Thromboxane A2 G Protein-Coupled Receptor Production and Crystallization for Structure Studies

G protein-coupled receptors (GPCRs) play vital roles in human physiology and pathophysiology. This makes the elucidation of the high-resolution blueprints of these high value membrane proteins of crucial importance for the structure-based design of novel therapeutics. However, the production and crystallization of GPCRs for structure determination comes with many challenges.In this chapter, we provide a comprehensive protocol for expressing and purifying the thromboxane A₂ receptor (TPR), an attractive therapeutic target, for use in structure studies. Guidelines for crystallizing the TPR are also included. Together, these procedures provide a template for generating crystal structures of the TPR and indeed other GPCRs in complex with pharmacologically interesting ligands.

Substrate specificity of 2-deoxy-D-ribose 5-phosphate aldolase (DERA) assessed by different protein engineering and machine learning methods

In this work, deoxyribose-5-phosphate aldolase (Ec DERA, EC 4.1.2.4) from Escherichia coli was chosen as the protein engineering target for improving the substrate preference towards smaller, non-phosphorylated aldehyde donor substrates, in particular towards acetaldehyde. The initial broad set of mutations was directed to 24 amino acid positions in the active site or in the close vicinity, based on the 3D complex structure of the E. coli DERA wild-type aldolase. The specific activity of the DERA variants containing one to three amino acid mutations was characterised using three different substrates. A novel machine learning (ML) model utilising Gaussian processes and feature learning was applied for the 3rd mutagenesis round to predict new beneficial mutant combinations. This led to the most clear-cut (two- to threefold) improvement in acetaldehyde (C2) addition capability with the concomitant abolishment of the activity towards the natural donor molecule glyceraldehyde-3-phosphate (C3P) as well as the non-phosphorylated equivalent (C3). The Ec DERA variants were also tested on aldol reaction utilising formaldehyde (C1) as the donor. Ec DERA wild-type was shown to be able to carry out this reaction, and furthermore, some of the improved variants on acetaldehyde addition reaction turned out to have also improved activity on formaldehyde. KEY POINTS: • DERA aldolases are promiscuous enzymes. • Synthetic utility of DERA aldolase was improved by protein engineering approaches. • Machine learning methods aid the protein engineering of DERA.

Kinetic and equilibrium adsorption of two post-harvest fungicides onto copper-exchanged montmorillonite: synergic and antagonistic effects of both fungicides' presence

The simultaneous adsorption of both imazalil (IMZ) and thiabendazole (TBZ) fungicides in a Cu²⁺-exchanged Mt was studied in this work. Kinetic studies were used to determine the rate law which describes the adsorption of individual fungicides onto the adsorbent. Adsorption isotherm of individual and combined fungicides was done to evaluate synergic or antagonistic effects. The Mt-Cu material considerably improved TBZ and/or IMZ adsorption from aqueous suspensions with respect to raw Mt, leading to removal efficiencies higher than 99% after 10 min of contact time for TBZ and IMZ C_i = 15 and 40 mg/L, respectively, when a solid dosage = 1 g/L was used. The adsorption sites involved were determined by a combination of X-ray diffraction (XRD) determinations and electron paramagnetic resonance (EPR), indicating that fungicides were bonded to Cu²⁺ cations, while the rate limiting step was the formation of coordination bonds. The adsorption mechanism proposed is that of ligand exchange between water and fungicide molecules in the metal coordination sphere. The single-crystal structure for the IMZ-Cu²⁺ complex indicated that four molecules were bounded to the copper centers, while two molecules of TBZ are bounded to copper explaining the higher IMZ uptake capacity for the Mt-Cu material. Graphical abstract.

The phase transition of Pb8F14I2

Abstract

The reversible phase transition of Pb₈F₁₄I₂ is of continuous type and takes place at about 107 °C as monitored by temperature-dependent single crystal and powder X-ray diffraction measurements, optical microscopy, and differential scanning calorimetry. The low-temperature ferroelastic phase crystallizes in the orthorhombic crystal system (23 °C, Bmmb, Z = 2, a = 6.0699(6) Å, b = 6.0165(6) Å, c = 25.077(2) Å, 1487 structure factors, 41 parameter, R(F²) = 0.0346, wR(F²) = 0.0771) and changes its symmetry to the tetragonal crystal system into the high-temperature paraelastic phase (130 °C, I4/mmm, Z = 1, a = 4.2667(12) Å, c = 25.388(7) Å, 430 structure factors, 303 parameter, R(F²) = 0.0575, wR(F²) = 0.1564). Group–subgroup relationships between the two structures and a hypothetical intermediate structure are presented.

Graphical abstract

Probing crystal packing of uniformly (13)C-enriched powder samples using homonuclear dipolar coupling measurements

The relationship between the crystal packing of powder samples and long-range (13)C-(13)C homonuclear dipolar couplings is presented and illustrated for the case of uniformly (13)C-enriched L-alanine and L-histidine·HCl·H2O. Dipolar coupling measurement is based on the partial reintroduction of dipolar interactions by spinning the sample slightly off-magic-angle, while the coupling of interest for a given spin pair is isolated with a frequency-selective pulse. A cost function is used to correlate the so-derived dipolar couplings to trial crystal structures of the samples under study. This procedure allowed for the investigation of the l-alanine space group and L-histidine·HCl·H2O space group and unit-cell parameters.