Search results for "Dimer"
showing 10 items of 558 documents
Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase.
2013
The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the …
Phosphatase-like Activity of Tetranuclear Iron(III) and Zinc(II) Complexes
2018
Three new tetranuclear iron(III) and zinc(II) complexes, [Fe4(cpdp)2(phth)2(OH)2]·8H2O (1), [Fe4(cpdp)2(terephth)2(OH)2] (2), and [Zn4(Hcpdp)2(suc)]Br2·12H2O (3), have been synthesized as models for the active site of phosphoester hydrolases by utilizing a polydentate ligand, N, N'-bis[2-carboxybenzomethyl]- N, N'-bis[2-pyridylmethyl]-1,3-diaminopropan-2-ol (H3cpdp) in combination with exogeneous phthalate (phth), terephthalate (terephth), and succinate (suc). Single crystal X-ray analyses reveal that the metallic core of complex 1 consists of four distorted octahedral iron(III) ions with average intraligand Fe---Fe separation of 3.656(2) A, while the structure 3 represents a tetranuclear m…
Piperazine bridged resorcinarene cages.
2010
The one-pot Mannich condensation of resorcinarenes with piperazine and an excess of formaldehyde under high dilution conditions results in a helical cage, namely, a covalently linked dimer of two resorcinarenes connected via four piperazine bridges in yields ranging from 20 to 40%. The compounds were analyzed by NMR spectroscopy, ESI mass spectrometry, and single crystal X-ray diffraction. The helical cages can encapsulate small guest molecules by adapting the cavity volume by changing the helical pitch according to the guest size.
Photoinduced Formation Mechanism of the Thymine−Thymine (6−4) Adduct
2013
The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just …
Insights into the catalytic mechanism of human sEH phosphatase by site-directed mutagenesis and LC-MS/MS analysis
2008
We have recently reported that human soluble epoxide hydrolase (sEH) is a bifunctional enzyme with a novel phosphatase enzymatic activity. Based on a structural relationship with other members of the haloacid dehalogenase superfamily, the sEH N-terminal phosphatase domain revealed four conserved sequence motifs, including the proposed catalytic nucleophile D9, and several other residues potentially implicated in substrate turnover and/or Mg(2+) binding. To enlighten the catalytic mechanism of dephosphorylation, we constructed sEH phosphatase active-site mutants by site-directed mutagenesis. A total of 18 mutants were constructed and recombinantly expressed in Escherichia coli as soluble pro…
Matrix Isolation and Ab Initio Study of Trans−Trans and Trans−Cis Dimers of Formic Acid
2010
Six trans-trans and five trans-cis dimeric structures of formic acid (HCOOH) are revealed by ab initio calculations. Four trans-trans and two trans-cis dimers are identified in the IR absorption spectra in argon matrices. The trans-cis dimers are obtained by narrow-band IR excitation of the vibrational transitions of the trans-trans dimers. Two trans-trans (tt3 and tt6) and one trans-cis (tc4) dimer are characterized experimentally for the first time. The tunneling decay rates of two trans-cis dimers (tc1 and tc4) are evaluated at different temperatures. A greater lifetime of the trans-cis dimers at elevated temperatures compared to the cis-monomer suggests that the high-energy conformers c…
Face-to-face held Pacman type porphyrin-fullerene dyads: design, synthesis, charge transfer interactions and photophysical studies
2008
Pacman-type face-to-face zinc-porphyrin-fullerene dyads have been newly synthesized and studied. Owing to the close proximity of the donor and acceptor entities, strong pi-pi intramolecular interactions between the porphyrin and fullerene entities resulted in modulating the spectral and electrochemical properties of the dyads. New absorption and emission bands that correspond to the charge-transfer interactions were observed in the near-IR region. Time-resolved transient absorption studies revealed efficient photoinduced electron transfer from the singlet excited porphyrin to the fullerene entity. The rate constants for photoinduced electron transfer are analyzed in terms of the Marcus theo…
Ferrocene compounds: methyl 1′-aminoferrocene-1-carboxylate
2010
The title compund, [Fe(C(5)H(6)N)(C(7)H(7)O(2))], features one strong intermolecular hydrogen bond of the type N-H...O=C [N...O = 3.028 (2) A] between the amine group and the carbonyl group of a neighbouring molecule, and vice versa, to form a centrosymmetric dimer. Furthermore, the carbonyl group acts as a double H-atom acceptor in the formation of a second, weaker, hydrogen bond of the type C-H...O=C [C...O = 3.283 (2) A] with the methyl group of the ester group of a second neighbouring molecule at (x, -y - 1/2, z - 1/2). The methyl group also acts as a weak hydrogen-bond donor, symmetry-related to the latter described C-H...O=C interaction, to a third molecule at (x, -y - 1/2, z + 1/2) t…
Transmembrane helix–helix interactions are modulated by the sequence context and by lipid bilayer properties
2012
Abstract Folding of polytopic transmembrane proteins involves interactions of individual transmembrane helices, and multiple TM helix–helix interactions need to be controlled and aligned to result in the final TM protein structure. While defined interaction motifs, such as the GxxxG motif, might be critically involved in transmembrane helix–helix interactions, the sequence context as well as lipid bilayer properties significantly modulate the strength of a sequence specific transmembrane helix–helix interaction. Structures of 11 transmembrane helix dimers have been described today, and the influence of the sequence context as well as of the detergent and lipid environment on a sequence spec…
Electrical Conductivity and Luminescence in Coordination Polymers Based on Copper(I)-Halides and Sulfur-Pyrimidine Ligands
2011
The solvothermal reactions between pyrimidinedisulfide (pym(2)S(2)) and CuI or CuBr(2) in CH(2)Cl(2):CH(3)CN lead to the formation of [Cu(11)I(7)(pymS)(4)](n) (pymSH = pyrimidine-2(1H)-thione) (1) and the dimer [Cu(II)(μ-Br)(Br)L](2) (L = 2-(pyrimidin-2-ylamino)-1,3-thiazole-4-carbaldehyde) (2). In the later reaction, there is an in situ S-S, S-C(sp(2)), and C(sp(2))-N multiple bond cleavage of the pyrimidinedisulfide resulting in the formation of 2-(pyrimidin-2-ylamino)-1,3-thiazole-4-carbaldehyde. Interestingly, similar reactions carried out just with a change in the solvent (H(2)O:CH(3)CN instead of CH(2)Cl(2):CH(3)CN) give rise to the formation of coordination polymers with rather diffe…