Binding of the Zn2+ ion to ferric uptake regulation protein from E. coli and the competition with Fe2+ binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur

The three dimensional structure of Ferric uptake regulation protein dimer from E. coli, determined by molecular modeling, was docked on a DNA fragment (iron box) and Zn²⁺ ions were added in two steps. The first step involved the binding of one Zn²⁺ ion to what is known as the zinc site which consists of the residues Cys 92, Cys 95, Asp 137, Asp141, Arg139, Glu 140, His 145 and His 143 with an average metal-Nitrogen distance of 2.5 Å and metal-oxygen distance of 3.1–3.2 Å. The second Zn²⁺ ion is bound to the iron activating site formed from the residues Ile 50, His 71, Asn 72, Gly 97, Asp 105 and Ala 109. The binding of the second Zn²⁺ ion strengthened the binding of the first ion as indicated by the shortening of the zinc-residue distances. Fe²⁺, when added to the complex consisting of 2Zn²⁺/Fur dimer/DNA, replaced the Zn²⁺ ion in the zinc site and when a second Fe²⁺ was added, it replaced the second zinc ion in the iron activating site. The binding of both zinc and iron ions induced a similar change in Fur conformations, but shifted residues closer to DNA in a different manner. This is discussed along with a possible role for the Zn²⁺ ion in the Fur dimer binding of DNA in its repressor activity. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Self-organized Segregation on the Grid

We consider an agent-based model with exponentially distributed waiting times in which two types of agents interact locally over a graph, and based on this interaction and on the value of a common intolerance threshold \(\tau \), decide whether to change their types. This is equivalent to a zero-temperature ising model with Glauber dynamics, an asynchronous cellular automaton with extended Moore neighborhoods, or a Schelling model of self-organized segregation in an open system, and has applications in the analysis of social and biological networks, and spin glasses systems. Some rigorous results were recently obtained in the theoretical computer science literature, and this work provides several extensions. We enlarge the intolerance interval leading to the expected formation of large segregated regions of agents of a single type from the known size \(\epsilon >0\) to size \(\approx 0.134\). Namely, we show that for \(0.433< \tau < 1/2\) (and by symmetry \(1/2<\tau <0.567\)), the expected size of the largest segregated region containing an arbitrary agent is exponential in the size of the neighborhood. We further extend the interval leading to expected large segregated regions to size \(\approx 0.312\) considering “almost segregated” regions, namely regions where the ratio of the number of agents of one type and the number of agents of the other type vanishes quickly as the size of the neighborhood grows. In this case, we show that for \(0.344 < \tau \le 0.433\) (and by symmetry for \(0.567 \le \tau <0.656\)) the expected size of the largest almost segregated region containing an arbitrary agent is exponential in the size of the neighborhood. This behavior is reminiscent of supercritical percolation, where small clusters of empty sites can be observed within any sufficiently large region of the occupied percolation cluster. The exponential bounds that we provide also imply that complete segregation, where agents of a single type cover the whole grid, does not occur with high probability for \(p=1/2\) and the range of intolerance considered.     

Efficient one-pot multienzyme synthesis of UDP-sugars using a promiscuous UDP-sugar pyrophosphorylase from Bifidobacterium longum (BLUSP)

A promiscuous UDP-sugar pyrophosphorylase (BLUSP) was cloned from Bifidobacterium longum strain ATCC55813 and used efficiently with a Pasteurella multocida inorganic pyrophosphatase (PmPpA) with or without a monosaccharide 1-kinase for one-pot multienzyme synthesis of UDP-galactose, UDP-glucose, UDP-mannose, and their derivatives. Further chemical diversification of a UDP-mannose derivative resulted in the formation of UDP-N-acetylmannosamine.     

Synthesis of D-mannitol substituted ether-linked bis-1,2,3-triazoles as models of gemini surfactants

Readily available and low cost D-mannitol was converted into 1,2,5,6-di-O-isopropylidene-D-mannitol (1) in the presence of acetone and zinc chloride. Williamson etherfication of 1 with propargyl bromide afforded the bisalkyne 2 in a very good yield. 1,3-Dipolar cycloaddition of 2 with four different alkyl azides using click conditions gave four novel bistriazoles 3a-d. Removal of the acetal groups of 3a-d afforded the deprotected bistriazoles 4a-d in excellent yields. Products 3 and 4 represent models of gemini surfactants.     

Indirubin Derivatives Modulate TGFβ/BMP Signaling at Different Levels and Trigger Ubiquitin-Mediated Depletion of Nonactivated R-Smads

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Highlights? Inhibition of TGFβ/BMP signaling by degradation of nonactivated R-Smads ? Total R-Smad pools are regulated through the ubiquitin-proteasome pathway ? Ubiquitin proteases USP9x and USP34 interact directly with R-Smads ? Indirubin derivative E738 controls BMP/TGFβ signaling though R-Smad depletion     

Antimicrobial photodynamic therapy with two photosensitizers on two oral streptococci: an in vitro study

Laser Physics - Periodontal diseases are caused by infection of tissues supporting the teeth due to complex aggregate of bacteria known as biofilm and firstly colonized by streptococci. The aim of...     

IBMA–metal containing polymers

A new convenient route to metal containing polymers is described. This method involves emulsion co(ter) polymerization of a polar hydrocarbon soluble monomer, N-isobutoxymethylacrylamide (IBMA), with styrene or styrene/butadiene, followed by addition of metals. Metal incorporation is effected by latex or solution techniques. Preparative, atomic adsorption, spectroscopic, film observation, and dilute solution data are presented in support of metal complexation. Structures for the complexes are proposed.     

Equilibrium geometry and electronic structure of benzylidene,arylethylidene, and heterocyclic arylidene malononitriles

The equilibrium geometry of some benzylidene, arylethylidene, and heterocyclic arylidene malononitriles has been calculated within the framework of the MNDO –MO formalism. Various structural factors are analyzed and discussed in terms of localized and delocalized MOS and π-interaction between methylene malononitrile (MMN) and aryl moieties. The possibility of charge transfer (CT ) from aryl to MMN moieties has been examined. The presence of a heterocyclic ring introduces a small perturbation into the MMN nuclear frame. p-Substituents have a pronounced effect on the magnitude and direction of the dipole moment. The variation of ionization potentials and bond order with the Hammet σ p are examined and a straight-line relationship is obtained. The correlation between physiological activity and quantum mechanical properties is analyzed in terms of heat of formation, ionization potential, dipole moment, and charge density on the aryl ring. © 1994 John Wiley & Sons, Inc.     

Solid catalysts for the production of fine chemicals: the use of natural phosphate alone and doped base catalysts for the synthesis of unsaturated arylsulfones

The inexpensive natural phosphate, both alone and doped with potassium fluoride, is a new basic catalyst for the synthesis of α,β-unsaturated arylsulfones. Activation by water and benzyltriethylammonium chloride has also been investigated. When using an ammonium salt, natural phosphate doped with potassium fluoride is an excellent solid support for the synthesis of α,β-unsaturated arylsulfones, leading to excellent yields in a few minutes.     

Determination of Some Metal Ions in Aquatic Environs by Atomic Absorption Spectrometry after Concentration with Modified Silica

The uptake behavior of porous silica modified with N‐propylsalicylaldimine (IE11) for Cd(II), Cr(III), Cu(II), Mn(II) and Pb(II) metal ions were studied. The Log k_d values were found to be within the range 2.19–5.16 depending on pH and time of stirring. IE11 was used in the separation and preconcentration of Cd(II), Cr(III), Cu(II), Mn(II) and Pb(II) from some natural water samples. The data were compared with those obtained by the solvent extraction method (APDC/MIBK). The method was found to be accurate and precise and not subject to random error.