Monodentate Binding Mode Research Articles

Excision of uranium oxide chains and ribbons in the novel one-dimensional uranyl iodates K(2)[(UO(2))3(IO(3))(4)O(2)] and Ba[(UO(2)2(IO(3))(2)O(2)](H(2)O).

The alkali metal and alkaline-earth metal uranyl iodates K(2)[(UO(2))(3)(IO(3))(4)O(2)] and Ba[(UO(2))(2)(IO(3))(2)O(2)](H(2)O) have been prepared from the hydrothermal reactions of KCl or BaCl(2) with UO(3) and I(2)O(5) at 425 and 180 degrees C, respectively. While K(2)[(UO(2))(3)(IO(3))(4)O(2)] can be synthesized under both mild and supercritical conditions, the yield increases from <5% to 73% as the temperature is raised from 180 to 425 degrees C. Ba[(UO(2))(2)(IO(3))(2)O(2)](H(2)O), however, has only been isolated from reactions performed in the mild temperature regime. Thermal measurements (DSC) indicate that K(2)[(UO(2))(3)(IO(3))(4)O(2)] is more stable than Ba[(UO(2))(2)(IO(3))(2)O(2)](H(2)O) and that both compounds decompose through thermal disproportionation at 579 and 575 degrees C, respectively. The difference in the thermal behavior of these compounds provides a basis for the divergence of their preparation temperatures. The structure of K(2)[(UO(2))(3)(IO(3))(4)O(2)] is composed of [(UO(2))(3)(IO(3))(4)O(2)](2)(-) chains built from the edge-sharing UO(7) pentagonal bipyramids and UO(6) octahedra. Ba[(UO(2))(2)(IO(3))(2)O(2)](H(2)O) consists of one-dimensional [(UO(2))(2)(IO(3))(2)O(2)](2)(-) ribbons formed from the edge sharing of distorted UO(7) pentagonal bipyramids. In both compounds the iodate groups occur in both bridging and monodentate binding modes and further serve to terminate the edges of the uranium oxide chains. The K(+) or Ba(2+) cations separate the chains or ribbons in these compounds forming bonds with terminal oxygen atoms from the iodate ligands. Crystallographic data: K(2)[(UO(2))(3)(IO(3))(4)O(2)], triclinic, space group P_1, a = 7.0372(5) A, b = 7.7727(5) A, c = 8.9851(6) A, alpha = 93.386(1) degrees, beta = 105.668(1) degrees, gamma = 91.339(1) degrees, Z = 1; Ba[(UO(2))(2)(IO(3))(2)O(2)](H(2)O), monoclinic, space group P2(1)/c, a = 8.062(4) A, b = 6.940(3) A, c = 21.67(1), beta= 98.05(1) degrees, Z = 4.

Binding of Bis-linked Netropsin Derivatives in the Parallel-Stranded Hairpin Form to DNA

Cis-diammine Pt(II)- bridged bis-netropsin and oligomethylene-bridged bis-netropsin in which two monomers are linked in a tail-to-tail manner bind to the DNA oligomer with the sequence 5′-CCTATATCC-3′ in a parallel-stranded hairpin form with a stoichiometry 1:1. The difference circular dichroism (CD) spectra characteristic of binding of these ligands in the hairpin form are similar. They differ from CD patterns obtained for binding to the same duplex of another bis-netropsin in which two netropsin moieties were linked in a head-to-tail manner. This reflects the fact that tail-to-tail and head-to-tail bis-netropsins use parallel and antiparallel side-by-side motifs, respectively, for binding to DNA in the hairpin forms. The binding affinity of cis -diammine Pt(II)- bridged bis-netropsin in the hairpin form to DNA oligomers with nucleotide sequences 5′-CCTATATCC-3′ (I), 5′-CCTTAATCC-3′ (II), 5′-CCTTATTCC-3′ (III), 5′-CCTTTTTCC-3′ (IV) and 5′-CCAATTTCC-3′ (V) decreases in the order I = II > III > IV> V. The binding of oligomethylene-bridged bis-netropsin in the hairpin form follows a similar hierarchy. An opposite order of sequence preferences is observed for partially bonded monodentate binding mode of the synthetic ligand.

Carboxylate Binding Modes in Zinc Proteins: A Theoretical Study

The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4–24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second-sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, ∼6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70–100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK a of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8–9.

DNA Binding Studies and Influence on the Activity of DNA Topoisomerases of Bis-Netropsins: Different Effects of Analogs Containing Cis and Trans Ethylene Linkers

Binding to DNA and synthetic duplex polymers of two bifunctional netropsins and effects on supercoiled plasmid DNA as well as their inhibitory potency on DNA. topoisomerases have been investigated. Characteristic differences were found in the DNA binding properties of the two bis-netropsins containing a cis and trans tether as reflected by CD, thermal melting and sedimentation measurements. CD results indicate, that the bis-netropsins interact with DNA by a two-step binding mode depending on the ligand concentration. The trans bis-netropsin may form stable complexes with different DNA's at high salt concentration, whereas for eis bis-netropsin DNA complexes the second binding step is completely abolished. The variations in the DNA binding ability of trans and cis bis-netropsin show a close relationship to the differences observed in their inhibitory effects on DNA topoisomerases. It appeared that trans bis-netropsin more strongly blocks topoisomerase activity than the cis isomer and represents the most potent inhibitor of DNA gyrase. Differences in the DNA binding ability of the bis-netropsins and their inhibitory potency on topoisomerase activity are explained in terms of a bidentate and monodentate binding mode of the trans and cis isomer, respectively.

Geometry of the soluble methane monooxygenase catalytic diiron center in two oxidation states

The hydroxylase component of soluble methane monooxygenase (sMMO) contains a dinuclear iron center responsible for the oxidation of methane to methanol. As isolated, the center is in the oxidized, diiron(III) state. The 2.2 A resolution X-ray structure of the oxidized hydroxylase, Hox, from Methylococcus capsulatus (Bath) was previously determined at 4 degrees C. In this structure the two iron atoms are bridged by a glutamate, a hydroxide ion, and an acetate ion, and additionally coordinated to two His residues, three Glu residues, and a water molecule. The 1.7 A resolution crystal structures of the sMMO hydroxylase from Methylococcus capsulatus (Bath) in both its oxidized diiron(III), Hox, and dithionite-treated, reduced diiron(II), Hred, oxidation states were determined at -160 degrees C. The structure of the diiron center in Hox differs from that previously reported at 2.2 A resolution and 4 degrees C. Although the hydroxide bridge is retained, the bidentate, bridging ligand assigned as acetate is replaced by a weakly coordinating monoatomic water bridge. In the resulting four-membered Fe(OH)Fe(OH2) ring, the Fe ... Fe distance is shortened from 3.4 A to 3.1 A. In protomer A of Hred, the hydroxide bridge is displaced by an oxygen atom of Glu243, which undergoes a carboxylate shift from its terminal monodentate binding mode in Hox to a mode in which the carboxylate is both monoatomic bridging and bidentate chelating. We therefore conclude that the center has been reduced to the diiron(II) oxidation state. Both iron atoms are coordinated to five ligands and weakly to a sixth water molecule in the resulting structure. The diiron center in protomer B of Hred has the same composition as those in Hox. In both the oxidized and reduced structures, the diiron core is connected through hydrogen bonds involving exogenous species to Thr213 in the active site cavity. The diiron center in Hox can change its exogenous ligand coordination and geometry, a property that could be important in the catalytic cycle of sMMO. In Hred, a carboxylate shift occurs, extruding hydroxide ion and opening coordination sites for reaction with O2 to form the diiron(III) peroxo intermediate, Hperoxo. Residue Thr213 may function in catalysis.