A structural and catalytic model for zinc phosphoesterases

A structural model for the active site of phosphoesterases, enzymes that degrade organophosphate neurotoxins, has been synthesised. The ligand 2-((2-hydroxy-3-(((2-hydroxyethyl)(pyridin-2-ylmethyl)amino)methyl)-5-methylbenzyl)(pyridin-2-ylmethyl)amino)acetic acid (H(3)L1) and two Zn(ii) complexes have been prepared and characterised as and The ligand (H(3)L1) and complex were characterised through (1)H NMR, (13)C NMR, mass spectroscopy and microanalysis. The X-ray crystal structure of revealed a tetramer of dinuclear complexes, bridged by two phosphate molecules and bifurcating acetic acid arms. Functional studies of the zinc complex with the substrate bis(4-nitrophenyl)phosphate (bNPP) determined the complex with HL1(2-) to be a competent catalyst with k(cat) = 1.26 0.06 x 10(-6) s(-1)

Synthesis and characterization of the tetranuclear iron(III) complex of a new asymmetric multidentate ligand. A structural model for purple acid phosphatases

The ligand, 2-((2-hydroxy-5-methyl-3-((pyridin-2-ylmethylamino)methyl)benzyl)(2-hydroxybenzyl)amino)acetic acid (H(3)HPBA), which contains a donor atom set that mimics that of the active site of purple acid phosphatase is described. Reaction of H(3)HPBA with iron(III) or iron(II) salts results in formation of the tetranuclear complex, [Fe-4(HPBA)(2)(OAc)(2)(mu-O)(mu-OH)(OH2)(2)]ClO4 center dot 5H(2)O. X-Ray structural analysis reveals the cation consists of four iron(III) ions, two HPBA(3-) ligands, two bridging acetate ligands, a bridging oxide ion and a bridging hydroxide ion. Each binucleating HPBA(3-) ligand coordinates two structurally distinct hexacoordinate iron(III) ions. The two metal ions coordinated to a HPBA(3-) ligand are linked to the two iron(III) metal ions of a second, similar binuclear unit by intramolecular oxide and hydroxide bridging moieties to form a tetramer. The complex has been further characterised by elemental analysis, mass spectrometry, UV-vis and MCD spectroscopy, X- ray crystallography, magnetic susceptibility measurements and variable-temperature Mossbauer spectroscopy

Chaste : Cancer, Heart and Soft Tissue Environment

Funding: UK Engineering and Physical Sciences Research Council [grant number EP/N509711/1 (J.K.)].Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology (‘Cardiac Chaste’), discrete cell-based modelling of soft tissues (‘Cell-based Chaste’), and modelling of ventilation in lungs (‘Lung Chaste’). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framewor kfor cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community.Publisher PDFPeer reviewe

Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues.

The growth and dynamics of epithelial tissues govern many morphogenetic processes in embryonic development. A recent quantitative transition in data acquisition, facilitated by advances in genetic and live-imaging techniques, is paving the way for new insights to these processes. Computational models can help us understand and interpret observations, and then make predictions for future experiments that can distinguish between hypothesised mechanisms. Increasingly, cell-based modelling approaches such as vertex models are being used to help understand the mechanics underlying epithelial morphogenesis. These models typically seek to reproduce qualitative phenomena, such as cell sorting or tissue buckling. However, it remains unclear to what extent quantitative data can be used to constrain these models so that they can then be used to make quantitative, experimentally testable predictions. To address this issue, we perform an in silico study to investigate whether vertex model parameters can be inferred from imaging data, and explore methods to quantify the uncertainty of such estimates. Our approach requires the use of summary statistics to estimate parameters. Here, we focus on summary statistics of cellular packing and of laser ablation experiments, as are commonly reported from imaging studies. We find that including data from repeated experiments is necessary to generate reliable parameter estimates that can facilitate quantitative model predictions

Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces

Embryogenesis is an extraordinarily robust process, exhibiting the ability to control tissue size and repair patterning defects in the face of environmental and genetic perturbations. The size and shape of a developing tissue is a function of the number and size of its constituent cells as well as their geometric packing. How these cellular properties are coordinated at the tissue level to ensure developmental robustness remains a mystery; understanding this process requires studying multiple concurrent processes that make up morphogenesis, including the spatial patterning of cell fates and apoptosis, as well as cell intercalations. In this work, we develop a computational model that aims to understand aspects of the robust pattern repair mechanisms of the Drosophila embryonic epidermal tissues. Size control in this system has previously been shown to rely on the regulation of apoptosis rather than proliferation; however, to date little work has been done to understand the role of cellular mechanics in this process. We employ a vertex model of an embryonic segment to test hypotheses about the emergence of this size control. Comparing the model to previously published data across wild type and genetic perturbations, we show that passive mechanical forces suffice to explain the observed size control in the posterior (P) compartment of a segment. However, observed asymmetries in cell death frequencies across the segment are demonstrated to require patterning of cellular properties in the model. Finally, we show that distinct forms of mechanical regulation in the model may be distinguished by differences in cell shapes in the P compartment, as quantified through experimentally accessible summary statistics, as well as by the tissue recoil after laser ablation experiments

A structural and catalytic model for zinc phosphoesterases

A structural model for the active site of phosphoesterases, enzymes that degrade organophosphate neurotoxins, has been synthesised. The ligand 2-((2-hydroxy-3-(((2-hydroxyethyl)(pyridin-2-ylmethyl)amino)methyl)-5-methylbenzyl)(pyridin-2-ylmethyl)amino)acetic acid (H(3)L1) and two Zn(ii) complexes have been prepared and characterised as and The ligand (H(3)L1) and complex were characterised through (1)H NMR, (13)C NMR, mass spectroscopy and microanalysis. The X-ray crystal structure of revealed a tetramer of dinuclear complexes, bridged by two phosphate molecules and bifurcating acetic acid arms. Functional studies of the zinc complex with the substrate bis(4-nitrophenyl)phosphate (bNPP) determined the complex with HL1(2-) to be a competent catalyst with k(cat) = 1.26 0.06 x 10(-6) s(-1)

A structural and catalytic model for zinc phosphoesterases

A structural model for the active site of phosphoesterases, enzymes that degrade organophosphate neurotoxins, has been synthesised. The ligand 2-((2-hydroxy-3-(((2-hydroxyethyl)(pyridin-2-ylmethyl)amino)methyl)-5-methylbenzyl)(pyridin-2-ylmethyl)amino)acetic acid (H(3)L1) and two Zn(ii) complexes have been prepared and characterised as and The ligand (H(3)L1) and complex were characterised through (1)H NMR, (13)C NMR, mass spectroscopy and microanalysis. The X-ray crystal structure of revealed a tetramer of dinuclear complexes, bridged by two phosphate molecules and bifurcating acetic acid arms. Functional studies of the zinc complex with the substrate bis(4-nitrophenyl)phosphate (bNPP) determined the complex with HL1(2-) to be a competent catalyst with k(cat) = 1.26 0.06 x 10(-6) s(-1)

A structural and catalytic model for zinc phosphoesterases

A structural model for the active site of phosphoesterases, enzymes that degrade organophosphate neurotoxins, has been synthesised. The ligand 2-((2-hydroxy-3-(((2-hydroxyethyl)(pyridin-2-ylmethyl)amino)methyl)-5-methylbenzyl)(pyridin-2-ylmethyl)amino)acetic acid (H(3)L1) and two Zn(ii) complexes have been prepared and characterised as and The ligand (H(3)L1) and complex were characterised through (1)H NMR, (13)C NMR, mass spectroscopy and microanalysis. The X-ray crystal structure of revealed a tetramer of dinuclear complexes, bridged by two phosphate molecules and bifurcating acetic acid arms. Functional studies of the zinc complex with the substrate bis(4-nitrophenyl)phosphate (bNPP) determined the complex with HL1(2-) to be a competent catalyst with k(cat) = 1.26 0.06 x 10(-6) s(-1)

Cadmium(II) complexes of the glycerophosphodiester-degrading enzyme GpdQ and a biomimetic N,O ligand

The glycerophosphodiester-degrading enzyme GpdQ from Enterobacter aerogenes is a promising bioremediator owing to its ability to degrade some organophosphate pesticides and diester products originating from the hydrolysis of nerve agents such as VX. Here, the cadmium derivative of GpdQ was prepared by reconstituting the apoenzyme. Catalytic measurements with (Cd2+)2-GpdQ and the phosphodiester substrate bis(4-nitrophenyl)phosphate yield k cat = 15 s−1. The pK a of 9.4, determined from the pH dependence of the catalytic activity, implicates a hydroxide ligand as the catalytic nucleophile. Also prepared was the cadmium-containing biomimetic [Cd2((HP)2B)(OAc)2(OH2)](PF6) (where (HP)2B is [2,6-bis([(2-pyridylmethyl)(2-hydroxyethyl)amino]methyl)-4-methylphenol]), which mimics the asymmetry of the metal ion coordination in the active site of GpdQ. The phosphoesterase-like activity of [Cd2((HP)2B)(OAc)2(OH2)](PF6) was studied using the substrate bis(2,4-dinitrophenyl)phosphate, yielding a kinetically relevant pK a of 8.9, with k cat = 0.004 s−1. In summary, the model is both an adequate structural and a reasonable functional mimic of GpdQ