Comparison of different approaches to derive classical bonded force-field parameters for a transition metal cofactor: a case study for non-heme iron site of ectoine synthase

Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase

Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.

Molecular Dynamics Simulations for the Michaelis Complex of Ectoine Synthase (EctC)

Ectoine is a chemical chaperone synthesised and used by bacteria to defend against osmotic stress. Although it has already gained attention from the pharmaceutical and cosmetic industries, thanks to its hydrating and cell-protecting properties, the reaction mechanism of its final synthesis step is still not fully understood. The ultimate step of ectoine biosynthesis is catalysed by the ectoine synthase enzyme (EctC), which requires an iron ion for substrate binding and overall enzymatic activity. Even though a crystal structure for Paenibacillus lautus EctC—substrate complex is available (PDB: 5ONN), it is not very informative with respect to the geometry of the active site because: (1) the crystal was obtained at a pH value far from the enzyme’s pH optimum, (2) the electron density at the Fe position is weak, and (3) the Fe-ligand distances are too long. To fill this gap, in this work we have used classical molecular dynamics simulations to model the enzyme-substrate (N-gamma-acetyl-L-2,4-diaminobutyric acid) complex of Paenibacillus lautus EctC (PlEctC). Since PlEctC is a homodimeric protein, MD simulations were carried out for a dimer with various plausible occupancies by the substrate and for two plausible coordination geometries around the catalytic Fe ion: tetrahedral and octahedral. MD results revealed that the presence of the ligand has a stabilising effect on the protein structure, most notably on a short helix 112–118, which flanks the entrance to the active site. The most important amino acids for substrate binding are Trp21, Arg25, Asn38, Thr40, and Tyr52, which were also identified in the crystal structure. Importantly, the substrate can easily adopt a conformation suitable for the progress of the catalytic reaction, and it does so spontaneously for the octahedral 6-coordinate geometry of the iron cofactor or with a low energy penalty (ca. 3 kcal/mol) in the case of 4-coordinate tetrahedral geometry. Simulations for different substrate occupancy states did not reveal any signs of cooperativity between the two monomers.

Comprehensive Study of the Ammonium Sulfamate-Urea Binary System

The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate-urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and theoretical (DFT, QTAIM, ELF, RDG, ADMP, etc.) techniques. It is shown that, at a temperature of 100 °C, the system under study remains thermally and chemically stable for up to 30 min. It was established using X-ray diffraction analysis that the heating time barely affects the X-ray characteristics of the system. Data on the aggregate states in specified temperature ranges were obtained with thermal analysis and determination of the melting point. The structures of the ammonium sulfamate-urea system with different component ratios were optimized within the density functional theory. The atom-centered density matrix propagation calculation of the ammonium sulfamate-urea system with different component ratios was performed at temperatures of 100, 300, and 500 K. Regardless of the component ratio, a regular increase in the potential energy variation (curve amplitude) with an increase in temperature from 100 to 500 K was found.

Microsolvation of lithium cation in xenon clusters: An octahedral growth pattern

The structural and energetic proprieties for the Li ⁺ Xe_n (n = 1-18) clusters are investigated using both Basin-Hopping combined with Potential Model description (BH-PM) and DFT methods. A structural transition from tetrahedral (4 coordination) form to octahedral (6 coordination) one is observed for n = 6. Above this size, all structures have an octahedral core. The cubic-face-centered arrangement for xenon atoms is detected for Li ⁺ Xe₁₄. To the best of our knowledge, the Li ⁺ Xe_n (n = 1-18) clusters are studied in the present work for the first time using the DFT theoretical approach. The M062X functional combined with aug-cc-pVDZ (for Li) and def2-TZVP (for Xe) basis sets reproduces accurately the CCSD(T) potential energy curve of Li + Xe system. Atom-Centered Density Matrix Propagation (ADMP) molecular dynamic calculations have been carried. Moreover, we investigate the larger sizes n = 31-35, 44, and 55 for the first time using the BH-PM theoretical approach. The closing of the first and second octahedron shells are proved for the n = 6 and 34 sizes, respectively. The relative stabilities of the Li ⁺ Xe_n molecules are also studied by computing the total energy, the binding energy per atoms for each size n. Then, the second energy difference between the size n and its two near neighbors allows identifying the magic number series. Our present data are analyzed, discussed and compared with the available theoretical and experimental data.