Browsing by Author "Chang, Cheng-Wen"

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Enzyme Reaction Annotation Using Cloud Techniques
(2013)
Huang, Chuan-Ching
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Lin, Chun-Yuan
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Chang, Cheng-Wen
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Tang, Chuan Yi
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應用化學系
An understanding of the activities of enzymes could help to elucidate the metabolic pathways of thousands of chemical reactions that are catalyzed by enzymes in living systems. Sophisticated applications such as drug design and metabolic reconstruction could be developed using accurate enzyme reaction annotation. Because accurate enzyme reaction annotation methods create potential for enhanced production capacity in these applications, they have received greater attention in the global market. We propose the enzyme reaction prediction (ERP) method as a novel tool to deduce enzyme reactions from domain architecture. We used several frequency relationships between architectures and reactions to enhance the annotation rates for single and multiple catalyzed reactions. The deluge of information which arose from high-throughput techniques in the postgenomic era has improved our understanding of biological data, although it presents obstacles in the data-processing stage. The high computational capacity provided by cloud computing has resulted in an exponential growth in the volume of incoming data. Cloud services also relieve the requirement for large-scale memory space required by this approach to analyze enzyme kinetic data. Our tool is designed as a single execution file; thus, it could be applied to any cloud platform in which multiple queries are supported.
Identification of Essential Residues of Human alpha-L-Fucosidase and Tests of Its Mechanism
(2009-01-13)
Liu, Sheng-Wen
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Chen, Chao-Sheng
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Chang, Shih-Shen
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Mong, Kwok-Kong Tony
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Lin, Chun-Hung
Fucosylated glycoconjugates have critical roles in biological processes, but a limited availability Of alpha-L-fucosidase has hampered research on this human enzyme (h-Fuc) at a molecular level. After overexpressing h-Fuc in Escherichia coli as an active form, we investigated the catalytic function of this recombinant enzyme. Based on sequence alignment and structural analysis of close homologues of h-Fuc, nine residues of glutamate and aspartate in h-Fuc were selected for mutagenic tests to determine the essential residues. Among the mutants, D225N, E289Q, and E289G lost catalytic activity significantly; their k(cat) values are 1/5700, 1/430, and 1/340, respectively, of that of the wild-type enzyme. The Bronsted plot for k(cat)/K(m) for the E289G mutant is linear with beta(1g) = -0.93, but that for k(cat) is biphasic, with beta(1g) for poor substrates being -0.88 and for activated substrates being -0.11. The small magnitude of Pig for the activated substrates may indicate that the rate-limiting step of the reaction is defucosylation, whereas the large magnitude of the latter Pig value for the poor substrates indicates that the rate-limiting step of the reaction becomes fucosylation. The kinetic outcomes support an argument that ASp(225) functions as a nucleophile and Glu(289) as a general acid/base catalyst. As further evidence, azide significantly reactivated D225G and E289G, and (1)H NMR spectral analysis confirmed the formation of beta-fucosyl azide and alpha-fucosyl azide in the azide rescues of D225G and E289G catalyses, respectively. As direct evidence to prove the function of Glu(289), an accumulation of fucosyl-enzyme intermediate was detected directly through ESI/MS analysis.
Long-term impacts of residue harvesting on soil quality
(2013-11-01)
Laird, David A.
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Chang, Cheng-Wen
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應用化學系
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Department of Applied Chemistry
Development of the cellulosic bioenergy industry raises the prospect of wide spread stover harvesting in the near future; however, the impact of stover harvesting on soil quality may not be apparent for several years. Here we evaluate the impact of 19 years of either zero or approximately 90% removal of above ground crop residue on soil quality. The 0-5, 5-15, and 15-30 cm soil depths of Waukegan silt loam (Typic Hapludoll) from east-central Minnesota were sampled from plots after 12 and 7 years of maize and soybean cropping, respectively. On average for the 0-5 and 5-15 cm depths, soil organic C was 12% less, total N was 12.6% less, N mineralization potential was 27.7% less, cation exchange capacity was 7.3% less, macro aggregation was 13.0% less, and total respiration was 12.3% less for plots with residue harvesting relative to plots where residue was not harvested. Minimal impacts of residue harvesting were apparent for the 15-30 cm soil samples, except N mineralization potential which was 28% lower for plots with residue harvesting. Declines in soil quality indicators due to residue harvesting were only slightly less severe for no-tillage plots relative to chisel and moldboard plow tillage plots. We conclude that harvesting 90% of above ground residue for 19 years resulted in substantial degradation of soil quality, and that the impact on N mineralization potential was substantially larger than the loss of total N, suggesting that labile organic N was selectively depleted. We also conclude that stover harvesting for bioenergy production could cause similar degradation of soil quality unless management practices that increase C inputs to soils are also implemented. (C) 2013 Elsevier B.V. All rights reserved.