as Fe, into streamwaters. In turn, the cycling of iron in aquatic systems can influence the fate of nutrients, alter primary productivity, enhance accumulation of trace metals and induce fractionation of rare earth elements (REE). In this study we examine a reach of a pristine oligotrophic alpine stream bracketing a 30 year-old landslide and explore the consequences of landslide-induced Fe mobilisation for aqueous geochemistry and the composition of benthic stream cobble biofilm. …

Late Pleistocene Glacial History And Magnetic Chronostratigraphy, Western Adirondack Borderland, New York, Donald Pair

Donald L. Pair

New lines of evidence from the western Adirondack borderland have been employed to assess the style of deglaciation and reconstruct the nature and timing of associated proglacial lacustrine and marine (Champlain Sea) events. Contrasting styles of deglaciation, controlled primarily by water depth, resulted in landfast ice withdrawing gradually on the northern slope of the Adirondacks while actively calving ice, retreating rapidly in the deep water of Lake Iroquois, quickly evacuated the western St. Lawrence Lowland of ice. The extent of ice retreat from the western St. Lawrence Lowland during the life of Lake Iroquois has been estimated on the basis …

Higher Order Dynamic Equations On Measure Chains: Wronskians, Disconjugacy, And Interpolating Families Of Functions, Martin Bohner, Paul Eloe

Paul W. Eloe

This paper introduces generalized zeros and hence disconjugacy of nth order linear dynamic equations, which cover simultaneously as special cases (among others) both differential equations and difference equations. We also define Markov, Fekete, and Descartes interpolating systems of functions. The main result of this paper states that disconjugacy is equivalent to the existence of any of the above interpolating systems of solutions and that it is also equivalent to a certain factorization representation of the operator. The results in this paper unify the corresponding theories of disconjugacy for nth order linear ordinary differential equations and for nth order linear difference …

Bifurcations In Steady State Solutions Of A Class Of Nonlinear Dispersive Wave Equation, Paul Eloe, Muhammad Usman

Paul W. Eloe

We consider the damped externally excited KdV and BBM equations and use an asymptotic perturbation method to analyze the stability of solutions. We consider the primary resonance by defining the detuning parameter. External-excitation and frequency-response curves are shown to exhibit jump and hysteresis phenomena (dis-continuous transitions between two stable solutions) for both KdV and BBM equations.

Soil Denitrification Fluxes From Three Northeastern North American Forests Across A Range Of Nitrogen Deposition, Jennifer Morse, Jorge Durán, Fred Beall, Eric Enanga, Irena Creed, Ivan Fernandez, Peter Groffman

Ivan J. Fernandez

In northern forests, large amounts of missing N that dominate N balances at scales ranging from small watersheds to large regional drainage basins may be related to N-gas production by soil microbes. We measured denitrification rates in forest soils in northeastern North America along a N deposition gradient to determine whether N-gas fluxes were a significant fate for atmospheric N inputs and whether denitrification rates were correlated with N availability, soil O2 status, or forest type. We quantified N2 and N2O fluxes in the laboratory with an intact-core method and monitored soil O2, temperature and moisture in three forests differing …

Maine's Climate Future: An Initial Assessment, George Jacobson, Ivan Fernandez, Paul Mayewski, Catherine Schmitt

Ivan J. Fernandez

Earth’s atmosphere is experiencing unprecedented changes that are modifying global climate. Discussions continue around the world, the nation, and in Maine on how to reduce and eventually eliminate emissions of carbon dioxide (CO2), other greenhouse gases, and other pollutants to the atmosphere, land, and oceans. These efforts are vitally important and urgent. However, even if a coordinated response succeeds in eliminating excess greenhouse gas emissions by the end of the century, something that appears highly unlikely today, climate change will continue, because the elevated levels of CO2 can persist in the atmosphere for thousands of years to come.

In late …

Tb134: A Laboratory Study To Assess Methods For Predicting Ph Change Of Ash Amended Forest Soils, Yvonne Unger, Ivan Fernandez

Ivan J. Fernandez

The objective of this study was to compare several commonly used lime requirement tests and soil capacity factors for their ability to predict pH change following wood-ash amendment. The ability to predict pH change is important because it is one of the criteria used to prescribe rates of ash amendment to forest soils.

Tb164: Precipitation Chemistry At The Greenville, Maine, Nadp/Ntn Station, Ivan Fernandez, Llew Wortman

Ivan J. Fernandez

This report details results from the Greenville, Maine, NADP/NTN site supported by the Maine Agricultural and Forest Experiment Station. The site is located in Piscataquis County at 69°39'52" longitude and 45°29'23" latitude at approximately 322 m elevation. The site consists of a single Aerochem Metrics® Automatic Sensing Wet/Dry Precipitation Collector that provides samples for chemical analysis and a Belfort® Recording Rain Gage and Event Recorder for accurate determinations of precipitation volume. Samples are collected every Tuesday morning 52 weeks a year.

Identifying Key Variables And Interactions In Statistical Models Of Building Energy Consumption Using Regularization, David Hsu

David Hsu

Statistical models can only be as good as the data put into them. Data about energy consumption continues to grow, particularly its non-technical aspects, but these variables are often interpreted differently among disciplines, datasets, and contexts. Selecting key variables and interactions is therefore an important step in achieving more accurate predictions, better interpretation, and identification of key subgroups for further analysis.

This paper therefore makes two main contributions to the modeling and analysis of energy consumption of buildings. First, it introduces regularization, also known as penalized regression, for principled selection of variables and interactions. Second, this approach is demonstrated by …

A New Undergraduate Curriculum On Mathematical Biology At University Of Dayton, Muhammad Usman, Amit Singh

Muhammad Usman

The beginning of modern science is marked by efforts of pioneers to understand the natural world using a quantitative approach. As Galileo wrote, "the book of nature is written in the language of mathematics". The traditional undergraduate course curriculum is heavily focused on individual disciplines like biology, physics, chemistry, mathematics rather than interdisciplinary courses. This fragmented teaching of sciences in majority of universities leave biology outside the quantitative and mathematical approaches. The landscape of biomedical science has transformed dramatically with advances in high throughput experimental approaches, which led to the huge amount of data. The best possible approach to generate …