Search results for "Models"

Theoretical study of the temperature dependence of dynamic effects in thymidylate synthase.

2010

A theoretical study of the temperature dependence of dynamic effects in the rate limiting step of the reaction catalyzed by thymidylate synthase is presented in this paper. From hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) optimizations of transition state structures within a fully flexible molecular model, free downhill molecular dynamics trajectories have been performed at four different temperatures. The analysis of the reactive and non-reactive trajectories in the enzyme environment has allowed us to study the geometric and electronic coupling between the substrate, the cofactor and the protein. The results show how the contribution of dynamic effects to the rate enhancement mea…

NMR structure of hypothetical protein TA0938 from Thermoplasma acidophilum.

2007

Structure, diversity and evolution of myriapod hemocyanins

2014

Oxygen transport in the hemolymph of many arthropods is mediated by hemocyanins, large copper-containing proteins that are well-studied in Chelicerata and Crustacea, but had long been considered unnecessary in the subphylum of Myriapoda. Only recently has it become evident that hemocyanins are present in Scutigeromorpha (Chilopoda) and Spirostreptida (Diplopoda). Here we present evidence for a more widespread occurrence of hemocyanin in the myriapods. By means of RT-PCR, western blotting and database searches, hemocyanins were identified in the symphylans Hanseniella audax and Symphylella vulgaris, the chilopod Scolopendra subspinipes dehaani and the diplopod Polydesmus angustus. No hemocya…

Structure, Spectroscopy, and Spectral Tuning of the Gas-Phase Retinal Chromophore: The β-Ionone "Handle" and Alkyl Group Effect

2005

The low-lying singlet states (i.e. S0, S1, and S2) of the chromophore of rhodopsin, the protonated Schiff base of 11-cis-retinal (PSB11), and of its all-trans photoproduct have been studied in isolated conditions by using ab initio multiconfigurational second-order perturbation theory. The computed spectroscopic features include the vertical excitation, the band origin, and the fluorescence maximum of both isomers. On the basis of the S0-->S1 vertical excitation, the gas-phase absorption maximum of PSB11 is predicted to be 545 nm (2.28 eV). Thus, the predicted absorption maximum appears to be closer to that of the rhodopsin pigment (2.48 eV) and considerably red-shifted with respect to that…

Equilibrium, Kinetic, and Computational Studies on the Formation of Cu2+ and Zn2+ Complexes with an Indazole-Containing Azamacrocyclic Scorpiand: Evi…

2015

Cu(2+) and Zn(2+) coordination chemistry of a new member of the family of scorpiand-like macrocyclic ligands derived from tris(2-aminoethyl)amine (tren) is reported. The new ligand (L1) contains in its pendant arm not only the amine group derived from tren but also a 6-indazole ring. Potentiometric studies allow the determination of four protonation constants. UV-vis and fluorescence data support that the last protonation step occurs on the indazole group. Equilibrium measurements in the presence of Cu(2+) and Zn(2+) reveal the formation of stable [ML1](2+), [MHL1](3+), and [ML1(OH)](+) complexes. Kinetic studies on the acid-promoted decomposition of the metal complexes were carried out usi…

Pentameric Circular Iron(II) Double Helicates and a Molecular Pentafoil Knot

2012

We report on the synthesis of 11 pentameric cyclic helicates formed by imine condensation of alkyl monoamines with a common bis(formylpyridine)bipyridyl-derived building block and iron(II) and chloride ions. The cyclic double-stranded helicates were characterized by NMR spectroscopy, mass spectrometry, and in the case of a 2,4-dimethoxybenzylamine-derived pentameric cyclic helicate, X-ray crystallography. The factors influencing the assembly process (reactant stoichiometry, concentration, solvent, nature and amount of anion) were studied in detail: the role of chloride in the assembly process appears not to be limited to that of a simple template, and larger circular helicates observed with…

Photoreaction Between Benzoylthiophenes and N-BOC-Tryptophan Methyl Ester‡

2005

Drug-induced photoallergy requires as the first step formation of covalent drug-protein photoadducts. One of the key amino acids involved in this process is tryptophan (Trp). In this context, several diaryl ketones, including 2-benzoylthiophene (BT), [2-(5-benzoyl-5-thienyl)]-2-methylpropanoic methyl ester (TPA methyl ester) and 4-(2-thienylcarbonyl)phenyl]-2-methylpropanoic methyl ester (SUP methyl ester) have been irradiated in the presence of N-BOC-(L)-tryptophan methyl ester. Laser flash photolysis has allowed to detect three neutral radicals (ketyl, indolyl and skatolyl radicals) resulting from formal hydrogen-atom abstraction. This correlates well with the isolation of homodimers, as …

Synthesis and Structural Model of an α(2,6)-Sialyl-T Glycosylated MUC1 Eicosapeptide under Physiological Conditions

2006

To study the effect of O-glycosylation on the conformational propensities of a peptide backbone, a 20-residue peptide (GSTAPPAHGVTSAPDTRPAP) representing the full length tandem repeat sequence of the human mucin MUC1 and its analogue glycosylated with the (2,6)-sialyl-T antigen on Thr11, were prepared and investigated by NMR and molecular modeling. The peptides contain both the GVTSAP sequence, which is an effective substrate for GalNAc transferases, and the PDTRP fragment, a known epitope recognized by several anti-MUC1 monoclonal antibodies. It has been shown that glycosylation of threonine in the GVTSAP sequence is a prerequisite for subsequent glycosylation of the serine at GVTSAP. Furt…

Solid-State Aggregation of Metallacyclophane-Based MnIICuII One-Dimensional Ladders

2012

Two distinct one-dimensional (1) and two-dimensional (2) mixed-metal-organic polymers have been synthesized by using the "complex-as-ligand" strategy. The structure of 1 consists of isolated ladderlike Mn(II)(2)Cu(II)(2) chains separated from each other by neutral Mn(II)(2) dimers, whereas 2 possesses an overall corrugated layer structure built from additional coordinative interactions between adjacent Mn(II)(2)Cu(II)(2) ladders. Interestingly, 1 and 2 show overall ferri- and antiferromagnetic behavior, respectively, as a result of their distinct crystalline aggregation in the solid state.

Artificial multiple criticality and phase equilibria: an investigation of the PC-SAFT approach

2005

The perturbed-chain statistical associating fluid theory (PC-SAFT) is studied for a wide range of temperature, T, pressure, p, and (effective) chain length, m, to establish the generic phase diagram of polymers according to this theory. In addition to the expected gas-liquid coexistence, two additional phase separations are found, termed "gas-gas" equilibrium (at very low densities) and "liquid-liquid" equilibrium (at densities where the system is expected to be solid already). These phase separations imply that in one-component polymer systems three critical points occur, as well as equilibria of three fluid phases at triple points. However, Monte Carlo simulations of the corresponding sys…