Investigation on substrate specificity and catalytic activity of serine protease neuropsin.

Neuropsin is one of serine proteases mainly found at the hippocampus and the amygdala, where it contributes to the long-term potentiation and memory acquisition by rebuilding of synaptic connections. Despite of the importance of neuropsin, the substrate specificity and regulation mechanisms of neuropsin have been unclear. Thus, we investigated the substrate specificity and the catalytic activity of neuropsin by the protein-ligand docking and molecular dynamics (MD) simulations and succeeded to reproduce the trend of the experimental results.

Molecular Dynamics Simulation Study on Allosteric Regulation of CD44-Hyaluronan Binding as a Force Sensing Mechanism.

CD44 protein exists on surfaces of a variety of human cells, acts as a receptor for the hyaluronan (HA) molecule, and mediates cell adhesion via the HA binding in leukocyte trafficking, cell rolling, and so on. The molecular structures of both CD44 and HA are well known, and the previous work shows that the external-mechanical force induces the partially disordered (PD) conformation from the ordered (O) conformation of CD44. The PD conformation has the higher HA affinity compared to the O conformation.

Intra-electron transfer induced by protonation in copper-containing nitrite reductase.

The inter- and intra-electron and proton transfers in the nitrite reduction of copper-containing nitrite reductase (CuNiR) were investigated by using the QM/MM method with the calculational models containing type 1 (T1) and type 2 (T2) Cu sites. The electron transfer from the outer electron donor protein to the T1 Cu site occurred both before and after nitrite binding, and nitrite binding lowered the reduction potential of the Cu T1 site. The protonation of catalytic His244 subsequent to nitrite binding and T1 Cu reduction induced partial intra-electron transfer from T1 to T2 Cu sites.

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 O 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.

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.

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.

Dynamic figure eight loop structure of meso-tetraaryl[32]octaphyrins(1.0.1.0.1.0.1.0).

3,3'-Diethyl substituents of the 2,2'-bipyrrole components in meso-tetraaryl[32]octaphyrins(1.0.1.

Direct determination of absolute configuration of carboxylic acids by cyclooctapyrrole.

Octaphyrin O1 has been found to be an effective sensor for the direct determination of absolute configuration of a variety of carboxylic acids at mM concentrations at room temperature based on CD exciton chirality method.

Supramolecular chirogenesis in zinc porphyrins: interaction with bidentate ligands, formation of tweezer structures, and the origin of enhanced optical activity.

The complexation behavior, binding properties, and spectral parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral bidentate guests (diamines and amino alcohols) have been studied by means of UV-vis, CD, fluorescence, (1)H NMR, and ESI MS techniques. It was found that the guest structure plays a decisive role in the chirogenesis pathway. The majority of bidentate ligands (except those geometrically unsuitable) exhibit two major equilibria steps: the first guest ligation leading to formation of the 1:1 host-guest tweezer structure (K(1)) and the second guest molecule ligation (K(2)) forming the anti bis-ligated species (1:2).

Direct determination of absolute configuration of monoalcohols by bis(magnesium porphyrin).

Ethane bridged bis(Mg porphyrin) has been found to be an effective sensor for the direct determination of the absolute configuration of a variety of monoalcohols at millimolar concentrations and room temperature based on the CD exciton chirality method. Examination of a variety of synthetic and natural monoalcohols, including alpha-substituted aliphatic and aromatic alkanols with one chiral center, as well as alicyclic alcohols with 2-5 chiral centers, gave consistent results. In the case of alcohols with multiple chiral centers, the absolute configuration of the carbon alpha to OH is always read out.

Remarkable stability and enhanced optical activity of a chiral supramolecular bis-porphyrin tweezer in both solution and solid state.

Interaction of the achiral syn (face-to-face) conformer of the ethane-bridged bis(zinc octaethylporphyrin) with the enantiopure 1,2-diaminocyclohexane results in the exclusive formation of a supramolecular chiral tweezer. This 1:1 host-guest complex exhibits remarkable stability in both solution (even upon photoexcitation) and solid-state phases, with a high degree of optical activity arising from the two-point interaction mode and optimal spatial geometry.

Supramolecular chirogenesis in zinc porphyrins: equilibria, binding properties, and thermodynamics.

Complexation mechanism, binding properties and thermodynamic parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral monoamine and monoalcohol guests have been studied by means of the UV-vis, CD, (1)H NMR, and ESI MS techniques. It was found that the chirogenesis process includes three major equilibria steps: the first guest ligation to a zinc porphyrin subunit of the host (K(1)), syn to anti conformational switching (K(S)), and further ligation by a second guest molecule to the remaining ligand-free zinc porphyrin subunit (K(2)), thus forming the final bis-ligated species possessing supramolecular chirality. The validity of this equilibria model is confirmed by the excellent match between the calculated and experimentally observed spectral parameters of the bis-ligated species.

Stoichiometry-controlled supramolecular chirality induction and inversion in bisporphyrin systems.

[reaction: see text] Stoichiometry is found to be an effective tool for controlling supramolecular chirality induction and inversion processes. Chirality induction in the achiral syn ethane-bridged bis(zinc octaethylporphyrin) is achieved upon interaction with the enantiopure (R,R)-1,2-diphenylethylenediamine at the low molar excess region, to yield the right-handed chiral 1:1 tweezer complex. Further increase of the ligand concentration results in chirality inversion as the equilibrium shifts toward the extended left-handed 1:2 anti complex as a result of switching of the complex helicity.