Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2

Recently, inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) have been proposed as potential therapeutic agents for COVID-19. Studying effects of amino acid mutations in the conformation of drug targets is necessary for anticipating drug resistance. In this study, with the structure of the SARS-CoV-2 Mpro complexed with a non-covalent inhibitor, we performed molecular dynamics (MD) simulations to determine the conformation of the complex when single amino acid residue in the active site is mutated. As a model of amino acid mutation, we constructed mutant proteins with one residue in the active site mutated to alanine. This method is called virtual alanine scan. The results of the MD simulations showed that the conformation and configuration of the ligand was changed for mutants H163A and E166A, although the structure of the whole protein and of the catalytic dyad did not change significantly, suggesting that mutations in His163 and Glu166 may be linked to drug resistance.     

Theoretical calculation of heat of formation and heat of combustion for several flammable gases

Heats of formation have been calculated by the Gaussian-2 (G2) and/or G2MP2 method for a number of flammable gases. As a result, it has been found that the calculated heat of formation for compounds containing, such atoms as fluorine and chlorine tends to deviate from the observed values more than calculations for other molecules do. A simple atom additivity correction (AAC) has been found effective to improve the quality of the heat of formation calculation from the G2 and G2MP2 theories for these molecules. The values of heat of formation thus obtained have been used to calculate the heat of combustion and related constants for evaluating the combustion hazard of flammable gases.     

Zn, Al, Rh-mixed oxides derived from hydrotalcite-like compound and their catalytic properties for N2O decomposition

The catalytic decomposition of nitrous oxide was studied over Zn, Al, Rh-mixed oxides derived from hydrotalcite-like compounds (HTlc) as a precursor. The study showed that, when the Zn/Al atomic ratio was 3, the rate of ZnAlRh-HTlc for N₂O decomposition increased with Rh loading up to 1.4 wt% (4.55 × 10⁴ μmol g⁻¹ h⁻¹ at 400°C), and levels off with further increase in Rh loading. Analogous behavior was found in the presence of NO₂ and water. In the presence of 0.5% water, the activity decreased with decreasing Zn/Al ratio, whereas the activity for N₂O decomposition in the presence of 0.1% NO₂ reached a maximum when the Zn/Al ratio was 3. The observed catalytic activities were comparable to those of the reported catalysts in the presence of NO₂ and water.     

A 500-megabyte/s data-rate 4.5 M DRAM

A 512-kb×9 DRAM with a 500-Mbyte/s data transfer rate was developed. This high data rate was achieved by designing a DRAM core with a very high internal column bandwidth, and coupling this core with a block-oriented, small-swing, synchronous interface that uses skew-canceling clocks. The DRAM has a 1-kbyte×2-line sense-amp cache and is assembled in a 32-pin vertical surface-mount-type plastic package. The measurement results clearly verified the 500-Mbyte/s data rate     

Hydrogen fermentation properties of undiluted cow dung

Anaerobic treatment of undiluted cow dung (15% total solids), so-called dry fermentation, produced hydrogen (743 ml-H(2)/kg-cow dung) at an optimum temperature of 60 degrees C, with butyrate and acetate formation. The hydrogen production was inhibited by the addition of NH(4)(+) in a dose-dependent manner. A bacterium with similarity to Clostridium cellulosi was detected in the fermented dung by a 16S rDNA analysis.     

Phylogenetic classification of Pseudomonas putida strains by MALDI-MS using ribosomal subunit proteins as biomarkers

A new method for phylogenetic classification of bacterial strains using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is proposed. This method was developed using a bioinformatics-based approach to the rapid identification of bacteria as previously proposed by Demirev and co-workers, which uses ribosomal proteins composed of approximately 50 subunit proteins as biomarkers. Although the amino acid sequences of ribosomal proteins are highly conserved, slight sequence variations can occur at the strain level. Since ribosomal subunit proteins are a complex of housekeeping proteins that have different phylogenetic evolution rates, sequence variation detected as mass differences by MALDI-MS may be useful for the phylogenetic classification of bacteria at strain level. In our proposed method, the first step is the selection of reliable biomarkers through characterization of the expressed ribosomal subunit proteins of a reference strain (usually a genome-sequenced strain) by MALDI-MS. The observed masses in the MALDI mass spectra of cell lysates of sample strains are then compared with the biomarker masses of the reference strain. The biomarkers for each sample strain were designated as present or absent at the reference masses, indicated by 1 or 0, respectively, which were summarized in a table. This table is processed by cluster analysis, generating a phylogenetic tree. In this study, the success of this approach was confirmed by classification of Pseudomonas putida strains because its classification is much more complicated than that of other bacterial strains. Forty-three reliable biomarkers were selected from ribosomal sub-unit proteins of a genome-sequenced strain, P. putida KT2440. The numbers and kinds of biomarkers observed for 16 strains of P. putida, including different biovars, were markedly different, reflecting the variety of the strains. The classification results by the proposed method were highly comparable to those based on the DNA gyrase subunit B gene (gyrB) sequence analysis, suggesting our proposed method would be a useful high-throughput method for phylogenetic classification of newly isolated bacteria.     

Production of recombinant human lysosomal acid lipase in Schizosaccharomyces pombe: development of a fed-batch fermentation and purification process

A fed-batch fermentation process has been developed to enable the production of large quantities of recombinant human lysosomal acid lipase (hLAL; EC 3.1.1.13), in Schizosaccharomyces pombe, for preclinical studies as a potential enzyme therapy drug. Recombinant S. pombe, clone ASP397-21, expressed enzymatically active hLAL in the secreted form. A feedback fed-batch system was used to determine the optimal feed rate of a 50% glucose solution used as the carbon source. The feed rate of the glucose solution was calculated by a computer-aided system according to the equation; F=q(sf)(VX)/S(in) (q(sf), specific substrate feed rate [gram substrate/gram dry cell weight/h]; V, volume of culture broth [l]; X, cell density [gram dry cell weight/l]; S(in), concentration of growth limiting substrate in feed solution [gram substrate/gram feed solution]). At the time of the initial consumption of glucose in the batch-phase culture, the nutrient supply was automatically initiated by means of monitoring the respiratory quotient change. The obtained profile of the feed rate was applied to the feed forward control fermentation. Finally, the cells were grown up to >50 g dry cell weight/l, and the hLAL expression level was approximately 16,000 U/l. Expressed hLAL protein was purified in a two-step process by hydrophobic interaction and anion exchange chromatographies. Purified recombinant hLAL exhibited a 90-150 kDa broad band upon SDS-PAGE with specific activity of about 300 U/mg. After endoglycosidase H treatment, the band converged to 45 kDa, equal to the calculated molecular weight, suggesting that hLAL produced in S. pombe was hyper-glycosylated. N-terminal analysis of de-glycosylated hLAL revealed that the signal sequence of hLAL was correctly processed in S. pombe.