New Aspects of the Structure of d-Amino Acid Oxidase from Porcine Kidney in Solution: Molecular Dynamics Simulation and Photoinduced Electron Transfer

Mammalian d-amino acid oxidase (DAAO) plays an important role for d-serine metabolism in the brain and regulation of glutamatergic neurotransmission. In the present work, the structures in solution obtained by the methods of molecular dynamic simulation (MDS) and analyses of photoinduced electron transfer (ET) from aromatic amino acids to the excited isoalloxazine (Iso*) are described based upon our recent works, comparing among DAAO dimer, monomer, DAAO-benzoate (DAOB) complex dimer and monomer. The fluorescence lifetimes of DAAO and DAOB in the time domain of picoseconds and femtoseconds are used for the ET analyses as experimental data. The ET parameters (static dielectric constants near isoalloxazine (Iso), standard free energy gap (SFEG) between the photoproducts and reactants), ET rates, and related physical quantities (solvent reorganization energy, net electrostatic energy between the photoproducts and ionic groups in the proteins), in addition to MDS structures, are used to compare the protein structures. The structure of the DAOB dimer in solution obtained by MDS is substantially different from the crystal structure, and the structures of the two subunits are not equivalent in solution. The ET rates and related physical quantities also differ between the two subunits

9,10-Dioxoanthracene-1,4-diyl bis­(4-methyl­benzene­sulfonate)

The title mol­ecule, C28H20O8S2, has a T-shaped conformation. The central 9,10-anthraquinone moiety is bow-shaped with the two outer aromatic rings being inclined to one another by 13.99 (11)°. The benzenesulfonate rings are inclined to one another by 47.35 (12)°, and by 34.51 (11) and 17.88 (11)° to the bridging aromatic ring of the 9,10-anthraquinone moiety. In the crystal, C—H⋯O interactions link the mol­ecules into ribbons in [100]

Comparison of the monomer structure of the FMN-binding protein from <i>Desulfovibrio vulgaris</i> obtained by NMR and molecular dynamics simulation approaches

<div><p>Flavin mononucleotide (FMN)-binding proteins (FBPs) play an important role in the electron transport process in bacteria. In this study, the structures of the FBP from <i>Desulfovibrio vulgaris</i> (<i>Dv</i>FBP) (Miyazaki F) were compared between those obtained experimentally by nuclear magnetic resonance (NMR) spectroscopy and those derived from molecular dynamics simulations (MDSs). A high-residue root of mean square deviation (RMSD) was observed in residues located at both sides of the wings (Gly22, Glu23, Asp24, Ala59, Arg60, Asp61, Glu62, Gly75, Arg76, Asn77, Gly78 and Pro79), while a low-residue RMSD was found in residues located in a hollow of the structure (Asn12, Glu13, Gly14, Val15, Val16, Asn30, Thr31, Trp32, Asn33, Ser34, Gly69, Ser70, Arg71 and Lys72). Inter-planar angles between the Phe7 and Iso and between the Phe7 and Trp106 residues were remarkably different between the MDS- and NMR-derived <i>Dv</i>FBP structures. Distribution of the torsion angles around the covalent bonds in the aliphatic chain of FMN was similar in the MDS- and NMR-derived structures, except for those around the C1′–C2′ and C5′–O5′ bonds. Hydrogen bond formation between IsoO2 and the Gly49 or Gly50 peptide NH was formed in both the NMR- and MDS-derived structures. Overall, the MDS-derived structures were found to be considerably different from the NMR-derived structures, which must be considered when the photoinduced electron transfer in flavoproteins is analysed with MDS-derived structures.</p></div

open access www.bioinformation.net Hypothesis Volume 9(8)

Binding mode prediction of biologically active compounds from plant Salvia Miltiorrhiza as integrase inhibito

Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products.

Staphylococcus aureus strains carrying enterotoxin A gene (sea) causes food poisoning and cannot be distinguished from non-pathogenic strains by the culture method. Here, we developed a rapid, specific and sensitive visual detection of sea using loop-mediated isothermal amplification (LAMP) combined with nanogold probe (AuNP) or styryl dye (STR). LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2 sea copies, respectively, which were lower than PCR (97 fg or 32 sea copies). The excellent performance of these new assays was demonstrated in food samples using crude DNA lysates. While the culture method detected 104 CFU/g in ground pork and 10 CFU/mL in milk in 5-7 days, LAMP-AuNP could detect down to 10 CFU/g for both samples in 27 minutes. Analyzing 80 pork and milk samples revealed that the LAMP-AuNP showed 100% sensitivity, 97-100% specificity and 97.5-100% accuracy, which were superior to the culture method, and comparable to PCR but without requirement of a thermal cycler. Furthermore, our LAMP-AuNP detect sea at a range below the food safety control (&lt;100 CFU/g). The LAMP-STR quantitated sea in 10-1,000 CFU (7.2-720 copies). Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facilitate appropriate control strategies

Source of High Pathogenicity of an Avian Influenza Virus H5N1: Why H5 Is Better Cleaved by Furin

The origin of the high pathogenicity of an emerging avian influenza H5N1 due to the –RRRKK– insertion at the cleavage loop of the hemagglutinin H5, was studied using the molecular dynamics technique, in comparison with those of the noninserted H5 and H3 bound to the furin (FR) active site. The cleavage loop of the highly pathogenic H5 was found to bind strongly to the FR cavity, serving as a conformation suitable for the proteolytic reaction. With this configuration, the appropriate interatomic distances were found for all three reaction centers of the enzyme-substrate complex: the arrangement of the catalytic triad, attachment of the catalytic Ser368 to the reactive S1-Arg, and formation of the oxyanion hole. Experimentally, the –RRRKK– insertion was also found to increase in cleavage of hemagglutinin by FR. The simulated data provide a clear answer to the question of why inserted H5 is better cleaved by FR than the other subtypes, explaining the high pathogenicity of avian influenza H5N1