Masami Lintuluoto

Theoretical study on the structure and energetics of alkali halide clusters

Abstract The structures of alkali halide clusters Na n F n , Li n F n and Na n Cl n , and their metal-excess clusters Na n F n −1 + , Li n F n −1 + and Na n Cl n −1 + were investigated by the ab initio molecular orbital method for cluster sizes from 1 to 14. The magic numbers for the neutral clusters Na n F n , Li n F n and Na n Cl n are 4, 6, and 8. The most stable structure for these cluster sizes is a perfect crystallite for Na n F n and Na n Cl n , and a double ring for Li n F n . The magic numbers for the metal-excess clusters are 5 and 8, which are near ideal cuboids with (100) facets.

Structural insights into the function of a thermostable copper-containing nitrite reductase

Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique η(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the η(1)-O coordination manner is proposed.

DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase

The reaction mechanism of copper-containing nitrite reductase (CuNiR) has been proposed to include two important events, an intramolecular electron transfer and a proton transfer. The two events have been suggested to be coupled, but the order of these events is currently under debate. We investigated the entire enzyme reaction mechanism of nitrite reduction at the T2 Cu site in thermophilic Geobacillus CuNiR from Geobacillus thermodenitrificans NG80-2 (GtNiR) using density functional theory calculations. We found significant conformational changes of His ligands coordinated to the T2 Cu site upon nitrite binding during the catalytic reaction. The reduction potentials and pKa values calculated for the relevant protonation and reduction states show two possible routes, A and B. Reduction of the T2 Cu site in the resting state is followed by endothermic nitrite binding in route A, while exothermic nitrite binding occurs prior to reduction of the T2 Cu site in route B. We concluded that our results support the random-sequential mechanism rather than the ordered mechanism.

DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase

Dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.

Adsorption of small molecules with the hydroxyl group on sodium halide cluster ions.

We have investigated adsorption of molecules with hydroxyl group, ROH, on sodium halide cluster ions, Na(n)X(n-1)(+) (X = F and I, n = 10-17) by mass spectrometry and by theoretical calculations. From analysis of the cluster ion intensities, the adsorption of one water molecule (R = H) is most efficient for Na(13)X(12)(+), whose structure has a NaX defect from a 3 x 3 x 3 cubic structure of n = 14. This result suggests that the defect has an important role in the adsorption reaction. However, it is also found that the reactivity diminishes with increasing bulk size of the R group from H to CH(3), (CH(3))(2)CH, and (CH(3))(3)C. These results imply that the adsorption reactivity is dominated by steric hindrance; the smaller molecules are adsorbed inside the basket structures of Na(13)X(12)(+). Reactivity dependence on the basket size is also discussed by comparing the results of Na(n)F(n-1)(+) and Na(n)I(n-1)(+).

QM/MM Calculation of the Enzyme Catalytic Cycle Mechanism for Copper- and Zinc-Containing Superoxide Dismutase

The entire enzyme catalytic mechanism including the electron and the proton transfers of the copper- and zinc-containing extracellular superoxide dismutase (SOD3) was investigated by using QM/MM method. In the first step, the electron transfer from O2·- to SOD3 occurred without the bond formation between the donor and the acceptor and formed the triplet oxygen molecule and reduced SOD3. In the reduced SOD3, the distorted tetrahedral structure of Cu(I) atom was maintained. The reduction of Cu(II) atom induced the protonation of His113, which bridges between the Cu(II) and Zn(II) atoms in the resting state. Since the protonation of His113 broke the bond between Cu(I) and His113, three-coordinated Cu(I) was formed. Further, we suggest the binding of O2·- formed hydrogen peroxide and the resting state after both the Cu reduction and the protonation of His113. The protonation of His113 caused the conformational change of Arg186 located at the entrance of the reactive site. The electrostatic potential surface around the reactive site showed that Arg186 plays an important role as electrostatic guidance for the negatively charged substrates only after the protonation of His113. The rotation of Arg186 switched the proton supply routes via Glu108 or Glu179 for transferring two protons from the bulk solvent.

Development of Chemical Compound Libraries for In Silico Drug Screening

Chemical compound libraries are the basic database for virtual (in silico) drug screening, and the number of entries has reached 20 million. Many drug-like compound libraries for virtual drug screening have been developed and released. In this review, the process of constructing a database for virtual screening is reviewed, and several popular databases are introduced. Several kinds of focused libraries have been developed. The author has developed databases for metalloproteases, and the details of the libraries are described. The library for metalloproteases was developed by improving the generation of the dominant-ion forms. For instance, the SH group is treated as S- in this library while all SH groups are protonated in the conventional libraries. In addition, metal complexes were examined as new candidates of drug-like compounds. Finally, a method for generating chemical space is introduced, and the diversity of compound libraries is discussed.

Size-dependent structures of NanIn−1+ cluster ions with a methanol adsorbate: A combined study by photodissociation spectroscopy and density-functional theory calculation

Methanol adsorption sites on NanI+n-1 ions were investigated. Photoexcitation to charge-transfer states of NanI+n-1 (methanol) predominantly produces two fragment ions: Nan-1I+n-2 (methanol) (neutral NaI loss) and Nan-1I+n-2(neutral NaI and methanol loss), without forming NanI+n-1 (methanol loss). The relative intensities of these fragments are correlated with the geometries and binding energies.

Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3G’s catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctd’s free energy, and we developed a new method that takes into account the distribution of the protein’s dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that this conformation is dominant in solution. In addition, β2-loop-β2’ configuration was stable throughout a 20-ns molecular dynamics (MD) simulation. This finding suggests that in solution A3Gctd is not likely to adopt the continuous β2 strand configuration present in the APOBEC2 crystal structure. In the NMR structure, the solvent water accessibility of the catalytic Zn2+ was limited throughout the 20-ns MD simulation. This result explains previous observations in which A3G did not bind or catalyze single cytosine nucleotide, even when at excessive concentrations.