Spatial geometric arrangements of disulfide-crosslinked loops in nonplanar proteins

The method presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7 , 67] for the classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.     

3-Aroylmethyl derivatives of 2(1H)quinoxalinone and 2H-l,4-benzoxazin-2-ones existing in the enamine form

Seventeen derivatives of 2(1H)quinoxalinone and 2H-l,4-benzoxazin-2-one have been synthesized for structural study. All of the compounds having a substituted phenacyl, isonicotinoylmethyl, or 2-furoylmethyl side chain are shown to exist in the enamine form with an internal chelation both in the crystalline and solution states as evidenced by the ir and pmr spectra, respectively. In the gas phase, however, o-hydroxyphenacyl derivatives can exist in another type of intramolecularly hydrogen-bonded form which is supported by their mass spectra.     

Non-linear structures in the non-critical NSR string

We investigate the Ward identities of theW symmetry in the super-Liouville theory coupled to the super-conformal matter of central charge . The theory is classified into two chiralities. For the positive chirality, all gravitationally dressed scaling operators are generated from theq–1 gravitational primaries by one of the ring generators in the R-sector acting on them repeatedly. After fixing the normalizations of the dressed scaling operators, we find that the Ward identities are expressed in the form of theusual W _q algebra constraints as in the bosonic case:W _n ^(k+1) ,=0, (k=1,...,q–1;nZ1–k), where the equations for even and oddn come from the currents in the NS- and the R-sector respectively. The non-linear terms come from the anomalous contributions at the boundaries of moduli space. The negative chirality is defined by interchanging the roles ofp andq. Then we get theW _p algebra constraints.     

A theorem on the average number of subfaces in arrangements and oriented matroids

It is known that for simple arrangements in thed-dimensional Euclidean spaceR ^d The average number ofj-dimensional subfaces of ak-dimensional face is less than . In this paper, we show that this is also true for all arrangements inR ^d and for all oriented matroids, and we give combinatorial proofs.     

Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format

Improvement of in-gel digestion efficiency is highly desirable for one- or two-dimensional gel electrophoretic separation and mass spectrometric (MS) analysis in proteomics, because the resultant increases in sequence coverage and MS signal intensity lead to higher confidence in protein identification. Here an optimized in-gel digestion system, in combination with thin-gel separation and negative staining in a high-throughput format using 96-well plates, is described. The combination of negative staining and protein separation on a 0.9 mm thick gel showed a clear improvement in in-gel digestion efficiency in comparison with the more typical protocols such as the combination of silver staining and a 1.0 mm gel. In addition, the use of 96-well plates to increase throughput did not decrease the efficiency of this strategy when the stirring of the gel pieces in processes such as destaining, washing, gel-shrinking and peptide extraction was performed by sonication instead of shaking the plates. This procedure was optimized and applied to identify proteins of the postsynaptic density fraction; 105 proteins were identified after SDS-PAGE separation.     

Post-oxidative conversion of thiol residue to sulfonic acid in the binding sites of molecularly imprinted polymers: disulfide based covalent molecular imprinting for basic compounds

An imprinted polymer using a disulfide derivative as a template was treated with NaBH4 to yield the polymer with thiol groups in the binding sites. The thiol groups were then oxidized with H2O2/AcOH to yield the molecularly imprinted polymer with sulfo groups in the binding sites. This site conversion can provide amine-imprinted polymers, in which amine is retained to the imprinted polymer by the strong electrostatic interaction between the amino group and the sulfo group in the binding sites.     

Radiation-induced heterogeneous polymerization of acrylamide in acetone and acetone–water mixtures

The effects of temperature, dose rate, and monomer concentration on the heterogeneous polymerization of acrylamide in acetone–water mixtures have been studied. Heterogeneous polymerization takes place in mixtures containing less than 60 vol-% water. The polymerization is steady in acetone and nonsteady in acetone an nonsteady in mixtures containing 10–50 vol-% water. The average rate of polymerization is highest in mixtures with about 20 vol-% water. Polymer molecular weight increases with the increasing water content in range 0–10 vol-% and does not change in the range of 30–70 vol-% water. For the polymerization in acetone and an acetone–water 60/40 mixture the activation energies are 2.3 and ?1.8 kcal/mole, the dose rate exponents of rate are 0.78 and 0.52, and the monomer concentration exponents of rate are 0.5 and 1.6, respectively. The polymer molecular weight increases with decreasing dose rate, decreasing temperature, and increasing monomer concentration. These results are discussed in connection with the mechanism of heterogeneous polymerization and the solvent effect.     

A long-range-corrected time-dependent density functional theory

We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.