Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Cubic phases of binary systems of 4′-n-tetradecyloxy-3′-nitrobiphenyl-4-carboxylic acid (ANBC-14)-n-alkane

The phase behaviour of the binary systems 4′- ⁿ -tetradecyloxy-3′-nitrobiphenyl-4-carboxylic acid (ANBC-14)- ⁿ -alkane ( ⁿ -tetradecane or ⁿ -hexadecane) was investigated by differential scanning calorimetry, polarizing optical microscopy, and X-ray diffraction. The phase behaviour was a function of temperature ( ^T ) and the effective carbon number of the system ( ^n*), where ^n* involves carbon atoms both from the alkoxy group of ANBC-14 and from the ⁿ -alkane added. ANBC-14 shows no cubic phase, but the addition of ⁿ -alkane induced cubic phases when ^n*≧c. 15. An interesting point is that the type of cubic phase is ^Ia 3 ^d for 15^≦n*≦17, while an ^Im 3 ^m type is formed for 18^≦n*≦20. Furthermore, for ^n* = 22, two types of cubic phase, one with ^Im 3 ^m symmetry in the low temperature region and the other with ^Ia 3 ^d in the high temperature region, were observed both on heating and cooling. The phase diagram with respect to ^T and ^n* is very similar to that of pure one-component ANBC- ⁿ , which is a function of ^T and the number of carbon atoms in the alkoxy group ⁿ .     

Modification effect of spherical zirconia with SiCl4 as a support of methylaluminoxane for heterogeneous single-site catalyst

Unmodified and SiCl₄-modified spherical zirconia-supported methylaluminoxane were used as cocatalyst for propylene polymerization as well as ethylene/1-hexene copolymerization in combined with Me₂Si(η³-C₁₃H₈)(η¹-N^tBu)TiMe₂ (1) at 0 °C. The modification with SiCl₄ improved the catalytic activity. The improvement was clearer in ethylene/1-hexene copolymerization than in propylene polymerization. The number average molecular weight (M_n) of polypropylenes increased linearly against the polymerization time regardless the cocatalyst used to give polymers with narrow molecular weight distribution (M_w/M_n < 1.32), indicating the living nature of the catalytic systems. Thus, propagation rate constant (k_p) and the number of active centers (C^*) were evaluated from M_n and the number of polymer-chains. When the zirconia was modified with SiCl₄, the k_p value decreased and the C^* increased. The latter effect was more significant to enhance the catalytic activity.     

Nonylphenol Polyethoxylates Degraded by Three Different Wavelengths of UV and Their Genotoxic Change—Detected by Generation of γ‐H2AX

UV rays in sunlight are an important factor in the degradation of chemicals. In this study, we investigated the degradation of nonionic surfactants, nonylphenol polyethoxylates (NPEOs) with 10 or 70 ethylene oxide (EO) units using UVA, B and C, and their genotoxic change based on phosphorylation of histone H2AX (γ‐H2AX), a marker of DNA damage. NPEOs were degraded dependent on the energy of UV, that is, UVC having the highest energy was most effective, whereas UVA having the lowest energy caused little change. The EO side chain of NPEO(70) was broken near the benzene ring by UV, producing NPEOs with a shortened EO chain (around 10 units). The generation of γ‐H2AX reflected the pattern of degradation; shortening of the EO chain changed NPEO(70) into an inducer for γ‐H2AX, and degradation of NPEO(10) attenuated the genotoxicity. The γ‐H2AX generated by NPEO(10) and UV‐degraded NPEO(70) was independent of the cell cycle. The formation of DNA double strand breaks detected by gel electrophoresis was consistent with the results for γ‐H2AX. These results suggested that UV rays can make NPEOs harmless or genotoxic according to the degradation of the EO side chain, the effects being dependent on wavelength.     

Global Structure-Acute Toxicity Relationships for Mice Using Structural Parameter Ratios: New Approach to Molecular Design and Screening

Abstract

A method for a preliminary survey of the relationship between molecular structure and performance was described using 1506 random data of structure-acute toxicity for mice (intravenously dosed). The structural patterns of the weakest toxic structures (111) were extracted from the data and the patterns discriminated for 64.2% of the other structures (1395). As for the 826 structures of strongest toxicity, 78.3% were discriminated by these structural patterns. These results were obtained by using structural parameter ratios to describe the structural patterns and the exhaustive elimination process to select the best parameter ratio from many candidates. The results were summarized in the form of a chart which can be used for practical screening for the weakest toxic structures.     

Cubic phases of 4′-n-alkoxy-3′-nitrobiphenyl-4-carboxylic acids (ANBC-n)

The structure of the thermotropic cubic phases of 4′- ⁿ -alkoxy-3′-nitrobiphenyl-4-carboxylic acids (ANBC- ⁿ , where ⁿ indicates the number of carbon atoms in the alkoxy group) was studied by X-ray diffraction. For the homologues with ⁿ = 15, 16, 17, and 18, the cubic phase was of an ^Ia 3 ^d type, whereas the homologues with ⁿ = 19, 20, and 21 exhibited an ^Im 3 ^m cubic structure; for these seven homologues the same type of cubic structure was observed both on heating and cooling. Further lengthening of the alkoxy chain to ⁿ = 22 and 26, however, gave two types of cubic structure in the cubic phase region on heating, one with ^Im 3 ^m symmetry in the low temperature region and the other with ^Ia 3 ^d symmetry in the high temperature region. On cooling, the two homologues exhibited the ^Ia 3 ^d cubic structure only. This is the first example in the cubic phase region of a series of homologues containing two types of structure, dependent on temperature and ⁿ . Such a complicated phase diagram in the cubic region is clearly understood qualitatively in terms of Gibbs free energy-temperature diagrams. The dependence of structural parameters such as the cubic lattice constant on the alkoxy chain length ⁿ are also presented and discussed.     

Injectable Polypeptide Hydrogel Depot System for Assessment of the Immune Response–Inducing Efficacy of Sustained Antigen Release Alone

Vaccines typically contain an antigen, delivery system (vehicle), and adjuvant, all of which contribute to inducing a potent immune response. Consequently, design of new vaccines is difficult, because the contributions and interactions of these components are difficult to distinguish. Here, it is aimed to develop an easy‐to‐use, non‐immunogenic, injectable depot system for sustained antigen release that will be suitable for assessing the efficacy of prolonged antigen exposure per se for inducing an immune response. This should mimic real‐life infections. Recombinant elastin‐like polypeptides with periodic cysteine residues (cELPs) are selected, which reportedly show little or no immunogenicity, as carriers and tetanus toxoid (Ttd) as an antigen. After subcutaneous injection of the mixture, cELP rapidly forms a disulfide cross‐linked hydrogel in situ, within which Ttd is physically incorporated, affording a biodegradable antigen depot. A series of Ttd‐containing hydrogels is examined. A single injection induces high levels of tetanus antibody with high avidity for at least 20 weeks in mice. The chain length of cELP proves critical, whereas differences in hydrophobicity has little effect, although hydrophilic cELPs are more rapidly biodegraded. This system's ability to distinguish the contribution of sustained antigen release to antibody induction should be helpful for rational design of next‐generation vaccines.