Computer-aided antibody design

Recent clinical trials using antibodies with low toxicity and high efficiency have raised expectations for the development of next-generation protein therapeutics. However, the process of obtaining therapeutic antibodies remains time consuming and empirical. This review summarizes recent progresses in the field of computer-aided antibody development mainly focusing on antibody modeling, which is divided essentially into two parts: (i) modeling the antigen-binding site, also called the complementarity determining regions (CDRs), and (ii) predicting the relative orientations of the variable heavy (V(H)) and light (V(L)) chains. Among the six CDR loops, the greatest challenge is predicting the conformation of CDR-H3, which is the most important in antigen recognition. Further computational methods could be used in drug development based on crystal structures or homology models, including antibody-antigen dockings and energy calculations with approximate potential functions. These methods should guide experimental studies to improve the affinities and physicochemical properties of antibodies. Finally, several successful examples of in silico structure-based antibody designs are reviewed. We also briefly review structure-based antigen or immunogen design, with application to rational vaccine development.     

Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon

We have cloned the gene encoding RNase HII (RNase HIIPk) from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 by screening of a library for clones that suppressed the temperature-sensitive growth phenotype of an rnh mutant strain of Escherichia coli. This gene was expressed in an rnh mutant strain of E. coli, the recombinant enzyme was purified, and its biochemical properties were compared with those of E. coli RNases HI and HII. RNase HIIPk is composed of 228 amino acid residues (molecular weight, 25,799) and acts as a monomer. Its amino acid sequence showed little similarity to those of enzymes that are members of the RNase HI family of proteins but showed 40, 31, and 25% identities to those of Methanococcus jannaschii, Saccharomyces cerevisiae, and E. coli RNase HII proteins, respectively. The enzymatic activity was determined at 30 degreesC and pH 8.0 by use of an M13 DNA-RNA hybrid as a substrate. Under these conditions, the most preferred metal ions were Co2+ for RNase HIIPk, Mn2+ for E. coli RNase HII, and Mg2+ for E. coli RNase HI. The specific activity of RNase HIIPk determined in the presence of the most preferred metal ion was 6. 8-fold higher than that of E. coli RNase HII and 4.5-fold lower than that of E. coli RNase HI. Like E. coli RNase HI, RNase HIIPk and E. coli RNase HII cleave the RNA strand of an RNA-DNA hybrid endonucleolytically at the P-O3' bond. In addition, these enzymes cleave oligomeric substrates in a similar manner. These results suggest that RNase HIIPk and E. coli RNases HI and HII are structurally and functionally related to one another.     

Palladium on Carbon‐Catalyzed One‐Pot N‐Arylindole Synthesis: Intramolecular Aromatic Amination,Aromatization, and Intermolecular Aromatic Amination

Indole and indoline derivatives were selectively and temperature dependently synthesized via the intramolecular cross‐coupling reaction between the amino and aromatic bromine functionalities of 2‐bromophenethylamine derivatives in the presence of 10% palladium on carbon (Pd/C), 1,1′‐bis(diphenylphosphino)ferrocene (DPPF), and sodium tert‐butoxide (NaO‐t‐Bu) in mesitylene at 140 and 200 °C, respectively. The neutralization using acetic acid after formation of the indoline derivatives effectively promoted their aromatization, and the corresponding indole derivatives were obtained at 140 °C. Furthermore, various aryl groups were also introduced to the N‐1 position of the indole, pyrrole, and carbazole rings by their direct intramolecular arylation with aryl halides and a one‐pot protocol for N‐arylindole synthesis from 2‐bromophenethylamine was developed.

     

Release of ‘soluble’ lignin fragments from orchardgrass during its passage through the rumen

Soluble lignin fractions were isolated with 90% (v/v) aqueous dioxane from the rumen digesta and faeces of a heifer fed on orchardgrass harvested at the pre-heading stage. Chemical analysis, UV and IR spectra indicated that the soluble lignin fractions were composed mostly of lignin components. The two solube lignin fractions showed wide distributions of molecular weight and had number-average molecular weights of 650–690 and weight-average molecular weights of 1450–1480. The results showed that, part of the orchardgrass lignin fed was released in the rumen as soluble lignin fragments with different molecular weights and excreted in the faeces possibly without further significant modifications.     

Energy level of minority carrier trap centers induced by light illumination in B-doped Cz-Si solar cells

The conversion efficiency of boron (B)-doped Czochralski silicon (Cz-Si) solar cells decreased by light illumination or minority carrier injection. Defects are induced by illumination and they act as trap centers, shorten the minority carrier (electron) lifetime. The energy level of this minority carrier trap center was determined by analyzing the open-circuit voltage (V_OC) changes as a function of substrate temperature. When substrate temperature is low, all electrons which are captured by the trap centers recombine with holes and they do not contribute to the generation of electric power. However, as the substrate temperature is increasing, some of the captured electrons are thermally excited to the conduction band before recombination. Hence, the lifetime of minority carriers are improved and V_OC is recovered. Based on this result, the energy level of trap center induced by light illumination is estimated to be 0.26 eV, which corresponds to the boron–oxygen-related defect (E_C-0.26 eV).     

Strategies for improving radiation tolerance of Si space solar cells

The present study explored first time the better radiation tolerance of gallium-doped silicon solar cells as compared to conventional boron-doped silicon solar cells after heavy fluence of 1 MeV electron irradiation. One of the approaches to improve the end of life of silicon solar cells is by increasing the effective base carrier concentrations. Analysis of the carrier removal rate R_C in boron, gallium and aluminum-doped Si solar cells showed that carrier removal effects can be partially offset by using gallium as dopant instead of boron.     

Electrochemical reduction of graphene oxide in organic solvents

Graphene oxide (GO) cast on conductive substrates was electrochemically reduced in some organic solvents. The amount of electricity required for the almost complete reduction of GO was 2.0 C for 1 mg GO, corresponding to attaching of a one-electron reducible species to each benzene ring in graphene. The electrochemically reduced GO film gave an electrical conductivity of about 3 S cm⁻¹ and exhibited a relatively high specific capacitance of 147.2 F g⁻¹ in propylene carbonate. The electrochemical reduction of GO was feasible on Al foils as well.     

Experimental study of flow and heat transfer characteristics of natural convection in an enclosure with horizontal parallel heated plates

We conducted an experimental investigation of natural convection in an enclosure containing horizontal parallel heated plates. Our experimental setup was as follows: Two heated plates were arranged vertically in an enclosure. The temperature of the ceiling was maintained at a constant low temperature, while the other sides satisfied thermal insulation boundary conditions. We examined flow characteristics in the enclosure and heat transfer around the horizontal heated plates. In the region between the cooled ceiling and the upper heated surface, vortex motion occurred when the accompanying flow from the lower region interfered with the ascending flow. Heat transfer around the heated surface was enhanced by this vortex motion. In other regions, the flow circulated along the heated surfaces in all cases. Generally speaking, for each flow pattern, the Nusselt number was proportional to some power of the modified Rayleigh number.     

Servo techniques for optical disk drives —high-speed and precise optical beam-positioning control—

We introduce advanced servo techniques for optical disk drives. High speed and precise optcal beam-positioning and following controls are required archival memories such as high density and high data transfer rate optical disk drives for recording many data and high quality moving pictures toward next generation systems. The zero phase error tracking-feed-forward (ZPET-FF) control method is effective for the next generation systems, which have high disk rotation speed beyond the limit of 10,000 rpm of optical disk drives such as current CDs, DVDs or Blu-ray discs. Copyright © 2009 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.     

Site-specific cleavage of MS2 RNA by a thermostable DNA-linked RNase H

A series of DNA-linked RNases H, in which the 15-mer DNA iscross-linked to the Thermus thermophilus RNase HI (TRNH) variantsat positions 135, 136, 137 and 138, were constructed and analyzedfor their abilities to cleave the complementary 15-mer RNA.Of these, that with the DNA adduct at position 135 most efficientlycleaved the RNA substrate, indicating that position 135 is themost appropriate cross-linking site among those examined. Toexamine whether DNA-linked RNase H also site-specifically cleavesa highly structured natural RNA, DNA-linked TRNHs with a seriesof DNA adducts varying in size at position 135 were constructedand analyzed for their abilities to cleave MS2 RNA. These DNAadducts were designed such that DNA-linked enzymes cleave MS2RNA at a loop around residue 2790. Of the four DNA-linked TRNHswith the 8-, 12-, 16- and 20-mer DNA adducts, only that withthe 16-mer DNA adduct efficiently and site-specifically cleavedMS2 RNA. Primer extension revealed that this DNA-linked TRNHcleaved MS2 RNA within the target sequence.