Structural studies on C-amidated amino acids and peptides: function of amide group in molecular association in crystal structures of Val-Gly-NH2, Ser-Phe-NH2, Gly-Tyr-NH2 and Pro-Tyr-NH2 hydrochloride salts

As part of a series of elucidation of the structural features of peptides caused by C-terminal alpha-amidation, the crystal structures of H-Val-Gly-NH2, H-Ser-Phe-NH2, H-Gly-Tyr-NH2, and H-Pro-Tyr-NH2 hydrochloride salts were analyzed by the X-ray diffraction method. Although respective molecules take energetically allowable torsion angles concerning the backbone and side chains, their conformations are not necessarily the same as the corresponding unamidated ones. This results from the different molecular packing requirements, rather than from different conformational features inherent in the C-amidated and -unamidated peptides. As for the molecular packing feature, each peptide tended to form a repeated structure through those hydrogen bonds in which both amide NH and O=C groups participate. The chloride ions are located between the neighboring peptides and are hydrogen-bonded to the respective amide NHs, leading to the sheet structure. The hydrogen-bonding feature of the amide group and its function in molecular packing was discussed based on the results analyzed so far.     

Two-stage feedforward tracking control system with error-based disturbance observer for optical discs

Recently, the scaling up of the storage capacity and data transfer rate of digital storage media has been required. However, increasing in the storage capacity and transfer rate makes optical head control more difficult. Thus, a tracking control system for optical discs must exhibit a high degree of precision control. Consequently, a new two-stage feedforward control (TSFFC) system for high-precision control is proposed in this paper. The proposed system is constructed using two zero phase error tracking (ZPET) control systems based on error prediction and an error-based disturbance observer (EDOB) that uses a notch filter to suppress non periodic disturbances. The proposed control system is designed for DDU-1000 for digital versatile discs (DVDs). The experimental results demonstrate that the proposed system effectively suppresses tracking errors.     

Bisecting a 4-connected graph with three resource sets

Let G=(V,E) be an undirected graph with a node set V and an arc set E. G has k pairwise disjoint subsets T₁,T₂,…,T_k of nodes, called resource sets, where |T_i| is even for each i. The partition problem with k resource sets asks to find a partition V₁ and V₂ of the node set V such that the graphs induced by V₁ and V₂ are both connected and |V₁∩T_i|=|V₂∩T_i|=|T_i|/2 holds for each i=1,2,…,k. The problem of testing whether such a bisection exists is known to be NP-hard even in the case of k=1. On the other hand, it is known that if G is (k+1)-connected for k=1,2, then a bisection exists for any given resource sets, and it has been conjectured that for k?3, a (k+1)-connected graph admits a bisection. In this paper, we show that for k=3, the conjecture does not hold, while if G is 4-connected and has K₄ as its subgraph, then a bisection exists and it can be found in O(|V|³log|V|) time. Moreover, we show that for an arc-version of the problem, the (k+1)-edge-connectivity suffices for k=1,2,3.     

A simple and rapid method of collecting radionuclides from rain water

A column of mixed powdered ion-exchange resins (Powdex) is proposed for the collection of radionuclides from rain water. The radionuclides are collected efficiently for γ-ray spectrometry. The procedure takes about 1.5 h for 10 l of rain water.     

Separation assay of histamine and its metabolites in biological specimens

This review summarizes the determination methods for histamine and the metabolites in biological specimens by separation techniques, such as gas chromatography, liquid chromatography and capillary electrophoresis. The typical applications using these methods are also described in this review together with the characteristics of the methods. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Capture of cationic ligands bound diffusely to base pairs during DNA refolding

We obtained the intrinsic binding affinity for metal ions, polyamines, and oligolysine peptides diffusely bound to base-paired sites in DNA by monitoring the shift of the hairpin-duplex equilibrium of the self-complementary DNA sequences, which can be widely used for capturing cationic ligands bound diffusely to nucleotide base pairs.     

Effect of DNA on filament formation of tau microtubule-binding domain: structural dependence of DNA

To examine whether or not DNA accelerates the paired helical filament (PHF) formation of tau, the effect of various types of DNAs on filament formations of three-repeated and four-repeated microtubule-binding domains (3RMBD and 4RMBD, respectively) of tau protein was investigated by monitoring the change of thioflavin S fluorescence intensity, that is parallel to the filament formation. Consequently, the followings were clarified: 1) the structurally rigid double-stranded DNA such as poly(dG-dC) or calf thymus DNA has the high potency of promoting the filament formations of 3RMBD and 4RMBD, 2) the filament formation of 3RMBD was more promoted than that of 4RMBD, due to the intermolecular dimer formation of 3RMBD, 3) the DNA-promoted filament formations of these MBDs were temperature-dependent, and the single-stranded DNA such as poly(dA) or poly(dT) reversely protected 4RMBD from the molecular assembly at 20 degrees C. These are the first report on the function of DNA for the PHF formation of tau protein.     

Magnetic resonance energies of heterocyclic conjugated molecules

Magnetic resonance energy (MRE), derived from ring-current diamagnetic susceptibility, can be interpreted as a kind of aromatic stabilization energy. For polycyclic conjugated hydrocarbons, this quantity correlates well with topological resonance energy (TRE). MREs for typical heterocyclic conjugated molecules were then calculated and analyzed. It was found that even for heterocycles MRE highly correlates with TRE. Thus, the MRE concept has been firmly established as a reliable indicator of aromaticity, which mediates magnetic criteria of aromaticity with energetic ones. The conformity of heterocycles to the rule of topological charge stabilization can be checked using not only TRE but also MRE.     

Advanced dress-up chiral columns: New removable chiral stationary phases for enantioseparation of chiral carboxylic acids

This paper describes the preparation of new dress-up columns featuring reproducibly removable and replaceable chiral stationary phases. After synthesizing perfluroalkylated quinine and quinidine derivatives as chiral stationary phase compounds (F-CSPs), we adsorbed them reversibly onto a fluorous LC column through pumping of their solutions. Using this dress-up chiral column and fluorophobic elution of aqueous ammonium formate/MeOH mixtures, we could enantioseparate four racemic N-acetyl amino acids, dichlorprop, and sixteen fluorescent 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC)-derivatized amino acids. Dressing and undressing of the coated F-CSPs could be controlled by varying the fluorophilicity and fluorophobicity of the eluent. The relative standard deviations of the retention times, the retention factors, the number of theoretical plates, the enantioseparation factors, and the resolutions of each of four preparations of such dress-up columns were all less than or equal to 5.26% (from 20 repeated analyses); the reproducibilities from four different preparations were all less than or equal to 10.6%. These columns also facilitated highly sensitive and selective analyses of AQC-amino acids when detected using LC–MS/MS.     

Photochemical dynamics of indolylmaleimide derivatives

On-the-fly nonadiabatic ab initio molecular dynamics simulations have been carried out for three anionic species of indolylmaleimides (3-(1H-3-indolyl)-2,5-dihydro-1H-2,5-pyrroledione, IM) to clarify the mechanisms of photochemical reactions. The results are obtained for (i) a monovalent anion with a deprotonated indole NH group (IM(-)'), (ii) a monovalent anion with a deprotonated maleimide NH group (IM(-)') and (iii) a divalent anion with doubly deprotonated indole and the maleimide NH groups (IM(2-)). Quantum chemical calculations are treated at the three state averaged complete-active space self-consistent field level for 6 electrons in 5 orbitals with the cc-pVDZ basis set (CAS (6, 5) SCF/cc-pVDZ). Molecular dynamics simulations are performed with electronically nonadiabatic transitions included using the Zhu-Nakamura version of the trajectory surface hopping (ZN-TSH) method. It is found that the nonadiabatic transitions occur accompanied by the stretching and shrinking motions of the N(7)-C(8) bond in the case of IM(-)' and the C(11)-N(12) bond in IM(2-) rather than the twisting motion of the dihedral angle. We also found that the ultrafast S(2)→ S(1) nonadiabatic transitions occur through the conical intersection (CoIn) right after photoexcitation to S(2) in IM(-)' and IM(2-). Furthermore, the S(1)→ S(0) nonadiabatic transitions are found to take place in IM(-)'. It is concluded that IM(2-) would mainly contribute to the photoemission, because the S(1)← S(0) and S(2)← S(0) transitions of IM(-)' are dipole-forbidden transitions and, moreover, IM(2-) is found to be the only species to stay in the S(1) state without non-radiative decay.