Kiattisak Lugsanangarm

Structural basis for the temperature-induced transition of D-amino acid oxidase from pig kidney revealed by molecular dynamic simulation and photo-induced electron transfer.

The structural basis for the temperature-induced transition in the D-amino acid oxidase (DAAO) monomer from pig kidney was studied by means of molecular dynamic simulations (MDS). The center to center (Rc) distances between the isoalloxazine ring (Iso) and all aromatic amino acids (Trp and Tyr) were calculated at 10 °C and 30 °C. Rc was shortest in Tyr224 (0.82 and 0.88 nm at 10 and 30 °C, respectively), and then in Tyr228. Hydrogen bonding (H-bond) formed between the Iso N1 and Gly315 N (peptide), between the Iso N3H and Leu51 O (peptide) and between the Iso N5 and Ala49 N (peptide) at 10 °C, whilst no H-bond was formed at the Iso N1 and Iso N3H at 30 °C. The H-bond of Iso O4 with Leu51 N (peptide) at 10 °C switched to that with Ala49 N (peptide) at 30 °C. The reported fluorescence lifetimes (228 and 182 ps at 10 and 30 °C, respectively) of DAAO were analyzed with Kakitani and Mataga (KM) ET theory. The calculated fluorescence lifetimes displayed an excellent agreement with the observed lifetimes. The ET rate was fastest from Tyr224 to the excited Iso (Iso*) at 10 °C and from Tyr314 at 30 °C, despite the fact that the Rc was shortest between Iso and Tyr224 at both temperatures. This was explained by the electrostatic energy in the protein. The differences in the observed fluorescence lifetimes at 10 and 30 °C were ascribed to the differences in electron affinity of the Iso* at both temperatures, in which the free energies of the electron affinity of Iso* at 10 and 30 °C were -8.69 eV and -8.51 eV respectively. The other physical quantities related to ET did not differ appreciably at both temperatures. The electron affinities at both temperatures were calculated with a semi-empirical molecular orbital method (MO) of PM6. Mean calculated electron affinities over 100 snapshots with 0.1 ps intervals were -7.69 eV at 10 °C and -7.59 eV at 30 °C. The difference in the calculated electron affinities, -0.11 eV, was close to the observed difference in the free energies, -0.18 eV. The present quantitative analysis predicts that the highest ET rate can occur from a donor with longer donor-acceptor distance, which was explained by differences in electrostatic energy.

Homology modelling and molecular dynamics simulations of wild type and mutated flavodoxins from Desulfovibrio vulgaris (Miyazaki F): insight into FMN–apoprotein interactions

The flavodoxin from Desulfovibrio vulgaris, strain Miyazaki F (FD-DvMF), binds one molecule of flavin mononucleotide (FMN) as a cofactor and is considered to associate with electron transport reactions. However, although the 3D structure of the related FD from D. vulgaris strain Hildenborough has been determined, that for FD-DvMF has not. In this study, we have predicted the protein structures of the wild type and the W59F, Y97F and W59F-Y97F substitutional mutants of FD-DvMF by a homology modelling approach. Subsequently, the dynamic properties of these four FD-DvMF variants were investigated by molecular dynamics simulations. The results revealed that peptide O of Trp59 formed H-bond with Tyr99OH only in Y97F, leading to FMN being buried deeper inside the protein than in the other three variants and reducing the accessibility of water to FMN. The phosphate oxygen atoms formed extensive H-bonds with amino acid residues in the 10-loop region in all variants resulting in the highest degree of stabilisation. The OH groups of the ribityl chain and the isoalloxazine ring formed H-bonds with amino acid residues of the 60- and 90-loop regions, respectively. The decomposition free energy calculations suggest that the greatest contribution come from the 10-loop region, which is compatible with the published data. That the calculated binding and decomposition free energies were both greatest in Y97F is proposed to be due to the H-bond between peptide O of Trp59 and Tyr99OH.

Theoretical analyses of the fluorescence lifetimes of the D-amino acid oxidase–benzoate complex dimer from porcine kidney: molecular dynamics simulation and photoinduced electron transfer

The mechanism of photoinduced electron transfer (ET) from benzoate (Bz) and aromatic amino acids to the excited isoalloxazine (Iso*) in the D-amino acid oxidase–benzoate complex (DAOB) dimer from porcine kidney was studied using molecular dynamics simulation (MDS) and an electron transfer theory, and compared with that in the DAOB monomer. The DAOB dimer displayed two fluorescent lifetime components of 0.85 ps and 4.8 ps, as reported. The ET parameters contained in the Kakitani and Mataga (KM) model were determined so as to reproduce these lifetimes with MDS atomic coordinates. The Bz–isoalloxazine (Iso) distances were 0.66 nm in subunit A (Sub A), 0.68 nm in subunit B (Sub B) and 0.61 nm in the monomer. The fluorescent lifetimes of 4.8 ps and 0.85 ps were found to originate from Sub A and Sub B, respectively. In Sub A, Tyr228 was the fastest ET donor followed by Bz and Tyr55, while Bz was followed by Tyr228 and Tyr314 in Sub B. The ET rate from Bz was fastest in Sub B, followed by that in Sub A and the DAOB monomer. The static dielectric constants obtained near Iso were 2.4–2.6 in the DAOB dimer and monomer and 5.8–5.9 in holo D-amino oxidase (DAAO). The different dielectric constants could account for the experimental fluorescence peak observed for DAOB (524 nm) and DAAO (530 nm). Logarithmic ET rates decreased linearly with the donor–acceptor distance expressed by both center to center distance (Rc) and edge to edge distance (Re) in Sub A and Sub B of DAOB dimer and monomer, which reveals that the conventional Dutton rule holds in the ET processes in DAOB. The logarithmic ET rates were decomposed into the electronic coupling (EC), square root (SQ) and exponential (GTRAM) terms. It was found that both the EC term and the GTRAM term also decreased linearly with Rc. The sum of the slopes in the EC and GTRAM vs. Rc plots coincided with the slopes in the logarithmic ET rate vs. Rc functions, suggesting that the GTRAM term makes a significant contribution to the linear relations between logarithmic ET rate and Rc.

Role of the electrostatic energy between the photo-products and ionic groups on the photoinduced electron transfer rates from aromatic amino acids to the excited flavin in five single-point substitution isoforms of the charged amino acid residue-13 in the FMN-binding protein

Effect of the charge (negative, positive or neutral) of amino acid residue-13 on the photoinduced electron transfer (ET) from Trp32, Tyr35 and Trp106 to the excited isoalloxazine was evaluated in the flavin mononucleotide-binding protein from Desulfovibrio vulgaris isolate Miyazaki F (DvFBP). The protein structures of the wild type and the four isoforms where glutamic acid-13 is replaced with lysine (E13K), arginine (E13R), threonine (E13T) and glutamine (E13Q) in aqueous solution were obtained by molecular dynamics simulation. The distances between the amino acid residue-13 and isoalloxazine (Iso), and between the amino acid residue-13 and the ET donors were longer than 1 nm. The ET rates were evaluated with the Kakitani and Mataga model (KM theory) from their ultrafast fluorescence dynamics by means of a non-linear least squares method. Electrostatic (ES) energies between the photo-products and other ionic groups in the proteins markedly varied among ET donors and among the DvFBP isoforms, while the other physical quantities related to the ET rates, the solvent reorganisation and ES energies between the Iso anion and the donor cations did not vary much between the proteins and donors. A plot of the logarithmic ET rates versus either the total free energy gaps or the net ES energies between the photo-products and the other ionic groups both displayed a parabolic function and so the net ES energies are an important influential factor upon the ET rate, in addition to the donor–acceptor distance.

Structural heterogeneity among four subunits in pyranose 2-oxidase: A molecular dynamics simulation study

The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates.

Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF)

The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, subunit A (Sub A) and subunit B (Sub B) were almost completely equivalent in all of the five FBP dimers. However, the predicted MDS structures of the two subunits were not equivalent in solution, revealed by the distances and inter-planar angles between isoalloxazine (Iso) and aromatic amino acids (Trp32, Tyr35 and Trp106) as well as the hydrogen bonding pairs between Iso and nearby amino acids. Residue root of mean square fluctuations (RMSF) also displayed considerable differences between Sub A and Sub B and in the five FBP dimers. The dynamics of the whole protein structures were examined with the distance (RNN) between the peptide N atom of the N terminal (Met1) and the peptide N atom of the C terminal (Leu122). Water molecules were rarely accessible to Iso in all FBP dimers which are in contrast with other flavoenzymes.

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

Integrase (IN), an essential enzyme for HIV-1 replication, has been targeted in antiretroviral drug therapy. The emergence of HIV-1 variants clinically resistant to antiretroviral agents has lead to the development of alternative IN inhibitors. In the present work, binding modes of a high potent IN inhibitor, M522 and M532, within the catalytic binding site of wild type (WT) IN were determined using molecular docking calculation. Both M522 and M532 displayed similar modes of binding within the IN putative binding pocket and exhibited favorable interactions with the catalytic Mg2+ ions, the nearby amino acids and viral DNA through metal-ligand chelation, hydrogen bonding and π-π stacking interactions. Furthermore, the modes of action of these two compounds against the mutated Y212R, N224H and S217H PFV IN were also predicted. Although the replacement of amino acid could somehow disturb inhibitor binding mode, almost key interactions which detected in the WT complexes were fairly conserved. Detailed information could highlight the application of M522 and M532 as candidate IN inhibitors for drug development against drug resistant strains.

Theoretical Analyses of Photoinduced Electron Transfer from Aromatic Amino Acids to the Excited Flavins in Some Flavoproteins

Kiattisak Lugsanangarm1, Nadtanet Nunthaboot2, Somsak Pianwanit1,3,*, Sirirat Kokpol1,3 and Fumio Tanaka1,4,* 1Department of Chemistry, Faculty of Science, Chulalongkorn University, 2Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 3Center of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University, Bangkok, 4Laser Biochemistry Division, Institute for Laser Technology, Osaka, 1,2,3Thailand 4Japan

Physical quantity of residue electrostatic energy in flavin mononucleotide binding protein dimer

The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obtained by a molecular dynamics (MD) simulation. ES is one of the most important energies among the interaction energies in a protein. It is determined from the RES, the residues which mainly contribute to stabilize the structure of each subunit, and the binding energy between two subunits can be estimated. The RES of all residues in subunit A (Sub A) and subunit B (Sub B) were attractive forces, even though the residues contain net negative or positive charges. This reveals that the ES energies of any of the residues can contribute to stabilize the protein structure. The total binding ES energy over all residues among the subunits was distributed between -0.2 to -1.2u202feV (meanu202f=u202f-0.67u202feV) from the MD simulation time.

Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation

Pyranose 2‐oxidase (P2O) from Trametes multicolor contains FAD as cofactor, and forms a tetramer. The protein structure of a mutated P2O, T169S (Thr169 is replaced by Ser), in solution was studied by means of molecular dynamics simulation and analyses of photoinduced electron transfer (ET) from Trp168 to excited isoalloxazine (Iso*), and was compared with wild type (WT) P2O. Hydrogen bonding between Iso and nearby amino acids was very similar as between T169S and WT protein. Distances between Iso and Tyr456 were extremely heterogeneous among the subunits, 1.7 (1.5 in WT) in subunit A (Sub A), 0.97 (2.2 in WT) in Sub B, 1.3 (2.1 in WT) in Sub C, 1.3 nm (2.0 in WT) in Sub D. Mean values of root of mean square fluctuation over all residues were greater by four times than those in WT. This suggests that the protein structure of T169S is much more flexible than that of WT. Electrostatic (ES) energies between Iso anion in one subunit and ionic groups in the entire protein were evaluated. It was found that more than 50% of the total ES energy in each subunit is contributed from other subunits. Reported fluorescence decays were analyzed by a method as WT, previously reported. Electron affinities of Iso* in T169S were appreciably higher than those in WT. Static dielectric constants near Iso and Trp168 were also quite higher in T169S than those in WT.