A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Bacterial response to eukaryotic cells. Analysis of differentially expressed proteins using nano liquid chromatography-electrospray ionization tandem mass spectrometry

Host-bacteria interactions have mostly been investigated with regard to the host response or to activities of pathogenic bacteria. In contrast, we aim to identify reactions of non-pathogenic bacteria that result from their contact with host cells of the gastrointestinal tract. In a proteomic approach, the response of non-pathogenic human Escherichia coli bacteria on gut epithelial cells (rat IEC-6) was investigated in an in vitro co-culture model. For this purpose, a sensitive analytical procedure was developed based on the identification of two-dimensional polyacrylamide gel electrophoresis separated proteins by online nanoLC-electrospray ionization MS/MS using a quadrupole time-of-flight tandem mass spectrometer for accurate mass determination. We demonstrate here the efficiency of this technique by the identification of a total of 43 differentially expressed proteins, out of which 25 were up-regulated and 18 were down-regulated. They represent a wide range of molecular weight and different metabolic and physiological functions.     

Weak dihydrogen bond interactions in organic crystals

Database analysis on H ? H interactions of the type CH₂ ? H₂C and N-H ? H-N in organic crystals substantiate the occurrence of dihydrogen bonds in the absence of metal atoms.     

Enthalpic interaction coefficients of formamides dissolved in N,N-dimethylformamide

Enthalpies of dilution of formamide, N-methylformamide, N-ethylformamide, N-propylformamide, N-butylformamide, N-pentylformamide, N,N-diethyl-formamide, N,N-dipropylformamide, N,N-dibutylformamide, and N,N-dipentyl-formamide dissolved in N,N-dimethylformamide as solvent have been measured calorimetrically at 25°C. The results are interpreted in terms of the McMillan-Mayer theory. Enthalpic interaction parameters are obtained for pairs, triplets, and in some cases, quadruplets of solute molecules. In general, the enthalpic pair interaction coefficients are negative, whereas the triplet coefficients are positive. The interaction enthalpies are positive only for N-methylformamide and formamide. The magnitudes of the enthalpic pair and triplet interaction coefficients increase with increasing number of C atoms in the N-alkyl groups. The results for the formamides presented in this paper are compared with those for corresponding acetamides published earlier. Although the trends are comparable, distinct differences are observed. The contribution of the -CH₃ group at the CO side of the dialkylacetamides to the enthalpic interaction coefficients appears to be negligible. The same is true for -CH₂ groups at the NH side of a number of amides and related compounds. The enthalpic pair interaction coefficients of the mono-N-alkylsubstituted formamides show a shift of about 100 J-kg-mol^–2 as compared with isomeric N-alkylacetamides. This is discussed in terms of the difference in proton donating and accepting ability of several types of amide molecules. It is concluded that substitution effects should be incorporated in additivity models for these type of systems.     

Ionic Association and Mobility IV. Ionophores in Dimethylsulfoxide at 25°C

The results of conductance measurements on pyridinium picrate, tetraphenylo-sonium picrate, potassium picrate, tetraphenylantimony picrate, tetrapropylam-monium, tetrafluoroborate, tetramethylammonium hexafluorophosphate ion association noncoulombic interaction in dimethyl sulfoxide (DMSO) at 25°C in the concentration range 1–15×10^–4 M are reported. The data were analyzed by the Justice modification of the Fuoss–Hsia equation. Except for pyridinium picrate all salts studied were found to be associated.Application of the Justice Barthel–Bjerrum model of ion association permitted calculation of the noncoulombic portion of the potential of mean force, W _±. Ionic limiting conductances were calculated for six ions using known values of previously determined transport numbers. A table of most current limiting ionic conductances for a variety of ions in DMSO at 25°C has been established.     

Thermodynamics of mixed electrolyte solutions. XI. An isopiestic study of the quaternary system NaCl−KCl−CaCl2−H2O at 25°C

Osmotic and activity coefficients in the aqueous quaternary system sodium chloride-potassium chloride-calcium chloride were derived from isopiestic measurements at 25°C. The isopiestic data were treated by the various procedures of Scatchard, Friedman, and Reilly, Wood, and Robinson. The results obtained showed good agreement with those obtained by pseudo-ternary transforms. Interaction parameters obtained indicated the preponderance of pairwise interactions. Excess Gibbs free energies of mixing were calculated.     

Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

In these years there was considerable interest inunderstanding of intermolecular forces in energetic(explosive) systems[1—3]. The supermolecular approach(SM) is widely adopted for calculating ab initio in-termolecular interactions. Nevertheless, it is unable toprovide physically meaningful interaction contribu-tions such as electrostatic, induction, repulsion anddispersion energies. In contrast, the symmetry-adaptedperturbation theory (SAPT)[4—8] has the ability to de-rive these correlated…     

Studies on Cyclodextrin Inclusion Complex by Fluorescence Anisotropy

An equation for determining the equilibrium association constant (KA) of cyclodextrin inclusion complex with fluorescence anisotropy is derived and used to determine KA of pyrene-B-cyclodextrin inclusion complex. The existing forms of cyclodextrin inclusion complex in solution, the interaction type of host with guest, and the possibility of application of B-cyclodextrin in the analysis of metal ions using naphthalene derivative as a ligand are discussed based on the equation derived along with the curve of fluorescence anisotropy versus cyclodextrin concentration of guest/cyclodextrin system.     

Metal-support interaction in mesoporous silica supported cobalt Fischer-Tropsch catalysts

Summary The pore structure of silica supports (SiO₂ or MCM-41) has little influence on the metal-support interaction in silica supported cobalt catalysts. Cobalt dispersion, reduction behavior, and catalytic properties for the Fischer-Tropsch synthesis were primarily affected by the metal particle size.     

Microcalorimetry, energetics and binding studies of DNA-dimethyltin dichloride complexes

The interaction of dimethyltin dichloride (Me₂SnCl₂) with calf thymus DNA was studied at 27 °C, pH 7.6 using various techniques including isothermal titration calorimetry (ITC) and UV-Vis, fluorescence and IR spectrophotometries. The binding isotherm and enthalpy curve for Me₂SnCl₂-DNA interaction was a biphasic transition process. This was determined by the analysis of the binding data with the Hill equation. The first phase of the enthalpy curve (exothermic process) was consistent with the first set of binding site, the second phase (endothermic process, less exothermicity) was consistent with second set of binding site from the cited interactions. Our results showed that the first set of binding sites is occupied by one mole of ligand bound per near 1 base pair of DNA. The DNA-ethidium bromide (EB) complex, in the presence of Me₂SnCl₂, caused the quenching of the fluorescence emission. The Scatchard plots illustrated a non-intercalating manner for such quenching. The DNA-EB complex results indicated that the binding of Me₂SnCl₂ is with the phosphate groups of DNA at low ligand concentrations (<9 mM). This was confirmed with the IR spectrophotometric spectra. However, the binding at higher ligand concentrations (>9 mM) was with the base groups of DNA. Therefore, these results suggest that the Me₂SnCl₂ binding to DNA at low concentrations occurs through an outside interaction by an exothermic process. However, the partial unfolding of the DNA caused at higher concentrations of Me₂SnCl₂ is through an endothermic process involving interactions with the base groups.