Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics

Asparagine glycosylation is one of the most common and important post-translational modifications of proteins in eukaryotic cells. N-glycosylation occurs when a triantennary glycan precursor is transferred en bloc to a nascent polypeptide (harboring the N-X-T/S sequon) as the peptide is cotranslationally translocated into the endoplasmic reticulum (ER). In addition to facilitating binding interactions with components of the ER proteostasis network, N-glycans can also have intrinsic effects on protein folding by directly altering the folding energy landscape. Previous work from our laboratories (Hanson et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 109, 3131-3136; Shental-Bechor, D.; Levy, Y. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261) suggested that the three sugar residues closest to the protein are sufficient for accelerating protein folding and stabilizing the resulting structure in vitro; even a monosaccharide can have a dramatic effect. The highly conserved nature of these three proximal sugars in N-glycans led us to speculate that introducing an N-glycosylation site into a protein that is not normally glycosylated would stabilize the protein and increase its folding rate in a manner that does not depend on the presence of specific stabilizing protein-saccharide interactions. Here, we test this hypothesis experimentally and computationally by incorporating an N-linked GlcNAc residue at various positions within the Pin WW domain, a small β-sheet-rich protein. The results show that an increased folding rate and enhanced thermodynamic stability are not general, context-independent consequences of N-glycosylation. Comparison between computational predictions and experimental observations suggests that generic glycan-based excluded volume effects are responsible for the destabilizing effect of glycosylation at highly structured positions. However, this reasoning does not adequately explain the observed destabilizing effect of glycosylation within flexible loops. Our data are consistent with the hypothesis that specific, evolved protein-glycan contacts must also play an important role in mediating the beneficial energetic effects on protein folding that glycosylation can confer.     

Behaviour of palladium(II), platinum(IV), and rhodium(III) in artificial and natural waters: influence of reactor surface and geochemistry on metal recovery

The recovery of dissolved platinum group elements (PGE: Pd(II), Pt(IV) and Rh(III)) added to Milli-Q^® water, artificial freshwater and seawater and filtered natural waters has been studied, as a function of pH and PGE concentration, in containers of varying synthetic composition. The least adsorptive and/or precipitative loss was obtained for borosilicate glass under most of the conditions employed, whereas the greatest loss was obtained for low-density polyethylene. Of the polymeric materials tested, the adsorptive and/or precipitative loss of PGE was lowest for fluorinated ethylene propylene (Teflon^®). The loss of Pd(II) in freshwater was significant due to its affinity for surface adsorption and its relatively low solubility. The presence of natural dissolved organic matter increases the recovery of Pd(II) but enhances the loss of Pt(IV). The loss of Rh(III) in seawater was significant and was mainly due to precipitation, whereas Pd(II) recovery was enhanced, compared to freshwater, because of its complexation with chloride. The results have important implications regarding protocols employed for sample preservation and controlled laboratory experiments used in the study of the speciation and biogeochemical behaviour of PGE.     

InspIRED by Nature: NADPH‐Dependent Imine Reductases (IREDs) as Catalysts for the Preparation of Chiral Amines

Imine reductases (IREDs) are NADPH‐dependent oxidoreductases that catalyse the asymmetric reduction of cyclic prochiral imines to amines, with excellent stereoselectivity. Since their discovery, stereocomplementary IREDs have been applied to the production of both (S) and (R) cyclic secondary amines, and the expansion in gene sequences recently identified has hinted at new substrate ranges that extend into acyclic imines and even suggest the possibility of asymmetric reductive amination from suitable ketone and amine precursors. Structural studies of various IREDs are beginning to reveal the complexities inherent in determining substrate range, stereoselectivity and mechanism in these enzymes, which represent a valuable emerging addition to the toolbox of available biocatalysts for chiral amine production.     

Translational diffusion constants of the amino acids: measurement by NMR and their use in modeling the transport of peptides

In this work, the translational self-diffusion constants, DT's, of 12 amino acids (Ala, Arg, Asn, Asp, Cys, Glu, His, Ile, Lys, Met, Phe, and Ser) are measured by field gradient NMR and extrapolated to infinite dilution. The experiments were carried out in D2O at 298 K at pD approximately =3.5 in 50 mM sodium phosphate buffer. Of these 12 amino acids, 6 are being reported for the first time (Asp, Cys, Glu, His, Lys, and Met) and the remaining 6 (Ala, Arg, Asn, Ile, Phe, and Ser) are compared with DT's from the literature. When corrected for differences in solvent viscosity and temperature, the discrepancy between DT's measured in the present work and those reported previously is always <8%, which is reasonable given the range of values reported previously by different groups. With the present work, DT's for all of the amino acids are now available. These diffusion constants are then used in modeling studies of the diffusion and free solution electrophoretic mobility, mu, of several model peptides. For this set of peptides, it is shown that modeling using revised input parameters results in improved agreement between model and experimental mobilities.     

Total phenol analysis of weakly supported water using a laccase-based microband biosensor

The monitoring of phenolic compounds in wastewaters in a simple manner is of great importance for environmental control. Here, a novel screen printed laccase-based microband array for in situ, total phenol estimation in wastewaters and for water quality monitoring without additional sample pre-treatment is presented. Numerical simulations using the finite element method were utilized for the characterization of micro-scale graphite electrodes. Anodization followed by covalent modification was used for the electrode functionalization with laccase. The functionalization efficiency and the electrochemical performance in direct and catechol-mediated oxygen reduction were studied at the microband laccase electrodes and compared with macro-scale electrode structures. The reduction of the dimensions of the enzyme biosensor, when used under optimized conditions, led to a significant improvement in its analytical characteristics. The elaborated microsensor showed fast responses towards catechol additions to tap water – a weakly supported medium – characterized by a linear range from 0.2 to 10 μM, a sensitivity of 1.35 ± 0.4 A M⁻¹ cm⁻² and a dynamic range up to 43 μM. This enhanced laccase-based microsensor was used for water quality monitoring and its performance for total phenol analysis of wastewater samples from different stages of the cleaning process was compared to a standard method.     

On the solid state structure of 4-iodobenzoic acid

The solid-state structure of 4-iodobenzoic acid has been confirmed by variable temperature X-ray diffraction, variable temperature solid-state NMR and differential scanning calorimetry. 4-iodobenzoic acid crystallizes in the space group P2(1)/n, and dimerizes in the solid state about a center of inversion. Using extensive X-ray crystallographic data collections, the placement of the carboxylate H atoms from the residual electron density in difference Fourier maps was determined. The position of the electron density associated with the proton is found to vary with temperature in that the population of the disordered sites changes with varying temperature. Determination of the crystal structure between the temperatures of 248 and 198 K was not possible due to a phase transition, an endothermic event occurring at 230.77 K. The phase transition is also indicated by a change in the relaxation time of the ring carbon atoms in the solid-state NMR data. Though the dominating force in the dimeric unit in the solid state is the presence of strong hydrogen bonds, there are also van der Waals forces present between the iodine atoms. In the layered structure, the iodine-iodine distance is within the van der Waals contact radii, an interaction which causes a deformation in the electron density of the iodine atoms.     

New cobalt(II) and zinc(II) coordination frameworks incorporating a pyridyl-pyrazole ditopic ligand

The metal-directed assembly of new molecular frameworks incorporating 4-(4-pyridyl)pyrazole (L), containing non-linear coordination vectors, is presented. Three metallo-arrays of types [Co(LH)2(NO3)4], [Co(LH)2(H2O)4][NO3]4.H2O and [Zn2(L-H)2Cl2].2EtOH are reported. The cobalt(II) in [Co(LH)2(NO3)4] displays distorted octahedral geometry, with the two protonated pyridyl-pyrazole ligands coordinated through their pyrazole nitrogen atoms in a trans-orientation; the remaining four coordination sites are occupied by nitrate anions. Two internal hydrogen bonds occur between each pyrazole NH and the oxygens of adjacent coordinated nitrato ligands. Short intermolecular hydrogen bonds also occur between the two pyridinium hydrogens and bound nitrate ligands on different molecules to yield a two-dimensional hydrogen-bonded array. Two of these arrays interpenetrate to form an extended two dimensional layer; such layers stack throughout the crystal structure. A second product of type [Co(LH)2(H2O)4][NO3]4.H2O exists as two crystallographically independent, but chemically similar, forms. In each form, the two protonated pyridyl-pyrazole ligands occupy trans positions about the cobalt, with the remaining four coordination sites being filled by water molecules to yield a distorted octahedral coordination geometry. Intramolecular hydrogen-bonding is observed between the two non-coordinated pyrazoyl nitrogen atoms and bound water oxygen atoms. The third complex, [Zn2(L-H)2Cl2].2EtOH, contains dimer units consisting of two zinc(II) ions bridged by two pyrazoylate groups in which the coordination geometry of each zinc approximates a tetrahedron. Each zinc is bound to two deprotonated pyridine-pyrazole ligands (L-H), one pyridyl group (from a different dimeric unit) and one chloro ligand. Each pyridyl nitrogen thus connects each of these zinc dimers to an adjacent dimer unit, forming a three-dimensional network containing small voids. The latter are occupied by ethanol molecules which form hydrogen bonds to the chloro ligands.     

Towards the development of multisensor for drugs of abuse based on molecular imprinted polymers

The synthetic receptors for cocaine, deoxyephedrine, methadone and morphine were computationally designed and produced using molecular imprinting. The structure and energy of the molecular complexes were analysed by computational techniques. The possible structures of the binding sites in the synthetic receptors have been compared with those of corresponding natural receptors. The composition of imprinted polymers was optimised to allow adequate performance under the same experimental conditions. All selected molecular imprinting polymers (MIPs) demonstrated stronger affinity in comparison with corresponding blank polymers resulting in imprinted factors (I) equal to 1.2 (cocaine), 2.5 (deoxyephedrine), 3.5 (methadone) and 3 (morphine) which suggested that the specific binding site for each molecule was successfully created. The polymers studied possessed good selectivity and affinity towards their templates and could be recommended for the integration with sensor devices. From a practical point of view, especially for multisensor requirements, the synthetic receptors based on imprinted polymers could be superior to natural receptors due to their stability, robustness and compatibility with automation processes required for sensor fabrication.