First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.     

Synthesis of 1-alkoxy-5-alkyluracils

1-Alkoxy-5-alkyluracils 2a-f have been prepared by the reaction of 2-alkyl-3-methoxyacryloyl isocyanates 8a-b with alkoxyamines 9a-c followed by cyclization of the resulting N-alkoxy-N'-(2-alkyl-3-methoxyacryloyl)ureas 10a-f. The isocyanates 8a-b were prepared from ethyl 2-alkylacrylates 3a-b in 5 steps.     

Depigmenting activity and low cytotoxicity of alkoxy benzoates or alkoxy cinnamte in cultured melanocytes

To obtain effective and safe topical depigmenting agents, we synthesized hydroxybenzoates, alkoxybenzoates, and 3,4,5-trimethoxycinnamate containing a thymol moiety and screened then for high-level inhibitory activity against melanin synthesis in cultured melanocytes. Eight compounds were tested for their depigmenting effect and cytotoxicity using a murine melanocyte cell line. We found that 3,4,5-trialkoxybenzoates and 3,4,5-trimethoxycinnamate, synthesized by conjugating 3,4,5-trialkoxybenzoic acids and 3,4,5-trimethoxycinnmic acid with thymol, showed a potent depigmenting effect and low cytotoxicity. Compound 4h, 5-methyl-2-(methylethyl)phenyl (2E)-3-(3,4,5-trimethoxyphenyl)prop-2-enoate, showed the most potent depigmenting effect (IC50=10 microM) with low cytotoxicity (IC50=200 microM).     

Uniqueness and clustering properties of Gibbs states for classical and quantum unbounded spin systems

We consider quantum unbounded spin systems (lattice boson systems) in -dimensional lattice space Z. Under appropriate conditions on the interactions we prove that in a region of high temperatures the Gibbs state is unique, is translationally invariant, and has clustering properties. The main methods we use are the Wiener integral representation, the cluster expansions for zero boundary conditions and for general Gibbs state, and explicitly -dependent probability estimates. For one-dimensional systems we show the uniqueness of Gibbs states for any value of temperature by using the method of perturbed states. We also consider classical unbounded spin systems. We derive necessary estimates so that all of the results for the quantum systems hold for the classical systems by straightforward applications of the methods used in the quantum case.     

Action on flag varieties: 2-Dimensional case

LetA be a finite dimensional commutative semisimple algebra over a fieldk and letV be a finitely generatedA-module. We examine the action of the general linear group GL _A (V) on the set of flags ofk-subspaces ofV. Also, let (V, B) be a finitely generated symplectic module overA. We also investigate the action of the symplectic group Sp _A (V, B) on the set of flags ofB-isotropick-subspaces ofV, whereB=°B is thek-symplectic form induced by a nonzerok-linear map :A k. In both cases, the orbits are completely classified in terms of certain integer invariants provided that dim _{k A}=2.This work is partially supported by a KOSEF research grant.     

Thermodynamics of electrolyte solutions. The system HCl + CaCl2 + H2O at 298.15°K

Activity coefficients of hydrochloric acid have been determined from electromotive-force measurements of cells containing mixtures of hydrochloric acid and calcium chloride at constant total ionic strengthsI=0.1, 0.5, 1.0, 2.0, and 3.0 mole-kg^–1 at 298.15°K. Interpretations based on Scatchard's and Pitzer's equations indicate that Pitzer's equations probably provide a more convenient guide to the thermodynamic properties of the mixed-electrolyte solutions. Activity coefficients for calcium chloride were derived from these equations.     

Determination of trace elements in human serum by inductively coupled plasma atomic emission spectrometry with flow injection

An analytical method for the simultaneous determination of some trace elements (Au, Fe, Mg, Li, Sr, Zn) in human serum by inductively coupled plasma atomic emission spectrometry (ICP-AES) with flow injection is described. Physical interference caused by the change of sample viscosity is discussed. When 100 μl of serum was injected, the relevant recoveries of > 99% for Li, > 98% for Cu and Mg, > 95% for Fe were obtained for an NIST SRM with R.S.D. > 1.3% using optimized flow injection parameters. The prepared lyophilized control serum for routine analysis in clinical laboratories was analyzed and verified for the validity of the technique employed in this experiment using NIST SRM 909 as a primary reference material.     

An ultraviolet-curable mold for sub-100-nm lithography

We describe a novel UV-curable mold that is stiff enough for replicating dense sub-100-nm features even with a high aspect ratio. It also allows for flexibility when the mold is prepared on a flexible support such that large area replication can be accomplished. The composite material of the mold is inert to chemicals and solvents. The surface energy is made low with a small amount of releasing agent such that the mold can be removed easily and cleanly after patterning. In addition, the material allows self-replication of the mold. These unique features of the mold material should make the mold quite useful for various patterning purposes.     

Redetermination of (6R,7S,9S,11S)‐(–)‐sparteinium monoperchlorate

The structure of the title compound, C₁₅H₂₇N₂⁺·ClO₄^?, consists of a monoprotonated sparteinium cation and a perchlorate anion. The two tertiary N atoms of the cation, one perchlorate O atom and a H atom form a bifurcated hydrogen bond, the four hydrogen‐bonding atoms being nearly in the same plane.     

Steric Stabilization of Colloids by Poly(dimethylsiloxane) in Carbon Dioxide: Effect of Cosolvents

Steric stabilization and flocculation of colloids with surface-grafted poly(dimethylsiloxane) (PDMS) chains are examined in liquid and supercritical carbon dioxide with and without hexane as a cosolvent. Neither poly(methyl methacrylate) (PMMA) nor silica particles with grafted 10,000 g/mol PDMS could be stabilized in pure CO(2) at pressures up to 345 bar at 25 degrees C and 517 bar at 65 degrees C without stirring. The addition of 15 wt% hexane to CO(2) led to stable dispersions with sedimentation velocities of 0.2 mm/min for 1-2 μm PMMA particles. The critical flocculation pressure of the colloids in the hexane/CO(2) mixture, determined from turbidity versus time measurements, was found to be the same for silica and PMMA particles and was well above the upper critical solution pressure for the PDMS-CO(2) system. The addition of a nonreactive cosolvent, hexane, eliminates flocculation of PMMA particles synthesized through dispersion polymerization in CO(2) with PDMS-based surfactants. Copyright 2000 Academic Press.