Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

Enzymatic transformations of macromolecular substrates such as DNA repair enzyme/DNA transformations are commonly interpreted primarily by active-site functional-group chemistry that ignores their extensive interfaces. Yet human uracil–DNA glycosylase (UDG), an archetypical enzyme that initiates DNA base-excision repair, efficiently excises the damaged base uracil resulting from cytosine deamination even when active-site functional groups are deleted by mutagenesis. The 1.8-Å resolution substrate analogue and 2.0-Å resolution cleaved product cocrystal structures of UDG bound to double-stranded DNA suggest enzyme–DNA substrate-binding energy from the macromolecular interface is funneled into catalytic power at the active site. The architecturally stabilized closing of UDG enforces distortions of the uracil and deoxyribose in the flipped-out nucleotide substrate that are relieved by glycosylic bond cleavage in the product complex. This experimentally defined substrate stereochemistry implies the enzyme alters the orientation of three orthogonal electron orbitals to favor electron transpositions for glycosylic bond cleavage. By revealing the coupling of this anomeric effect to a delocalization of the glycosylic bond electrons into the uracil aromatic system, this structurally implicated mechanism resolves apparent paradoxes concerning the transpositions of electrons among orthogonal orbitals and the retention of catalytic efficiency despite mutational removal of active-site functional groups. These UDG/DNA structures and their implied dissociative excision chemistry suggest biology favors a chemistry for base-excision repair initiation that optimizes pathway coordination by product binding to avoid the release of cytotoxic and mutagenic intermediates. Similar excision chemistry may apply to other biological reaction pathways requiring the coordination of complex multistep chemical transformations.

The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis

The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ΔpKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ΔpKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo substantially larger increases in nonaqueous media than aqueous solutions as the charge density on the donor or acceptor atom increases. These results support a general mechanism for enzymatic catalysis, in which hydrogen bonding to a substrate is strengthened as charge rearranges in going from the ground state to the transition state; the strengthening of the hydrogen bond would be greater in a nonaqueous enzymatic active site than in water, thus providing a rate enhancement for an enzymatic reaction relative to the solution reaction. We suggest that binding energy of an enzyme is used to fix the substrate in the low-dielectric active site, where the strengthening of the hydrogen bond in the course of a reaction is increased.

A host–guest system to study structure–function relationships of membrane fusion peptides

We designed a host–guest fusion peptide system, which is completely soluble in water and has a high affinity for biological and lipid model membranes. The guest sequences are those of the fusion peptides of influenza hemagglutinin, which are solubilized by a highly charged unstructured C-terminal host sequence. These peptides partition to the surface of negatively charged liposomes or erythrocytes and elicit membrane fusion or hemolysis. They undergo a conformational change from random coil to an obliquely inserted (≈33° from the surface) α-helix on binding to model membranes. Partition coefficients for membrane insertion were measured for influenza fusion peptides of increasing lengths (n = 8, 13, 16, and 20). The hydrophobic contribution to the free energy of binding of the 20-residue fusion peptide at pH 5.0 is −7.6 kcal/mol (1 cal = 4.18 J). This energy is sufficient to stabilize a “stalk” intermediate if a typical number of fusion peptides assemble at the site of membrane fusion. The fusion activity of the fusion peptides increases with each increment in length, and this increase strictly correlates with the hydrophobic binding energy and the angle of insertion.

The evolution and masses of the neutron star and donor star in the high mass X-ray binary OAO 1657−415

We report near-infrared radial velocity (RV) measurements of the recently identified donor star in the high mass X-ray binary (HMXB) system OAO 1657−415 obtained in the H band using ISAAC on the Very Large Telescope. Cross-correlation methods were employed to construct a RV curve with a semi-amplitude of 22.1 ± 3.5 km s−1. Combined with other measured parameters of this system it provides a dynamically determined neutron star (NS) mass of 1.42 ± 0.26 M⊙ and a mass of 14.3 ± 0.8 M⊙ for the Ofpe/WN9 highly evolved donor star. OAO 1657−415 is an eclipsing HMXB pulsar with the largest eccentricity and orbital period of any within its class. Of the 10 known eclipsing X-ray binary pulsars OAO 1657−415 becomes the ninth with a dynamically determined NS mass solution and only the second in an eccentric system. Furthermore, the donor star in OAO 1657−415 is much more highly evolved than the majority of the supergiant donors in other HMXBs, joining a small but growing list of HMXBs donors with extensive hydrogen depleted atmospheres. Considering the evolutionary development of OAO 1657−415, we have estimated the binding energy of the envelope of the mass donor and find that there is insufficient energy for the removal of the donor’s envelope via spiral-in, ruling out a common envelope evolutionary scenario. With its non-zero eccentricity and relatively large orbital period the identification of a definitive evolutionary pathway for OAO 1657−415 remains problematic, we conclude by proposing two scenarios which may account for OAO 1657−415 current orbital configuration.

Dynamical properties of a strongly correlated model for quarter-filled layered organic molecular crystals

The dynamical properties of an extended Hubbard model, which is relevant to quarter-filled layered organic molecular crystals, are analyzed. We have computed the dynamical charge correlation function, spectral density, and optical conductivity using Lanczos diagonalization and large-N techniques. As the ratio of the nearest-neighbor Coulomb repulsion, V, to the hopping integral, t, increases there is a transition from a metallic phase to a charge-ordered phase. Dynamical properties close to the ordering transition are found to differ from the ones expected in a conventional metal. Large-N calculations display an enhancement of spectral weight at low frequencies as the system is driven closer to the charge-ordering transition in agreement with Lanczos calculations. As V is increased the charge correlation function displays a collective mode which, for wave vectors close to (pi,pi), increases in amplitude and softens as the charge-ordering transition is approached. We propose that inelastic x-ray scattering be used to detect this mode. Large-N calculations predict superconductivity with d(xy) symmetry close to the ordering transition. We find that this is consistent with Lanczos diagonalization calculations, on lattices of 20 sites, which find that the binding energy of two holes becomes negative close to the charge-ordering transition.

Comparative study of hydrogen storage in Li- and K-doped carbon materials - theoretically revisited

Hydrogen adsorption in alkali-doped carbon materials is investigated theoretically. Our calculations show that hydrogen molecules can be physically adsorbed on alkali-doped graphite at 0 K but such an adsorption is thermodynamically unfavourable. The binding energy of hydrogen adsorption decreases significantly with the increase in temperature and becomes nearly zero at ambient temperature. We suggest that it may be unlikely to observe any hydrogen uptake in alkali-doped carbon materials at or above ambient temperature in the TGA (thermogravimetric) system, the previously reported hydrogen uptake in alkali-doped carbon materials was caused by either uncyclable chemisorbed hydrogen on the defects of carbon (defects were produced by repeated heat treatment) and/or moisture adsorption. (C) 2004 Elsevier Ltd. All rights reserved.

Coherent molecular bound states of bosons and fermions near a Feshback resonance

We analyze molecular bound states of atomic quantum gases near a Feshbach resonance. A simple, renormalizable field theoretic model is shown to have exact solutions in the two-body sector, whose binding energy agrees well with observed experimental results in both Bosonic and Fermionic cases. These solutions, which interpolate between BEC and BCS theories, also provide a more general variational ansatz for resonant superfluidity and related problems.

XPS study of the major minerals in bauxite: Gibbsite, bayerite and (pseudo-)boehmite

Synthetic corundum (Al2O3), gibbsite (Al(OH)(3)), bayerite (Al(OH)(3)), boehmite (AlO(OH)) and pseudoboehmite (AlO(OH)) have been studied by high resolution XPS. The chemical compositions based on the XPS survey scans were in good agreement with the expected composition. High resolution A12p scans showed no significant changes in binding energy, with all values between 73.9 and 74.4 eV. Only bayerite showed two transitions, associated with the presence of amorphous material in the sample. More information about the chemical and crystallographic environment was obtained from the 0 Is high resolution spectra. Here a clear distinction could be made between oxygen in the crystal structure, hydroxyl groups and adsorbed water. Oxygen in the crystal structure was characterised by a binding energy of about 530.6 eV in all minerals. Hydroxyl groups, present either in the crystal structure or on the surface, exhibited binding energies around 531.9 eV, while water on the surface showed binding energies around 533.0 eV. A distinction could be made between boehmite and pseudoboehmite based on the slightly lower ratio of oxygen to hydroxyl groups and water in pseudoboehmite. (c) 2005 Elsevier Inc. All rights reserved.

Electrostatically mediated specific adsorption of small molecules in metallo-organic frameworks

We investigate the interaction of ethylene and ethane with a Cu-tricarboxylate complex and show that at low loadings the lighter molecule has a higher binding energy as a result of an increased interaction with the framework Cu and stronger hydrogen bonding with the basic framework oxygens. This leads to selective adsorption of ethylene by a factor of about 2 at low pressure, which is overcome by the stronger van der Waals interaction of ethane at high loadings, explaining recent literature data. The results suggest the possibility of separation of light hydrocarbons at low pressures or in trace amounts.

Pluronic F127-modified liposome-containing tacrolimus-cyclodextrin inclusion complexes:improved solubility, cellular uptake and intestinal penetration

Objective The aim of this study was to investigate Pluronic F127-modified liposome-containing cyclodextrin (CD) inclusion complex (FLIC) for improving the solubility, cellular uptake and intestinal penetration of tacrolimus (FK 506) in the gastrointestinal (GI) tract. Methods Molecular modelling was performed to screen the optimal CD for the solubilization of FK 506. FLIC was prepared by thin-lipid film hydration with the inclusion complex solutions followed by membrane extrusion. Dilution tests were conducted in simulated gastric fluids and phosphate-buffered solution of sodium taurocholate to investigate the solubility improvement of FK506. The cellular uptake of nanocarriers was studied in Caco-2 cells, and intestinal mucous membrane penetration in the GI tract was evaluated in Sprague-Dawley rats. Key findings The results showed that β-CD had the strongest binding energy with the guest molecule among the CDs. The prepared FLIC has an average diameter of 180.8 ± 8.1 nm with a spherical shape. The solubility and cellular uptake of FK 506 was greatly improved by the incorporation of CD complexes in the Pluronic F127-modified liposomes. Intestinal mucous membrane penetration was also significantly improved by the preparation of FLIC. Conclusion With improved drug solubility and intestinal mucous membrane penetration, FLIC shows a promising oral delivery system for FK 506. © 2013 Royal Pharmaceutical Society.

Metastable de-excitation spectroscopy and density functional theory study of the selective oxidation of crotyl alcohol over Pd(111)

The extremely surface sensitive technique of metastable de-excitation spectroscopy (MDS) has been utilized to probe the bonding and reactivity of crotyl alcohol over Pd(111) and provide insight into the selective oxidation pathway to crotonaldehyde. Auger de-excitation (AD) of metastable He (23S) atoms reveals distinct features associated with the molecular orbitals of the adsorbed alcohol, corresponding to emission from the hydrocarbon skeleton, the O n nonbonding, and C═C π states. The O n and C═C π states of the alcohol are reversed when compared to those of the aldehyde. Density functional theory (DFT) calculations of the alcohol show that an adsorption mode with both C═C and O bonds aligned somewhat parallel to the surface is energetically favored at a substrate temperature below 200 K. Density of states calculations for such configurations are in excellent agreement with experimental MDS measurements. MDS revealed oxidative dehydrogenation of crotyl alcohol to crotonaldehyde between 200 and 250 K, resulting in small peak shifts to higher binding energy. Intramolecular changes lead to the opposite assignment of the first two MOs in the alcohol versus the aldehyde, in accordance with DFT and UPS studies of the free molecules. Subsequent crotonaldehyde decarbonylation and associated propylidyne formation above 260 K could also be identified by MDS and complementary theoretical calculations as the origin of deactivation and selectivity loss. Combining MDS and DFT in this way represents a novel approach to elucidating surface catalyzed reaction pathways associated with a “real-world” practical chemical transformation, namely the selective oxidation of alcohols to aldehydes.

Fast x-ray spectroscopy study of ethene on clean and SO4 precovered Pt{111}

The adsorption and decomposition of ethylene over a Pt{111} single crystalsurface has been investigated by fast x-ray spectroscopy. At 100 K ethene displays precursor-mediated adsorption kinetics, adopting a single environment with a saturation C2H4 coverage of 0.25 ML and binding energy of 283.2 eV. Thermal decomposition proceeds above 240 K via dehydrogenation to ethylidyne with an activation barrier of 57±3 kJ mol−1 and preexponential factor ν=1×1010±0.5 s−1. Site-blocking by preadsorbed SO4 reduces the saturation ethene coverage but induces a new, less reactive π-bonded ethene species centered around 283.9 eV, which in turn decomposes to ethylidyne at 350 K.

Computational modeling of biodegradable starch based polymer composites

Purpose. The goal of this study is to improve the favorable molecular interactions between starch and PPC by addition of grafting monomers MA and ROM as compatibilizers, which would advance the mechanical properties of starch/PPC composites. ^ Methodology. DFT and semi-empirical methods based calculations were performed on three systems: (a) starch/PPC, (b) starch/PPC-MA, and (c) starch-ROM/PPC. Theoretical computations involved the determination of optimal geometries, binding-energies and vibrational frequencies of the blended polymers. ^ Findings. Calculations performed on five starch/PPC composites revealed hydrogen bond formation as the driving force behind stable composite formation, also confirmed by the negative relative energies of the composites indicating the existence of binding forces between the constituent co-polymers. The interaction between starch and PPC is also confirmed by the computed decrease in stretching CO and OH group frequencies participating in hydrogen bond formation, which agree qualitatively with the experimental values. ^ A three-step mechanism of grafting MA on PPC was proposed to improve the compatibility of PPC with starch. Nine types of 'blends' produced by covalent bond formation between starch and MA-grafted PPC were found to be energetically stable, with blends involving MA grafted at the 'B' and 'C' positions of PPC indicating a binding-energy increase of 6.8 and 6.2 kcal/mol, respectively, as compared to the non-grafted starch/PPC composites. A similar increase in binding-energies was also observed for three types of 'composites' formed by hydrogen bond formation between starch and MA-grafted PPC. ^ Next, grafting of ROM on starch and subsequent blend formation with PPC was studied. All four types of blends formed by the reaction of ROM-grafted starch with PPC were found to be more energetically stable as compared to the starch/PPC composite and starch/PPC-MA composites and blends. A blend of PPC and ROM grafted at the ' a&d12; ' position on amylose exhibited a maximal increase of 17.1 kcal/mol as compared with the starch/PPC-MA blend. ^ Conclusions. ROM was found to be a more effective compatibilizer in improving the favorable interactions between starch and PPC as compared to MA. The ' a&d12; ' position was found to be the most favorable attachment point of ROM to amylose for stable blend formation with PPC.^

Modelagem molecular voltada para a construção de um nanobiossensor para detecção do herbicida Imazaquin

In this study, our goal was develop and describe a molecular model of the enzyme-inhibiting interaction which can be used for an optimized projection of a Microscope Force Atomic nanobiosensor to detect pesticides molecules, used in agriculture, to evaluate its accordance with limit levels stipulated in valid legislation for its use. The studied herbicide (imazaquin) is a typical member of imidazolinone family and is an inhibitor of the enzymatic activity of Acetohydroxiacid Synthase (AHAS) enzyme that is responsible for the first step of pathway for the synthesis of side-chains in amino acids. The analysis of this enzyme property in the presence of its cofactors was made to obtain structural information and charge distribution of the molecular surface to evaluate its capacity of became immobilized on the Microscopy Atomic Force tip. The computational simulation of the system, using Molecular Dynamics, was possible with the force-field parameters for the cofactor and the herbicides obtained by the online tool SwissParam and it was implemented in force-field CHARMM27, used by software GROMACS; then appropriated simulations were made to validate the new parameters. The molecular orientation of the AHAS was defined based on electrostatic map and the availability of the herbicide in the active site. Steered Molecular Dynamics (SMD) Simulations, followed by quantum mechanics calculations for more representative frames, according to the sequential QM/MM methodology, in a specific direction of extraction of the herbicide from the active site. Therefore, external harmonic forces were applied with similar force constants of AFM cantilever for to simulate herbicide detection experiments by the proposed nanobiosensor. Force value of 1391 pN and binding energy of -14048.52 kJ mol-1 were calculated.

The Flotation of Niobium Oxide Minerals from Carbonatite Ores

Global niobium production is presently dominated by three operations, Araxá and Catalão (Brazil), and Niobec (Canada). Although Brazil accounts for over 90% of the world’s niobium production, a number of high grade niobium deposits exist worldwide. The advancement of these deposits depends largely on the development of operable beneficiation flowsheets. Pyrochlore, as the primary niobium mineral, is typically upgraded by flotation with amine collectors at acidic pH following a complicated flowsheet with significant losses of niobium. This research compares the typical two stage flotation flowsheet to a direct flotation process (i.e. elimination of gangue pre-flotation) with the objective of circuit simplification. In addition, the use of a chelating reagent (benzohydroxamic acid, BHA) was studied as an alternative collector for fine grained, highly disseminated pyrochlore. For the amine based reagent system, results showed that while comparable at the laboratory scale, when scaled up to the pilot level the direct flotation process suffered from circuit instability because of high quantities of dissolved calcium in the process water due to stream recirculation and fine calcite dissolution, which ultimately depressed pyrochlore. This scale up issue was not observed in pilot plant operation of the two stage flotation process as a portion of the highly reactive carbonate minerals was removed prior to acid addition. A statistical model was developed for batch flotation using BHA on carbonatite ore (0.25% Nb2O5) that could not be effectively upgraded using the conventional amine reagent scheme. Results showed that it was possible to produce a concentrate containing 1.54% Nb2O5 with 93% Nb recovery in ~15% of the original mass. Fundamental studies undertaken included FT-IR and XPS, which showed the adsorption of both the protonized amine and the neutral amine onto the surface of the pyrochlore (possibly at niobium sites as indicated by detected shifts in the Nb3d binding energy). The results suggest that the preferential flotation of pyrochlore over quartz with amines at low pH levels can be attributed to a difference in critical hemimicelle concentration (CHC) values for the two minerals. BHA was found to be absorbed on pyrochlore surfaces by a similar mechanism to alkyl hydroxamic acid. It is hoped that this work will assist in improving operability of existing pyrochlore flotation circuits and help promote the development of niobium deposits globally. Future studies should focus on investigation into specific gangue mineral depressants and inadvertent activation phenomenon related to BHA flotation of gangue minerals.