Thermodynamics Research Today is a free monthly online journal that collates and summarizes the latest research about Thermodynamics, including details on enthalpy, entropy, energy transitions. | ||||||
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Impact of phosphorylation on structure and thermodynamics of the interaction between the N-terminal domain of enzyme I and the histidine phosphocarrier protein of the bacterial phosphotransferase system.Suh JY, Cai M, Clore GM Chemical Physics, NIDDK/NIH, Bethesda, MD 20892-0520. The structural and thermodynamic impact of phosphorylation on the interaction of the N-terminal domain of enzyme I (EIN) and the histidine phosphocarrier protein HPr, the two common components of all branches of the bacterial phosphotransferase system (PTS), have been examined using NMR spectroscopy and isothermal titration calorimetry. His189 is located at the interface of the a and a/ss domains of EIN, resulting in rather widespread chemical shift perturbation upon phosphorylation, in contrast to the highly localized perturbations seen for HPr where His15 is fully exposed to solvent. Residual dipolar coupling (RDC) measurements, however, demonstrate unambiguously that no significant changes in backbone conformation of either protein occur upon phosphorylation: for EIN, the relative orientation of the a and a/ss domains remains unchanged; for HPr, the backbone f/ torsion angles of the active site residues are unperturbed within experimental error. HisGlu/Asp mutations of the active site histidines designed to mimic the phosphorylated states reveal binding equilibria that favor phosphoryl transfer from EIN to HPr. Although binding of phospho-EIN to phospho-HPr is reduced by a factor of ~21 relative to the unphosphorylated complex, RDC measurements reveal that the structures of the unphosphorylated and biphosphorylated complexes are the same. Hence, the phosphorylation states of EIN and HPr shift the binding equilibria predominantly by modulating intermolecular electrostatic interactions without altering either the backbone scaffold or binding interface. This facilitates highly efficient phosphoryl transfer between EIN and HPr, which is estimated to occur at a rate of ~850 s-1 from exchange spectroscopy. Published 30 April 2008 in J Biol Chem. Articles on Thermodynamics published 30 April 2008: Double Affinity Amplification of Galectin-Ligand Interactions through Arginine-Arene Interactions: Synthetic, Thermodynamic, and Computational Studies with Aromatic Diamido Thiodigalactosides. Chemistry, 14(14): 4233-4245. A series of aromatic mono- or diamido-thiodigalactoside derivatives were synthesized and studied as ligands for galectin-1, -3, -7, -8N terminal domain, and -9N terminal domain. The affinity determination in vitro with competitive fluorescence-polarization experiments and thermodynamic analysis by isothermal microcalorimetry provided a coherent picture of structural requirements for arginine-arene interactions in galectin-ligand binding. Computational studies were employed to explain binding ... [Abstract] [Full-text] Thermodynamic characterization of a highly thermoactive extracellular pectate lyase from a new isolate Bacillus pumilus DKS1. Bioresour Technol. An extracellular pectate lyase (EC 4.2.2.2) was purified from the culture filtrate of a newly isolated Bacillus pumilus DKS1 grown in pectin containing medium. Using ion-exchange and gel filtration chromatography, this enzyme was purified and found to have a molecular weight of around 35kDa. The purified enzyme exhibited maximal activity at a temperature of 75 degrees C and pH 8.5. The presence of 1mM calcium and manganese enhanced pectate lyase activity and was strongly inhibited by zinc, ... [Abstract] [Full-text] Articles on Thermodynamics published 29 April 2008: Membrane insertion pathway of annexin B12: thermodynamic and kinetic characterization by fluorescence correlation spectroscopy and fluorescence quenching. Biochemistry, 47(18): 5078-87. Experimental determination of the free energy stabilizing the structure of membrane proteins in their native lipid environment is undermined by the lack of appropriate methods and suitable model systems. Annexin B12 (ANX) is a soluble protein which reversibly inserts into lipid membranes under mildly acidic conditions, which makes it a good experimental model for thermodynamic studies of folding and stability of membrane proteins. Here we apply fluorescence correlation spectroscopy for ... [Abstract] [Full-text] Articles on Thermodynamics published 28 April 2008: Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. J Struct Biol, 162(2): 237-47. We propose a coarse-grained (CG) model to study the native structure and physical properties of helical membrane proteins (HMPs) using off-lattice computer simulations. Instead of considering sequence heterogeneity explicitly, we model its effect on the packing of helices by employing a mean packing parameter r(0), which is calculated from an all-atom (AA) model. Specifically, this CG model is applied to investigate the packing of helices in bacteriorhodopsin (BR), and predicts the seven helix ... [Abstract] [Full-text] Surface complexation modeling of uranium(VI) sorbed onto zirconium oxophosphate versus temperature: Thermodynamic and structural approaches. J Colloid Interface Sci. This work presents an investigation of the interaction mechanisms between uranyl ions and a solid phosphate, the zirconium oxophosphate: Zr(2)O(PO(4))(2). Both thermodynamic and structural points of view are developed. Indeed, prior to any simulation of the retention data, it is necessary to precisely characterize the system under study in order to gain information at a molecular scale. First, the intrinsic surface properties of this synthetic compound have been investigated for different ... [Abstract] [Full-text] anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics, 9: 199. BACKGROUND: Compared to other omics techniques, quantitative metabolomics is still at its infancy. Complex sample preparation and analytical procedures render exact quantification extremely difficult. Furthermore, not only the actual measurement but also the subsequent interpretation of quantitative metabolome data to obtain mechanistic insights is still lacking behind the current expectations. Recently, the method of network-embedded thermodynamic (NET) analysis was introduced to address some ... [Abstract] [Full-text] Articles on Thermodynamics published 24 April 2008: Equilibrium and thermodynamic studies on biosorption of Pb(II) onto Candida albicans biomass. J Hazard Mater. Biosorption of Pb(II) ions from aqueous solutions was studied in a batch system by using Candida albicans. The optimum conditions of biosorption were determined by investigating the initial metal ion concentration, contact time, temperature, biosorbent dose and pH. The extent of metal ion removed increased with increasing contact time, initial metal ion concentration and temperature. Biosorption equilibrium time was observed in 30min. The Freundlich and Langmuir adsorption models were used for ... [Abstract] [Full-text] Monte Carlo simulations of thermodynamic and structural properties of Mie(14,7) fluids. J Chem Phys, 128(15): 154514. The vapor-liquid phase envelope of Mie(14,7) fluids is determined by the Gibbs ensemble Monte Carlo (MC) simulation technique. The NVT-MC simulation method is then utilized to compute the equation of state and the pair correlation function over a wide range of densities and temperatures. The effective diameters are calculated via the virial minimization method and the results are applied as the repulsion-attraction splitting distance within the generic van der Waals (GvdW) theory to compute the ... [Abstract] [Full-text] © 2005-2008 Thermodynamics Research Today. All Rights Reserved. |
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