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Triwahyono, S., Jalil, A. A., Mukti, R. R., Musthofa, M., Razali, N. A. M., & Aziz, M. A. A. (2011). Hydrogen spillover behavior of Zn/HZSM-5 showing catalytically active protonic acid sites in the isomerization of n-pentane. Applied Catalysis A: General, 407(1-2), 91–99.
Abstract: The impregnation of zinc particles into MFI zeolite (HZSM-5) caused the formation of catalytically active protonic acid sites for isomerizing n-pentane in the presence of hydrogen. An infrared (IR) study with preadsorbed pyridine revealed that these protonic acid sites originated from the spillover of molecular hydrogen from the zinc species onto the zeolite surface. The requirements for this spillover effect were further studied by IR spectroscopy of adsorbed ammonia and carbon monoxide. The presence of zinc species in HZSM-5 suggested the exchange of acidic character towards strong Lewis acids rather than Brønsted acid sites. The isomerization of n-pentane over the Zn/HZSM-5 catalyst resulted in high activity and stability and the conversion to iso-pentane depends on the promotive effect of hydrogen as a carrier gas.
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Parikesit, A. A., Stadler, P. F., & Prohaska, S. J. (2011). Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes, 2(4), 912–924.
Abstract: The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints.
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Nurachman, Z., Kono, A., Radjasa, O. K., & Natalia, D. (). Identification a Novel Raw-Starch-Degrading-α-Amylase from a Tropical Marine Bacterium. American Journal of Biochemistry and Biotechnology, 6(4), 300–306.
Abstract: Problem statement: Bacteria from the surface of the tropical marine hard coral Acropora sp. were screened for producing raw-starch-degrading-á-amylase. Approach: Based on its 16s rDNA sequence, a bacterium that produced the highest amylolitic activity was identified as Bacillus amyloliquifaciens ABBD. The bacterial isolate secreted a á-amylase extracellularly and then the enzyme was partially purified by ammonium sulfate precipitation followed by anion exchange chromatography. Results: Electrophoresis results both SDS-PAGE and native PAGE suggested that the enzyme was a heterodimeric protein (97 kDa) consisting of 45 and 55 kDa subunits. The á-amylase had an optimum pH of 7.0 and temperature of 60°C. More than 80% activity of the enzyme was retained under high salt conditions (up to 20% NaCl). The enzyme remained stable at 50°C for 1 h. Starch hydrolysis by the enzyme at 70°C yielded oligosaccharides (G2-G4) and at room temperature yielded glucose/maltose (G1 and G2). Conclusion: The B. amyloliquifaciens ABBD á-amylase was capable of degrading various raw starch granules from corn, rice, cassava and sago at room temperature.
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Nurachman, Z., Akanuma, S., Sato, T., Oshima, T., & Tanaka, N. (2000). Crystal structures of 3-isopropylmalate dehydrogenases with mutations at the C-terminus: crystallographic analyses of structure–stability relationships. Protein Engineering, 13(4), 253–258.
Abstract: Thermal stability of the Thermus thermophilus isopropylmalate dehydrogenase enzyme was substantially lost upon the deletion of three residues from the C-terminus. However, the stability was partly recovered by the addition of two, four and seven amino acid residues (called HD177, HD708 and HD711, respectively) to the C-terminal region of the truncated enzyme. Three structures of these mutant enzymes were determined by an X-ray diffraction method. All protein crystals belong to space group P21 and their structures were solved by a standard molecular replacement method where the original dimer structure of the A172L mutant was used as a search model. Thermal stability of these mutant enzymes is discussed based on the 3D structure with special attention to the width of the active-site groove and the minor groove, distortion of β-sheet pillar structure and size of cavity in the domain–domain interface around the C-terminus. Our previous studies revealed that the thermal stability of isopropylmalate dehydrogenase increases when the active-site cleft is closed (the closed form). In the present study it is shown that the active-site cleft can be regulated by open–close movement of the minor groove located at the opposite side to the active-site groove on the same subunit, through a paperclip-like motion.
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Nurachman, Z., Kurniasih, S. D., Puspitawati, F., Hadi, S., Radjasa, O. K., & Natalia, D. (). Cloning of the Endoglucanase Gene from a Bacillus amyloliquefaciens PSM 3.1 in Escherichia coli Revealed Catalytic Triad Residues Thr-His-Glu. American Journal of Biochemistry and Biotechnology, 6(4), 268–274.
Abstract: Problem statement: An Indonesian marine bacterial isolate, Bacillus amyloliquefaciens PSM 3.1 was isolated for hydrolyzing cellulose. A 1500-bp nucleotide fragment was amplified from the chromosomal DNA by the use of primers directed against the conserved sequence of Bacilli endoglucanase genes obtained from GenBank. Approach: The fragment was cloned and expressed in Escherichia coli. Results: The endoglucanase gene (eglII gene) had an open reading frame of 1500 nucleotides encoding a protein of 499 amino acids. The EglII protein belonged to Glycosyl Hydrolase family 5 (GH5) with a Cellulose Binding Module 3 (CBM 3). The structure model of the EglII protein revealed that the catalytic residues seemed to be Glu169 (as proton donor) and Glu257 (as nucleophile) and the catalytic triad residues were Thr256, His229 and Glu169. The EglII endoglucanase exhibited an optimum pH of 6.0 and temperature of 50°C and the enzyme tolerated to high salt concentration. Conclusion/Recommendations: This EglII endoglucanase is a promising candidate for many applications in biomass degradation.
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