Combining gel and capillary electrophoresis, nano-LC and mass spectrometry for the elucidation of post-translational modifications of Trichoderma reesei cellobiohydrolase I

N-Glycosylation of cellobiohydrolase I from the fungus Trichoderma reesei (strain Rut-C30) is studied using a combination of electrophoretic, chromatographic and mass spectrometric techniques. As four potential N-glycosylation sites and several uncharged and phosphorylated high-mannose glycans are present, a large number of glycoforms and phospho-isoforms can be expected. Isoelectric focusing both in gel and in capillary format was successfully applied for the separation of the phospho-isoforms. They were extracted in their intact form from the gel and subsequently analysed by nanospray-Q-TOF-MS, thereby making use of a powerful two-dimensional technique. Nano-LC/MS/MS on a Q-Trap MS further allowed the determination of the glycosylation sites. As a novel approach, an oxonium ion was used in precursor ion scanning for selective detection of glycopeptides containing phosphorylated high-mannose glycans.     

Superbeads: immobilization in "sweet" chemistry

Enzymatic oligosaccharide synthesis using recombinant glycosyltransferases is able to overcome the difficulties associated with chemical methods. Nonetheless, sugar nucleotide regeneration cycles are necessary for the glycosylation. The multistep enzyme reaction can be efficiently carried out on superbeads that are prepared by immobilizing multienzyme mixtures on bead support through fused binding domains.     

Dünnschicht-Chromatographie höherer Fettsäuren

Zusammenfassung Die Dünnschichtchromatographie von Fettsäuren wurde mit der Papierchromatographie solcher Säuren hinsichtlich ihrer Trennwirkung verglichen. Ein Verfahren zur quantitativen Bestimmung auf Dünn-schichten getrennter Fettsäuren wurde ausgearbeitet.

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Summary The thin layer chromatography of fatty acids was compared with the paper chromatography of such acids with respect to their separation. A method was worked out for the quantitative determination of fatty acids separated on thin layers.

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Résumé On compare la chromatographie en couche mince des acides gras avec celle sur papier, du point de vue de leur pouvoir de séparation. On a mis au point un procédé de dosage quantitatif des acides gras séparés sur couches minces.

     

Magnetic-Field-Orientation Dependent Thermal Entanglement of a Spin-1 Heisenberg Dimer: The Case Study of Dinuclear Nickel Complex with an Uniaxial Single-Ion Anisotropy

The bipartite entanglement in pure and mixed states of a quantum spin-1 Heisenberg dimer with exchange and uniaxial single-ion anisotropies is quantified through the negativity in a presence of the external magnetic field. At zero temperature the negativity shows a marked stepwise dependence on a magnetic field with two abrupt jumps and plateaus, which can be attributed to the quantum antiferromagnetic and quantum ferrimagnetic ground states. The magnetic-field-driven phase transition between the quantum antiferromagnetic and quantum ferrimagnetic ground states manifests itself at nonzero temperatures by a local minimum of the negativity, which is followed by a peculiar field-induced rise of the negativity observable in a range of moderately strong magnetic fields. The rising temperature generally smears out abrupt jumps and plateaus of the negativity, which cannot be distinguished in the relevant dependencies above a certain temperature. It is shown that the thermal entanglement is most persistent against rising temperature at the magnetic field, for which an energy gap between a ground state and a first excited state is highest. Besides, temperature variations of the negativity of the spin-1 Heisenberg dimer with an easy-axis single-ion anisotropy may exhibit a singular point-kink, at which the negativity has discontinuity in its first derivative. The homodinuclear nickel complex [Ni2(Medpt)2(μ-ox)(H2O)2](ClO4)2·2H2O provides a suitable experimental platform of the antiferromagnetic spin-1 Heisenberg dimer, which allowed us to estimate a strength of the bipartite entanglement between two exchange-coupled Ni2+ magnetic ions on the grounds of the interaction constants reported previously from the fitting procedure of the magnetization data. It is verified that the negativity of this dinuclear compound is highly magnetic-field-orientation dependent due to presence of a relatively strong uniaxial single-ion anisotropy.     

Large configuration interaction calculations of nuclear spin-spin coupling constants: III. Vibrational effects in ammonia

Large configuration interaction calculations of the proton—proton coupling constant for several geometrical configurations of the ammonia molecules are reported. The analytical expressions for the energy surface and the coupling constant as functions of two cartesian displacement coordinates are fitted to the calculated values. The potential is used for the calculation of the vibrational wavefunctions for ¹⁵NH₃ and ¹⁵ND₃ species and the vibrational averaging of the coupling constant is carried out using these functions. Though the value of the coupling constants shows a very strong geometry dependence, the vibrational corrections are found to be small. A possible correlation of the proton—proton coupling constant with an angular parameter in the NH₂ group in RNH₂ compounds is indicated.     

Hamiltonian replica exchange molecular dynamics using soft-core interactions

To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25 ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1 ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8 ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].     

Characterization of oxidation progress by chemiluminescence: A study of polyethylene with pro-oxidant additives

Non-isothermal chemiluminescence measurements in nitrogen and isothermal measurements in oxygen were used for the evaluation of degradation in pre-oxidized polyethylene either pure or containing Mn-based pro-oxidant additives. The results were compared with infrared spectroscopy data. Chemiluminescence measurements of pure polyethylene and polyethylene with additive made it possible to calculate the set of rate constants, based on the Bolland-Gee oxidation scheme. The oxidation rate constants of polyethylene with additive were significantly higher, while the activation energy of the process appeared lower (65 kJ mol⁻¹), than those of pure polyethylene. The method provides an access to study oxidation processes during the induction period of oxidation when infrared spectroscopy cannot provide sufficient information.     

MALDI-TOF/TOF de novo sequence analysis of 2-D PAGE-separated proteins from Halorhodospira halophila, a bacterium with unsequenced genome

Because protein identifications rely on matches with sequence databases, high-throughput proteomics is currently largely restricted to those species for which comprehensive sequence databases are available. The identification of proteins derived from organisms with unsequenced genomes mainly depends on homology searching. Here, we report the use of a simplified, gel-based, chemical derivatization strategy for de novo sequence analysis using a MALDI-TOF/TOF mass spectrometer. This approach allows the determination of de novo peptide sequences of up to 20 amino acid residues in length. The protocol was applied on a proteomic study of 2-D PAGE-separated proteins from Halorhodospira halophila, an extremophilic eubacterium with yet unsequenced genome. Using three different homology-based search algorithms, we were able to identify more than 30 proteins from this organism using subpicomole quantities of protein.