Multi‐material incompressible flow simulation using the moment‐of‐fluid method

This paper compares the numerical performance of the moment‐of‐fluid (MOF) interface reconstruction technique with Youngs, LVIRA, power diagram (PD), and Swartz interface reconstruction techniques in the context of a volume‐of‐fluid (VOF) based finite element projection method for the numerical simulation of variable‐density incompressible viscous flows. In pure advection tests with multiple materials MOF shows dramatic improvements in accuracy compared with the other methods. In incompressible flows where density differences determine the flow evolution, all the methods perform similarly for two material flows on structured grids. On unstructured grids, the second‐order MOF, LVIRA, and Swartz methods perform similarly and show improvement over the first‐order Youngs' and PD methods. For flow simulations with more than two materials, MOF shows increased accuracy in interface positions on coarse meshes. In most cases, the convergence and accuracy of the computed flow solution was not strongly affected by interface reconstruction method. Published in 2009 by John Wiley & Sons, Ltd.     

Structural and mechanistic studies on γ-butyrobetaine hydroxylase

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Highlights? Crystal structure of γ-butyrobetaine hydroxylase in complex with substrate and inhibitor ? N-terminal Zn-binding domain involved in dimerization ? The clinically used inhibitor, THP, is also a substrate for BBOX ? BBOX catalyzed rearrangement reaction     

Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases.     

Studies on ternary metallo-β lactamase-inhibitor complexes using electrospray ionization mass spectrometry

Metallo-beta-lactamases (MBLs) are targets for medicinal chemistry as they mediate bacterial resistance to beta-lactam antibiotics. Electrospray-ionization mass spectrometry (ESI-MS) was used to study the inhibition by a set of mercaptocarboxylates of two representative MBLs with different optimal metal stoichiometries for catalysis. BcII is a dizinc MBL (Class B1), whilst the CphA MBL (Class B2) exhibits highest activity with a single zinc ion in the active site. Experimental parameters for the detection of the metallo-enzyme and the metallo-enzyme-inhibitor complexes were evaluated and optimized. Following investigations on the stoichiometry of metal binding, the affinity of the inhibitors was investigated by measuring the relative abundance of the complex compared to the metalloprotein. The results for the BcII enzyme were in general agreement with solution assays and demonstrated that the inhibitors bind to the dizinc form of the BcII enzyme. The results for the CphA(ZnII) complex unexpectedly revealed an increased affinity for the binding of a second metal ion in the presence of thiomandelic acid. The results demonstrate that direct ESI-MS analysis of enzyme:inhibitor complexes is a viable method for screening inhibitors and for the rapid assay of the enzyme:metal:inhibitor ratios.     

Monitoring Conformational Changes in the NDM‐1 Metallo‐β‐lactamase by 19F NMR Spectroscopy

The New Delhi metallo‐β‐lactamase (NDM‐1) is involved in the emerging antibiotic resistance problem. Development of metallo‐β‐lactamases (MBLs) inhibitors has proven challenging, due to their conformational flexibility. Here we report site‐selective labeling of NDM‐1 with 1,1,1‐trifluoro‐3‐bromo acetone (BFA), and its use to study binding events and conformational changes upon ligand–metal binding using ¹⁹F NMR spectroscopy. The results demonstrate different modes of binding of known NDM‐1 inhibitors, including L ‐ and D ‐captopril by monitoring the changing chemical environment of the active‐site loop of NDM‐1. The method described will be applicable to other MBLs and more generally to monitoring ligand‐induced conformational changes.     

Photoactivable peptides for identifying enzyme-substrate and protein-protein interactions

Photoactivated cross-linking of peptides to proteins is a useful strategy for identifying enzyme-substrate and protein-protein interactions in cell lysates as demonstrated by studies on the human hypoxia inducible factor system.     

Structural and biochemical analyses reveal how ornithine acetyl transferase binds acidic and basic amino acid substrates

Structural and biochemical analyses reveal how ornithine acetyl-transferases catalyse the reversible transfer of an acetyl-group from a basic (ornithine) to an acidic (glutamate) amino acid by employing a common mechanism involving an acetyl-enzyme intermediate but using different side chain binding modes.