Photochemical Reaction of Ketoprofen with Proteinogenic Amino Acids.

Ketoprofen (KP) is one of the most popular nonsteroidal anti-inflammatory drugs; however, drug-induced photosensitivity of KP has been reported as a serious adverse effect. KP incorporated into a protein can produce an allergen under UV irradiation, which causes drug-induced photosensitivity. The photochemistry of KP with 20 kinds of proteinogenic amino acids in phosphate buffer solutions at pH 7.

Thermal and Nonthermal Microwave Effects of Ethanol and Hexane-Mixed Solution as Revealed by In Situ Microwave Irradiation Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

Microwave heating is widely used to accelerate the organic synthesis reaction. However, the role of the nonthermal microwave effect in the chemical reaction has not yet been well characterized. The microwave heating processes of an ethanol-hexane mixed solution were investigated using in situ microwave irradiation nuclear magnetic resonance spectroscopy and molecular dynamics (MD) simulation.

Aggregability of β(1→4)-linked glucosaminoglucan originating from a sulfur-oxidizing bacterium .

β-1,4-glucosaminoglucan (GG) was prepared from the sheath of a sulfur-oxidizing bacterium . Recently, GG was found to be adsorbed by cellulose (paper) and is therefore potentially applicable as an aminating agent for cellulose. We attempted to increase the yield of GG using a fed-batch cultivation method.

Separation of D-amino acid-containing peptide phenylseptin using 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns.

Several D-amino acid-containing peptides (DAACPs) with antimicrobial, cardio-excitatory, or neuronal activities have been found in several species. Here, we demonstrated the chiral separation of the antimicrobial peptide diastereomers, D-phenylseptin and L-phenylseptin using (S) and (R) 3,3'-phenyl-1,1'-binaphthyl-18-crown-6-ether columns (CR-I (+) and CR-I (-), respectively) and also investigated the underlying mechanism. First, using D-amino acid-containing tripeptide Phe-Phe-Phe-OH, we found that CR-I (+) could be used to recognize diastereomeric tripeptides containing an L-amino acid as the first residue.

DFT study of the influence of acetyl groups of cellulose acetate on its intrinsic birefringence and wavelength dependence.

The effect of the acetyl groups of cellulose acetate (CA) on its intrinsic birefringence and its wavelength dependence was investigated using density functional theory (DFT). Seven types of CA repeating-unit models that differ in their degree of substitution (DS) and substitution sites were used in the calculations. The results suggested that the intrinsic birefringence (Δn°) and its wavelength dependence significantly depended on the conformations of the acetyl group at C6.

Retinal Configuration of ppR Intermediates Revealed by Photoirradiation Solid-State NMR and DFT.

Pharanois phoborhodopsin (ppR) from Natronomonas pharaonis is a transmembrane photoreceptor protein involved in negative phototaxis. Structural changes in ppR triggered by photoisomerization of the retinal chromophore are transmitted to its cognate transducer protein (pHtrII) through a cyclic photoreaction pathway involving several photointermediates. This pathway is called the photocycle.

Acetylacetonato-based pincer-type nickel(ii) complexes: synthesis and catalysis in cross-couplings of aryl chlorides with aryl Grignard reagents.

In this work, three different types of acetylacetonato-based pincer-type nickel(ii) complexes (2) were prepared. Complex 2a possessed the tridentate ONN ligand, which was constructed by the condensation reaction of acetylacetone with N,N-diethylethylenediamine. Complex 2b contained the PPh2 donor group in contrast to the NEt2 group in 2a, i.

The role of d-allo-isoleucine in the deposition of the anti-Leishmania peptide bombinin H4 as revealed by P solid-state NMR, VCD spectroscopy, and MD simulation.

Bombinin H4 is an antimicrobial peptide that was isolated from the toad Bombina variegata. Bombinin H family peptides are active against gram-positive, gram-negative bacteria, and fungi as well as the parasite Leishmania. Among them, bombinin H4 (H4), which contains d-allo-isoleucine (d-allo-Ile) as the second residue in its sequence, is the most active, and its l-isomer is bombinin H2 (H2).

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra.

The role of CH/π interactions in the high affinity binding of streptavidin and biotin.

The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10mol) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood.

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs.

Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation.

Melittin is a venom peptide that disrupts lipid bilayers at temperatures below the liquid-crystalline to gel phase transition temperature (T). Notably, the ability of melittin to disrupt acidic dimyristoylphosphatidylglycerol (DMPG) bilayers was weaker than its ability to disrupt neutral dimyristoylphosphatidylcholine bilayers. The structure and orientation of melittin bound to DMPG bilayers were revealed by analyzing the C chemical shift anisotropy of [1-C]-labeled melittin obtained from solid-state C NMR spectra.

Discrimination between naphthacene and triphenylene using cellulose tris(4-methylbenzoate) and cellulose tribenzoate: A computational study.

The mechanisms of naphthacene and triphenylene discrimination using commercially available cellulose tris(4-methylbenzoate) (CMB) and cellulose tribenzoate (CB) chiral stationary phases were investigated using molecular mechanics calculations. Naphthacene and triphenylene could be separated by liquid chromatography on CMB and CB, with triphenylene being eluted earlier than naphthacene on both phases. However, the corresponding separation factor is much larger for CMB than for CB.

Achiral Molecular Recognition of Aromatic Position Isomers by Polysaccharide-Based CSPs in Relation to Chiral Recognition.

Chromatographic separation of several sets of aromatic position isomers on three cellulose- and one amylose-based chiral stationary phases was performed to evaluate the potential of a polysaccharide-based chiral stationary phase (CSP) in the separation of isomeric or closely similar molecules, and to understand the interaction mechanism of this type of CSP with analytes. Their ability of molecular recognition was quite outstanding, but the selection rule was particular to each polysaccharide derivative. In the series of analytes, cellulose tris(4-methylbenzoate) and tris(3,5-dimethylphenylcarbamate) exhibited a contrasting selection rule, and the recognition mechanism was considered based on the computer-simulation of the former polymer.

Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well.

Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation.

The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region.

Computational study to evaluate the birefringence of uniaxially oriented film of cellulose triacetate.

The intrinsic birefringence of a cellulose triacetate (CTA) film is evaluated using the polarizability of the monomer model of the CTA repeating unit, which is calculated using the density functional theory (DFT). Since the CTA monomer is known to have three rotational isomers, referred to as gg, gt, and tg, the intrinsic birefringence of these isomers is evaluated separately. The calculation indicates that the monomer CTA with gg and gt structures shows a negative intrinsic birefringence, whereas the monomer unit with a tg structure shows a positive intrinsic birefringence.

Interaction of extracellular loop II of κ-opioid receptor (196-228) with opioid peptide dynorphin in membrane environments as revealed by solid state nuclear magnetic resonance, quartz crystal microbalance and molecular dynamics simulation.

κ-Opioid receptor is a member of the opioid receptor family and selectively interacts with the opioid peptide dynorphin. Extracellular loop II (ECL-II) of the κ-opioid receptor displays an amphiphilic helix in membrane environments and the N-terminal α-helix of dynorphin A(1-17) (hereafter DynA17) is inserted into the membrane with the tilt angle of 21° to the bilayer normal. ECL-II peptides (1-33), corresponding to 196-228 of κ-opioid receptor with [1-(13)C]- or [3-(13)C]-labeled amino acids were incorporated into large [dimyristoylphosphatidyl choline (DMPC)/ dihexanoylphosphatidyl choline (DHPC) = 3, q = 3] and small bicelle (q = 1) systems.

Investigation of the structure and interaction of cellulose triacetate I crystal using ab initio calculations.

The crystal structure of cellulose triacetate I (CTA I) was investigated using first-principles density functional theory (DFT) calculations. The results are in good agreement with the experimental structure obtained by Sikorski et al. when performing the calculation with inclusion of the dispersion correction.

Computational study on the interactions and orientation of monoclonal human immunoglobulin G on a polystyrene surface.

Having a theoretical understanding of the orientation of immunoglobulin on an immobilized solid surface is important in biomedical pathogen-detecting systems and cellular analysis. Despite the stable adsorption of immunoglobulin on a polystyrene (PS) surface that has been applied in many kinds of immunoassays, there are many uncertainties in antibody-based clinical and biological experimental methods. To understand the binding mechanism and physicochemical interactions between immunoglobulin and the PS surface at the atomic level, we investigated the binding behavior and interactions of the monoclonal immunoglobulin G (IgG) on the PS surface using the computational method.

Folded-chain structure of cellulose II suggested by molecular dynamics simulation.

We investigated the possibility of a folded-chain crystal of the cellulose II polymorph by molecular dynamics (MD) simulation. The molecular direction of cellulose chains in cellulose II is anti-parallel, which allows the crystal to have folded-chain packing. It is impossible for cellulose I to form such a structure due to its parallel up assembly.

Role of aromatic residues in amyloid fibril formation of human calcitonin by solid-state 13C NMR and molecular dynamics simulation.

Calcitonin (CT) is an amyloid fibril forming peptide. Since salmon calcitonin (sCT), having Leu residues (Leu12, Leu16 or Leu19) instead of Tyr12, Phe16 or Phe19 for human calcitonin (hCT), is known to form the fibrils much slower than hCT, hCTs mutated to Leu residues at the position of 16 (F16L-hCT), 19 (F19L-hCT), and 12, 16 and 19 (TL-hCT) were examined to reveal the role of aromatic side-chains on amyloid fibrillation using solid-state (13)C NMR. The detailed kinetics were analyzed using a two-step reaction mechanism such as nucleation and fibril elongation with the rate constants of k1 and k2, respectively.

Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation.

Bovine lactoferrampin (LFampinB) is a newly discovered antimicrobial peptide found in the N1-domain of bovine lactoferrin (268-284), and consists of 17 amino-acid residues. It is important to determine the orientation and structure of LFampinB in bacterial membranes to reveal the antimicrobial mechanism. We therefore performed (13)C and (31)P NMR, (13)C-(31)P rotational echo double resonance (REDOR), potassium ion-selective electrode, and quartz-crystal microbalance measurements for LFampinB with mimetic bacterial membrane and molecular-dynamics simulation in acidic membrane.

Conformational analysis of an extracellular polysaccharide produced by Sphaerotilus natans.

Sphaerotilus natans is a filamentous sheath-forming bacterium, commonly found in bulking activated sludge. The bulky nature of this bacterium is caused by an extracellular polysaccharide (EPS). EPS is a linear acidic polysaccharide with the following chemical structure: [ → 4)-α-D-Glcp-(1 → 2)-β-D-GlcpA-(1 → 2)-α-L-Rhap-(1 → 3)-β-L-Rhap-(1 → ](n).

Molecular dynamics simulation of the dissolution process of a cellulose triacetate-II nano-sized crystal in DMSO.

An understanding of the dissolution process of cellulose derivatives is important not only for basic research but also for industrial purposes. We investigated the dissolution process of cellulose triacetate II (CTA II) nano-sized crystal in DMSO solvent using molecular dynamics simulations. The nano-sized crystal consists of 18 CTA chains.