Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

NMR measurements of a large set of protein backbone one-bond dipolar couplings have been carried out to refine the structure of the third IgG-binding domain of Protein G (GB3), previously solved by X-ray crystallography at a resolution of 1.1 A. Besides the commonly used bicelle, poly(ethylene glycol), and filamentous phage liquid crystalline media, dipolar couplings were also measured when the protein was aligned inside either positively or negatively charged stretched acrylamide gels. Refinement of the GB3 crystal structure against the (13)C(alpha)-(13)C' and (13)C'-(15)N dipolar couplings improves the agreement between experimental and predicted (15)N-(1)H(N) as well as (13)C(alpha)-(1)H(alpha) dipolar couplings. Evaluation of the peptide bond N-H orientations shows a weak anticorrelation between the deviation of the peptide bond torsion angle omega from 180 degrees and the angle between the N-H vector and the C'-N-C(alpha) plane. The slope of this correlation is -1, indicating that, on average, pyramidalization of the peptide N contributes to small deviations from peptide bond planarity ( = 179.3 +/- 3.1 degrees ) to the same degree as true twisting around the C'-N bond. Although hydrogens are commonly built onto crystal structures assuming the N-H vector orientation falls on the line bisecting the C'-N-C(alpha) angle, a better approximation adjusts the C(alpha)-C'-N-H torsion angle to -2 degrees. The (15)N-(1)H(N) dipolar data do not contradict the commonly accepted motional model where angular fluctuations of the N-H bond orthogonal to the peptide plane are larger than in-plane motions, but the amplitude of angular fluctuations orthogonal the C(alpha)(i-1)-N(i)-C(alpha)(i) plane exceeds that of in-plane motions by at most 10-15 degrees. Dipolar coupling analysis indicates that for most of the GB3 backbone, the amide order parameters, S, are highly homogeneous and vary by less than +/-7%. Evaluation of the H(alpha) proton positions indicates that the average C(alpha)-H(alpha) vector orientation deviates by less than 1 degrees from the direction that makes ideal tetrahedral angles with the C(alpha)-C(beta) and C(alpha)-N vectors.     

Structural determination of neutral O-linked oligosaccharide alditols by negative ion LC-electrospray-MS<Superscript>n</Superscript>.

Neutral O-linked oligosaccharides released from the salivary mucin MUC5B were separated and detected by negative ion LC-MS and LC-MS(2). The resolution of the chromatography and the information obtained from collision induced dissociation of detected [M - H](-) ions were usually sufficient to identify the sequence of individual oligosaccharides, illustrated by the fact that 50 different oligosaccharides ranging from disaccharides to nonasaccharides could be assigned from the sample. Fragmentation was shown to yield mostly reducing end sequence fragments (Z(i) and Y(i)), enabling primary sequence assignment. Specific fragmentation pathways or patterns were also detected giving specific linkage information. The reducing end core (Gal/GlcNAcbeta1-3GalNAcol or Gal/GlcNAcbeta1-3(GlcNAcbeta1-6)GalNAcol) could be deduced from the pronounced glycosidic C-3 cleavage and A(i) type cleavages of the reducing end GalNAcol, together with the non reducing end fragment from the loss of a single substituted GalNAcol. Substitution patterns on GlcNAc residues were also found, indicative for C-4 substitution ((0,2)A(i) - H(2)O cleavage) and disubstitution of C-3 and C-4 (Z(i)/Z(i) cleavages). This kind of fragmentation can be used for assigning the mode of chain elongation (Galbeta1-3/4GlcNAcbeta1-) and identification of Lewis type antigens like Lewis a/x and Lewis b/y on O-linked oligosaccharides. In essence, negative ion LC-MS(2) was able to generate extensive data for understanding the overall glycosylation pattern of a sample, especially when only a limited amount of material is available.     

Phytochromes with noncovalently bound chromophores: the ability of apophytochromes to direct tetrapyrrole photoisomerization

Chromophore-apoprotein interactions were studied with recombinant apoproteins, oat phytochrome (phyA) and CphB of the cyanobacterium Calothrix PCC7601, which were both incubated with the bilin compounds biliverdin (BV) IXalpha, phycocyanobilin (PCB) and the 3'-methoxy derivative of PCB. Previously it was shown that CphB and its homolog in Calothrix, CphA, show strong sequence similarities with each other and with the phytochromes of higher and lower plants, despite the fact that CphB carries a leucine instead of a cysteine at the chromophore attachment position and thus holds the chromophore only noncovalently. CphA binds tetrapyrrole chromophores in a covalent, phytochrome-like manner. For both eyanobacterial phytochromes, red and far-red light-induced photochemistry has been reported. Thus, the role of the binding site of CphB in directing the photochemistry of noncovalently bound tetrapyrroles was analyzed in comparison with the apoprotein from phyA phytochrome. Both the aforementioned compounds, which were used as chromophores, are not able to form covalent bonds with a phytochrome-type apoprotein because of their chemical structure (vinyl group at position 3 or methoxy group at position 3'). The BV adducts of both apoproteins showed phytochrome-like photochemistry (formation of red and far-red-absorbing forms of phytochrome [P(r) and P(fr) forms]). However, incubation of the oat apophytochrome with BV primarily yields a 700 nm form from which the P(r)-P(fr) photochemistry can be initiated and to which the system relaxes in the dark after illumination. The results for CphB were compared with a CphB mutant where the chromophore-binding cysteine had been introduced, which, upon incubation with PCB, shows spectral properties nearly identical with its (covalently binding) CphA homolog. A comparison of the spectral properties (P(r) and P(fr) forms) of all the PCB- and BV-containing chromoproteins reveals that the binding site of the cyanobacterial apoprotein is better suited than the plant (oat) phytochrome to noncovalently incorporate the chromophore and to regulate its photochemistry. Our findings support the proposal that the recently identified phytochrome-like prokaryotic photoreceptors, which do not contain a covalently bound chromophore, may trigger a light-induced physiological response.     

New structures in the bi­pyridine–copper(II) nitrate–methanol system: [(bpy)2Cu(NO3)]NO3·CH3OH and [(bpy)2Cu(NO3)]NO3

Reaction of 2,2′‐bi­pyridine (bpy) and copper(II) nitrate in methanol results in two complexes, namely light‐blue bis(2,2′‐bi­pyridine)­nitrato­copper(II) nitrate methanol solvate, [Cu(NO₃)(C₁₀H₈N₂)₂]NO₃·CH₃OH, (I), which is unstable in air, and the product of its decomposition, catena‐poly­[[[bis(2,2′‐bi­pyridine)copper(II)]‐μ‐nitrato‐O:O′] nitrate], {[Cu(NO₃)(C₁₀H₈N₂)₂]NO₃}_n, (II). The crystal structures of both compounds were determined from one crystal at room temperature. Later, the structure of (I) was redetermined at low temperature. In (I) and (II), the Cu atom is coordinated by two bpy and one or two nitrate ions, respectively. The second nitrate ion in (I), along with the methanol solvent mol­ecule, is found in the outer coordination sphere, not bonded to Cu. The nitrate in (I) is chelating, while in (II), it bridges (bpy)₂Cu complexes, forming a one‐dimensional chain structure. The Cu cation in (II) lies on a twofold axis and the uncoordinated NO₃^? ion is located close to a twofold axis and is therefore disordered. Compound (I) converts into (II) upon loss of solvent.     

Elucidating the initial dynamics of electron photodetachment from atoms in liquids using variably-time-delayed resonant multiphoton ionization

We study the photodetachment of electrons from sodium anions in room temperature liquid tetrahydrofuran (THF) using a new type of three-pulse pump-probe spectroscopy. Our experiments use two variably-time-delayed pulses for excitation in what is essentially a resonant 1+1 two-photon ionization: By varying the arrival time of the second excitation pulse, we can directly observe how solvent motions stabilize and trap the excited electron prior to electron detachment. Moreover, by varying the arrival times of the ionization (excitation) and probe pulses, we also can determine the fate of the photoionized electrons and the distance they are ejected from their parent Na atoms. We find that as solvent reorganization proceeds, the second excitation pulse becomes less effective at achieving photoionization, and that the solvent motions that stabilize the excited electron following the first excitation pulse occur over a time of approximately 450 fs. We also find that there is no spectroscopic evidence for significant solvent relaxation after detachment of the electron is complete. In combination with the results of previous experiments and molecular dynamics simulations, the data provide new insight into the role of the solvent in solution-phase electron detachment and charge-transfer-to-solvent reactions.     

Temperature effects for isothermal polymer crystallization kinetics

We adopt the cluster size distribution model to investigate the effect of temperature on homogeneous nucleation and crystal growth for isothermal polymer crystallization. The model includes the temperature effects of interfacial energy, nucleation rate, growth and dissociation rate coefficients, and equilibrium solubility. The time dependencies of polymer concentration, number and size of crystals, and crystallinity (in Avrami plots) are presented for different temperatures. The denucleation (Ostwald ripening effect) is also investigated by comparing moment and numerical solutions of the population balance equations. Agreement between the model results and temperature-sensitive experimental measurements for different polymer systems required strong temperature dependence for the crystal-melt interfacial energy.     

Application of relaxation periods during electrodialysis of a casein solution: Impact on anion-exchange membrane fouling

Electrodialysis (ED) is a membrane process used on a large scale. However, one of the common problems is fouling of ion-exchange membranes stacked in the cell. The use of pulsed power, consisting in applying a constant current density during a fixed time of application (T_on) followed by a pause duration (T_off), was demonstrated recently as an effective fouling mitigation method for electrodialysis. Up until now, no work has investigated the potential of electrodialysis using pulsed electric field on protein fouling. The aim of the present work was to study the influence of pulsed electric field (PEF) with a low frequency square shaped periodic signal (T_on = 10 s–T_off = 10 s, T_on = 10 s–T_off = 40 s) in comparison with dc current during electrodialysis of a casein solution at different current densities (10, 20 and 30 mA/cm²) on membrane fouling. It appeared from these results that PEF, under certain conditions of pulse, would avoid fouling on anion-exchange membranes. For 10 s–40 s pulsed electric field conditions, no fouling was observed with any density, while for 10 s–10 s PEF conditions, fouling appeared only at current density over 10 mA/cm². dc current, whatever the current density conditions, led to a fouling on the diluate side of the AEM. Furthermore, when fouling occurred, magnitude layer thickness and dry weight increased with the applied current density. The nature of the fouling was identified as 97% protein. The protein fouling would be due to the dissociation of water molecules and/or heat increase at the anion-exchange membrane interface. The relaxation time of the pulse would limit both phenomena on the membrane.     

Electrospun Nanofibrous Adsorption Membranes for Wastewater Treatment: Mechanical Strength Enhancement

Functional nanofibrous membranes fabricated by electrospinning technology have attracted much attention in the removal of heavy metal ions from contaminated wastewater. The high specific surface area, high porosity and ease of functionality create an enhanced throughput and high adsorption capacity of the nanofibrous membrane. However, the relatively poor mechanical properties of the membrane with a non-woven nanofibrous structure are one of the major concerns, which can limit the applications in wastewater treatment. Different strategies and methodologies were explored to address the problems and were reviewed in this work, highlighting the possibilities of overcoming the poor mechanical properties of the nanofibrous membrane and to ensure the recyclability and reusability of the membrane during the adsorption process.     

Screening an In-House Isoquinoline Alkaloids Library for New Blockers of Voltage-Gated Na+ Channels Using Voltage Sensor Fluorescent Probes: Hits and Biases

Voltage-gated Na⁺ (Na_V) channels are significant therapeutic targets for the treatment of cardiac and neurological disorders, thus promoting the search for novel Na_V channel ligands. With the objective of discovering new blockers of Na_V channel ligands, we screened an In-House vegetal alkaloid library using fluorescence cell-based assays. We screened 62 isoquinoline alkaloids (IA) for their ability to decrease the FRET signal of voltage sensor probes (VSP), which were induced by the activation of Na_V channels with batrachotoxin (BTX) in GH3b6 cells. This led to the selection of five IA: liriodenine, oxostephanine, thalmiculine, protopine, and bebeerine, inhibiting the BTX-induced VSP signal with micromolar IC₅₀. These five alkaloids were then assayed using the Na⁺ fluorescent probe ANG-2 and the patch-clamp technique. Only oxostephanine and liriodenine were able to inhibit the BTX-induced ANG-2 signal in HEK293-hNa_V1.3 cells. Indeed, liriodenine and oxostephanine decreased the effects of BTX on Na⁺ currents elicited by the hNa_V1.3 channel, suggesting that conformation change induced by BTX binding could induce a bias in fluorescent assays. However, among the five IA selected in the VSP assay, only bebeerine exhibited strong inhibitory effects against Na⁺ currents elicited by the hNav1.2 and hNav1.6 channels, with IC₅₀ values below 10 µM. So far, bebeerine is the first BBIQ to have been reported to block Na_V channels, with promising therapeutical applications.     

Strengthening the Connection between Science,Society and Environment to Develop Future French and European Bioeconomies: Cutting-Edge Research of VAALBIO Team at UCCS

The development of the future French and European bioeconomies will involve developing new green chemical processes in which catalytic transformations are key. The VAALBIO team (valorization of alkanes and biomass) of the UCCS laboratory (Unité de Catalyse et Chimie du Solide) are working on various catalytic processes, either developing new catalysts and/or designing the whole catalytic processes. Our research is focused on both the fundamental and applied aspects of the processes. Through this review paper, we demonstrate the main topics developed by our team focusing mostly on oxygen- and hydrogen-related processes as well as on green hydrogen production and hybrid catalysis. The social impacts of the bioeconomy are also discussed applying the concept of the institutional compass.