Structural explanation for the tunable substrate specificity of an <Emphasis Type="Italic">E. coli</Emphasis> nucleoside hydrolase: insights from molecular dynamics simulations

Parasitic protozoa rely on nucleoside hydrolases that play key roles in the purine salvage pathway by catalyzing the hydrolytic cleavage of the N-glycosidic bond that connects nucleobases to ribose sugars. Cytidine–uridine nucleoside hydrolase (CU–NH) is generally specific toward pyrimidine nucleosides; however, previous work has shown that replacing two active site residues with Tyr, specifically the Thr223Tyr and Gln227Tyr mutations, allows CU–NH to process inosine. The current study uses molecular dynamics (MD) simulations to gain atomic-level insight into the activity of wild-type and mutant E. coli CU–NH toward inosine. By examining systems that differ in the identity and protonation states of active site catalytic residues, key enzyme-substrate interactions that dictate the substrate specificity of CU–NH are identified. Regardless of the wild-type or mutant CU–NH considered, our calculations suggest that inosine binding is facilitated by interactions of the ribose moiety with active site residues and Ca²⁺, and π-interactions between two His residues (His82 and His239) and the nucleobase. However, the lack of observed activity toward inosine for wild-type CU–NH is explained by no residue being correctly aligned to stabilize the departing nucleobase. In contrast, a hydrogen-bonding network between hypoxanthine and a newly identified general acid (Asp15) is present when the two Tyr mutations are engineered into the active site. Investigation of the single CU–NH mutants reveals that this hydrogen-bonding network is only maintained when both Tyr mutations are present due to a π-interaction between the residues. These results rationalize previous experiments that show the single Tyr mutants are unable to efficiently hydrolyze inosine and explain how the Tyr residues work synergistically in the double mutant to stabilize the nucleobase leaving group during hydrolysis. Overall, our simulations provide a structural explanation for the substrate specificity of nucleoside hydrolases, which may be used to rationally develop new treatments for kinetoplastid diseases.

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A Banach space-valued ergodic theorem and the uniform approximation of the integrated density of states

In this paper we consider bounded operators on infinite graphs, in particular Cayley graphs of amenable groups. The operators satisfy an equivariance condition which is formulated in terms of a colouring of the vertex set of the underlying graph. In this setting it is natural to expect that the integrated density of states (IDS), or spectral distribution function, exists. We show that it can be defined as the uniform limit of approximants associated to finite matrices. The proof is based on a Banach space valued ergodic theorem which even allows explicit convergence estimates. Our result applies to a variety of group structures and colouring types, in particular to periodic operators and percolation-type Hamiltonians.     

Quantitative analysis of erythropoietin in human plasma by tandem mass spectrometry

The extended use of protein drugs in therapeutics has created the need for their quantification in human plasma. A methodology using the therapeutic protein itself as internal standard for quantitative analysis by multiple reaction monitoring (MRM) has been designed and applied to epoetin beta, a recombinant human erythropoietin (rhEPO). After depletion of major proteins, plasma samples were desalted and enriched in rhEPO by reversed phase liquid chromatography prior to tryptic cleavage. Differential isotopic labeling of peptides was performed by derivatization with 2-methoxy-4,5-dehydro-imidazole. A light version (four hydrogen atoms) of this reagent was used for plasma peptides. Tryptic peptides obtained from pure rhEPO were derivatized with a heavy version (four deuterium atoms) of the same reagent and used as internal standards. Two rhEPO tryptic peptides with three MRM transitions per peptide were selected for quantification. This strategy provided a quantification limit close to 50 amol of epoetin beta per microliter of plasma (equivalent to 1.7 ng/mL), i.e., well below the expected therapeutic concentrations in plasma (around 100–500 amol/μL).     

Selenium speciation in anaerobic granular sludge

Chromatographic (IC-CD, GC-FID) and spectroscopic (XRD) techniques that allow the specific determination of several selenium species present or formed during bioremediation processes of selenate contaminated drinking, ground, or wastewaters have been established. The developed techniques are shown to be applicable in determining selenium species in the range of target concentrations for emissions and are thus appropriate to characterize bioremediation processes. The applied techniques offer advantages regarding short analytical times without loss of satisfactory accurateness towards more sophisticated methods. By means of IC-CD, selenate and selenite can be detected specifically to concentrations far below allowance levels for metal finishing industries (20?µg?L^?1 selenate, 40?µg?L^?1 selenite) within 16.0?min. Thus, the removal of selenate from the liquid phase by anaerobic granular sludge was quantified by IC-CD, and the concomitantly formed red precipitates were analysed by XRD. Hexagonal elemental selenium was found to be present in the XRD analysis. Even if the precipitate contained iron and zinc, as shown by ICP-OES, no iron- or zinc-containing selenium minerals were detected by XRD. The GC-FID method described determines dimethylselenide and dimethyldiselenide at a detection limit of 1?ng and 2?ng, respectively, without further chemical derivatization within 7.4?min. Thus, the GC-FID offers adequate detection of two major volatile organic selenium species potentially formed during bioremediation of selenium contaminated waters.     

Ultra-sensitive magnetometry based on free precession of nuclear spins

We discuss the design and performance of a very sensitive low-field magnetometer based on the detection of free spin precession of gaseous, nuclear polarized ³He or ¹²⁹Xe samples with a SQUID as magnetic flux detector. The device will be employed to control fluctuating magnetic fields and gradients in a new experiment searching for a permanent electric dipole moment of the neutron. Furthermore, with the detection of the free precession of co-located ³He/¹²⁹Xe nuclear spins it can be used as ultra-sensitive probe for non-magnetic spin interactions, since the magnetic dipole interaction (Zeeman-term) drops out. Characteristic spin precession times T₂ ^* of up to 60 h were measured. The achieved signal-to-noise ratio of more than 5000:1 leads to an expected sensitivity level (Cramer-Rao lower bound) of δB≈1 fT after an integration time of 220 s and of δB≈10^-4 fT after one day. By means of a co-located ³He/¹²⁹Xe magnetometer, noise sources inherent in the magnetometer could be investigated, showing that CRLB is fulfilled, at least down to δB≈10^-2 fT. The reason for such a high sensitivity is that free precessing ³He (¹²⁹Xe) nuclear spins are almost completely decoupled from the environment. Therefore, this type of magnetometer is particularly attractive for precision field measurements where long-term stability is required.     

Spin-pumping-enhanced magnetic damping in ultrathin Cu(0 0 1)/Co/Cu and Cu(0 0 1)/Ni/Cu films

The influence of the Cu capping layer thickness on the spin pumping effect in ultrathin epitaxial Co and Ni films on Cu(0 0 1) was investigated by in situ ultrahigh vacuum ferromagnetic resonance. A pronounced increase in the linewidth is observed at the onset of spin pumping for capping layer thicknesses d_Cu larger than 5 ML, saturating at d_Cu = 20 ML for both systems. The spin mixing conductance for Co/Cu and Ni/Cu interfaces was evaluated.     

ChemInform Abstract: Two Structure Types Based on Si6O15 Rings: Synthesis and Structural and Spectroscopic Characterization of Cs1.86K1.14DySi6O15 and Cs1.6K1.4SmSi6O15.

Single crystals of Cs_1.86K_1.14DySi₆O₁₅ (I) and Cs_1.6K_1.4SmSi₆O₁₅ (II) are grown by reaction of SmF₃ or Dy₂O₃, DyF₃, SiO₂, K₂CO₃, and Cs₂CO₃ in a MoO₃ or MoO₃/RbF flux (Pt crucible, 950 °C, 3—6 h; controlled cooling).     

Copolymerization of β-butyrolactone and β-benzyl malolactone with aluminoxane catalysts

Poly (β-hydroxylbutyrate-co-benzyl β-malolactonate), (P-HB-co-BML) copolymers, were prepared by the ring-opening copolymerizations of β-butyrolactone (BL) and benzyl β-malolactone (BML) with several alkyl aluminoxane catalysts, including ethylaluminoxane (EAO), methylaluminoxane (MAO), and isobutylaluminoxane (IBAO). The copolymers had very broad molecular weight distributions with weight average molecular weights, M̄_w, greater than 200,000. The products were fractionated by solubility into acetone-soluble and insoluble copolymers. The former were random, atactic copolymers while the latter were stereoblock copolymers. Random, atactic copolyesters of these two monomers were also obtained with the diethylzinc-water, ZnEt₂-H₂O (0.6:1), and the (5,10,15,20-tetraphenylporphinato)aluminium chloride, TPPAlCl, catalysts. The copolymerization reactions with the latter two catalysts gave much higher yields (up to 98%) and better control of both the copolymer compositions and the molecular weight distributions, but these copolymers had M̄_w values of only 20,000 or less. The copolymer tacticities and comonomer sequences were determined by ¹³C NMR spectroscopy.