Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T_m = 73.5 °C; ΔT_m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.

Illustration of cooperative thermostabilization effects of the double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site.     

Enzymatic in-capillary derivatization for glucose determination by electrophoresis with spectrophotometric detection

The following paper compares several procedures of in-capillary bienzymatic derivatization with regard to glucose determination with the use of glucose oxidase and horseradish peroxidase. The procedures discussed below include continuous contact in the capillary, plug-plug injection, and sequential injection with incubation in the capillary inlet. The reaction of hydrogen peroxide catalyzed by peroxidase was performed using two different substrates. The best results were achieved for nicotinamide adenine dinucleotide, reduced disodium salt (NADH) acting both as a chromogenic reagent and a substrate for peroxidase, while the method employed was sequential injection and incubation at the capillary inlet. The LOD was estimated to be 25 nM with a linear response up to 0.1 microM.     

An engine breaking the ΩEP-property

We present a construction which shows that some special continua do not have the nonwandering-eventually-periodic property. The construction applies e.g. to the topologist's sin curve and to the harmonic fan.     

129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity,dynamics, and explicit solvent

The isotropic ¹²⁹Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C₆₀ dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the ¹²⁹Xe NMR CS. The ¹²⁹Xe shielding constant was obtained by averaging the ¹²⁹Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C₆₀ system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit–Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C₆₀ system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated ¹²⁹Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental ¹²⁹Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of ¹²⁹Xe NMR parameters in different Xe atom guest–host systems. © 2013 Wiley Periodicals, Inc.     

Microsolvation of the [Ni(acac)(tmen)]+ complex

Microsolvation of the [Ni(acac)(tmen)]⁺ complex by a series of aliphatic n-alcohols (Solv) has been studied in ClCH₂CH₂Cl solutions by spectrophotometry. Based on the changes in the electronic spectrum of the afore-mentioned complex, observed under the influence of any alcohol, the equilibrium constants for the formation of the [Ni(acac)(tmen)Solv]⁺ and [Ni(acac)(tmen)Solv₂]⁺ species have been computed according to the algorithm presented in this work. It was found that, in all the systems studied, the stability of five-coordinated [Ni(acac)(tmen)Solv]⁺ is higher than that of octahedral [Ni(acac)(tmen)Solv₂]⁺. The resulting values are discussed in terms of the Lewis basicity of alcohols.     

Modification of Polylactide Nonwovens with Carbon Nanotubes and Ladder Poly(silsesquioxane)

Electrospun nonwovens of poly(L-lactide) (PLLA) modified with multiwall carbon nanotubes (MWCNT) and linear ladder-like poly(silsesquioxane) with methoxycarbonyl side groups (LPSQ-COOMe) were obtained. MWCNT and LPSQ-COOMe were added to the polymer solution before the electrospinning. In addition, nonwovens of PLLA grafted to modified MWCNT were electrospun. All modified nonwovens exhibited higher tensile strength than the neat PLA nonwoven. The addition of 10 wt.% of LPSQ-COOMe and 0.1 wt.% of MWCNT to PLLA increased the tensile strength of the nonwovens 2.4 times, improving also the elongation at the maximum stress.     

Heteroclinic solutions for a class of the second order Hamiltonian systems

We shall be concerned with the existence of heteroclinic orbits for the second order Hamiltonian system , where q∈Rn and V∈C¹(R×Rn,R), V?0. We will assume that V and a certain subset M⊂Rn satisfy the following conditions. M is a set of isolated points and #M?2. For every sufficiently small ε>0 there exists δ>0 such that for all (t,z)∈R×Rn, if d(z,M)?ε then −V(t,z)?δ. The integrals , z∈M, are equi-bounded and −V(t,z)→∞, as |t|→∞, uniformly on compact subsets of Rn?M. Our result states that each point in M is joined to another point in M by a solution of our system.     

Synthesis,spectroscopic and structural characterisation of vanadium(IV) and oxovanadium(IV) complexes with arsenic donor ligands

The reaction of o-C₆H₄(AsMe₂)₂ with VCl₄ in anhydrous CCl₄ produces orange eight-coordinate [VCl₄{o-C₆H₄(AsMe₂)₂}₂], whilst in CH₂Cl₂ the product is the brown, six-coordinate [VCl₄{o-C₆H₄(AsMe₂)₂}]. In dilute CH₂Cl₂ solution slow decomposition occurs to form the V^III complex [V₂Cl₆{o-C₆H₄(AsMe₂)₂}₂]. Six-coordination is also found in [VCl₄{MeC(CH₂AsMe₂)₃}] and [VCl₄{Et₃As)₂]. Hydrolysis of these complexes occurs readily to form vanadyl (VO²⁺) species, pure samples of which are obtained by reaction of [VOCl₂(thf)₂(H₂O)] with the arsines to form green [VOCl₂{o-C₆H₄(AsMe₂)₂}], [VOCl₂{MeC(CH₂AsMe₂)₃}(H₂O)] and [VOCl₂(Et₃As)₂]. Green [VOCl₂(o-C₆H₄(PMe₂)₂}] is formed from [VOCl₂(thf)₂(H₂O)] and the ligand. The [VOCl₂{o-C₆H₄(PMe₂)₂}] decomposes in thf solution open to air to form the diphosphine dioxide complex [VO{o-C₆H₄(P(O)Me₂)₂}₂(H₂O)]Cl₂, but in contrast, the products formed from similar treatment of [VCl₄{o-C₆H₄(AsMe₂)₂}_x] or [VOCl₂{o-C₆H₄(AsMe₂)₂}] contain the novel arsenic(V) cation [o-C₆H₄(AsMe₂Cl)(μ-O)(AsMe₂)]⁺. X-ray crystal structures are reported for [V₂Cl₆{o-C₆H₄(AsMe₂)₂}₂], [VO(H₂O){o-C₆H₄(P(O)Me₂)₂}₂]Cl₂, [o-C₆H₄(AsMe₂Cl)(μ-O)(AsMe₂)]Cl·[VO(H₂O)₃Cl₂] and powder neutron diffraction data for [VCl₄{o-C₆H₄(AsMe₂)₂}₂].     

Origin of the magnetic field induced changes of the transverse plasma mode in the c-axis infrared response of underdoped YBa2Cu3O(7-δ)

We report on results of our theoretical study of magnetic field induced changes of the c-axis infrared response of bilayer cuprate superconductors using the phenomenological multilayer model involving the conductivity of the spacing layers and that of the bilayer units. For H perpendicular to the planes, the local conductivities have been expressed in terms of a two-fluid approximation--as weighted averages of the superconducting state ones and the normal state ones representing contributions of the vortex cores, the weight of the latter increasing linearly with the field. This allows us to reproduce and interpret the fast decrease with increasing H of the well known 400 cm(-1) peak (transverse plasma mode) in the c-axis conductivity, observed by LaForge and co-workers. For the local conductivities of underdoped YBa(2)Cu(3)O(7-δ) with T(c)=58 K reported by Dubroka and co-workers and the fraction of the normal state (T ≈ T(c)) component given by (μ(0)H/25 T), the computed field induced changes of the reflectivity are in quantitative agreement with the data. This suggests that the response at H=0 and T ≈ T(c) is close to that at H=25 T < H(c2) and T ? T(c), in accord with theories attributing the above T(c) state to that of a superconductor lacking long-range phase coherence. Also discussed are changes of the response induced by H parallel to the CuO(2) planes.     

Photoinitiation by radical-cationic mechanism in the polymerization of isobutylene with lewis acids

ESR spectra of Lewis acids (VCl₄, TiCl₄, TiBr₄, SnCl₄, and AlBr₃) and their mixtures with isobutylene were investigated in a n-heptane solution in the dark and under irradiation at 400–480 nm at ?80 to ?150°C. A signal was observed only upon irradiating mixtures of VCl₄, TiCl₄, or TiBr₄ and isobutylene. The signal was identified as an isobutylene radical-cation by comparison with a simulated spectrum. A signal indicating the presence of peroxy radicals were recorded in measurements carried out in the presence of oxygen; these radicals originated from reaction of the isobutylene radical-cation with oxygen. Radical-cation initiation by visible light is indicated by the polymerization of isobutylene by VCl₄, TiCl₄, and TiBr₄ and by ESR spectra. The inhibiting effect of oxygen in photochemically initiated polymerization of isobutylene was also elucidated.