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31.
Family 47 alpha-1,2-mannosidases are crucial enzymes involved in N-glycan maturation in the endoplasmic reticula and Golgi apparati of eukaryotic cells. High-resolution crystal structures of the human and yeast endoplasmic reticulum alpha-1,2-mannosidases have been recently determined, the former complexed with the inhibitors 1-deoxymannojirimycin and kifunensine, both of which bind in its active site in the unusual 1C4 conformation. However, unambiguous identification of the catalytic proton donor and nucleophile involved in glycoside bond hydrolysis was not possible from this structural information. In this work, alpha-D-galactose, alpha-D-glucose, and alpha-D-mannose were computationally docked in the active site in the energetically stable 4C1 conformation as well as in the 1C4 conformation to compare their interaction energetics. From these docked structures, a model for substrate and conformer selectivity based on the dimensions of the active site was proposed. Alpha-D-galactopyranosyl-(1-->2)-alpha-D-mannopyranose, alpha-D-glucopyranosyl-(1-->2)-alpha-D-mannopyranose, and alpha-D-mannopyranosyl-(1-->2)-alpha-D-mannopyranose were also docked into the active site with their nonreducing-end residues in the 1C4 and E4 (representing the transition state) conformations. Based on the docked structure of alpha-D-mannopyranosyl-E4-(1-->2)-alpha-D-mannopyranose, the catalytic acid and base are Glu132 and Glu435, respectively. 相似文献
32.
33.
Komal Bajaj Sandeep Burudkar Pranay Shah Ashish Keche Usha Ghosh Prashant Tannu Smriti Khanna Ankita Srivastava Nitin J. Deshmukh Amol Dixit Yogesh Ahire Anagha Damre Kumar V.S. Nemmani Asha Kulkarni-Almeida Chandrika B-Rao Rajiv Sharma H. Sivaramakrishnan 《Bioorganic & medicinal chemistry letters》2013,23(3):834-838
We report our attempts at improving the oral efficacy of low-nanomolar inhibitors of xanthine oxidase from isocytosine series through chemical modifications. Our lead compound had earlier shown good in vivo efficacy when administered intraperitoneally but not orally. Several modifications are reported here which achieved more than twofold improvement in exposure. A compound with significant improvement in oral efficacy was also obtained. 相似文献
34.
Rao A Pimprikar P Bendigiri C Kumar AR Zinjarde S 《Applied microbiology and biotechnology》2011,92(5):951-959
Amplification of the tyrosinase gene (melO) from the genomic DNA of Aspergillus oryzae NCIM 1212 yielded a 1.6-kb product. This gene was cloned into pYLEX1, and the resulting pTyro-YLEX1 vector was transformed
in Yarrowia lipolytica strain Po1g. A clone displaying the highest specific activity for tyrosinase (10.94 U/mg) was used for obtaining the complementary
DNA (cDNA) and for protein expression studies. cDNA sequence analysis indicated the splicing of an intron present in the melO gene by Po1g. Native polyacrylamide gel electrophoresis, acidification at pH 3.0 followed by activity staining with l-DOPA indicated the expression of an active tyrosinase. The clone over-expressing the tyrosinase transformed l-tyrosine to l-DOPA. On optimization of conditions for the biotransformation (pH 4.0, temperature 60°C and with 3.5 mg of biomass), 0.4 mg/ml
of l-DOPA was obtained. 相似文献
35.
In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern
biology. 相似文献
36.
Cellooligosaccharides were computationally docked using AutoDock into the active sites of the glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly Trichoderma reesei) cellobiohydrolase and Thermobifida fusca endoglucanase. Subsite -2 exerts the greatest intermolecular energy in binding beta-glucosyl residues, with energies progressively decreasing to either side. Cumulative forces imparting processivity exerted by these two enzymes are significantly less than by the equivalent glycoside hydrolase Family 7 enzymes studied previously. Putative subsites -4, -3, +3, and +4 exist in H. jecorina cellobiohydrolase, along with putative subsites -4, -3, and +3 in T. fusca endoglucanase, but they are less important than subsites -2, -1, +1, and +2. In general, binding adds 3-7 kcal/mol to ligand intramolecular energies because of twisting of scissile glycosidic bonds. Distortion of beta-glucosyl residues to the (2)S(O) conformation by binding in subsite -1 adds approximately 7 kcal/mol to substrate intramolecular energies. 相似文献
37.
38.
M. Chandrika Thoyajaksha V. Ravishankar Rai K. Ramachandra Kini 《Biologia Plantarum》2008,52(4):735-739
In the present study, a polymerase chain reaction (PCR)-based method namely inter simple sequence repeat (ISSR) was employed
to assess genetic stability in tissue culture-derived Dictyospermum ovalifolium plantlets. To study genomic stability of micropropagated plants, 14 individuals were randomly tagged among a population of
2500 regenerants and were compared with single donor mother plant. A total of 51 clear and reproducible bands ranging from
200 bp to 2.1 kb were scored corresponding to an average of 3.64 bands per primer. Two of the 51 bands were polymorphic (3.92
%) among 14 individuals, thus indicating the occurrence of low level genomic variation in the micropropagated plants. Cluster
analysis indicates that genetic similarity values were 0.978 which allows classification of the plants to distinct groups.
Further an attempt was made to reintroduce the micropropagated plants into their natural habitat. Over one thousand six hundred
fifty plants were successfully established. 相似文献
39.
Comparative genomics using data mining tools 总被引:3,自引:0,他引:3
We have analysed the genomes of representatives of three kingdoms of life, namely, archaea, eubacteria and eukaryota using
data mining tools based on compositional analyses of the protein sequences. The representatives chosen in this analysis wereMethanococcus jannaschii, Haemophilus influenzae andSaccharomyces cerevisiae. We have identified the common and different features between the three genomes in the protein evolution patterns.M. jannaschii has been seen to have a greater number of proteins with more charged amino acids whereasS. cerevisiae has been observed to have a greater number of hydrophilic proteins. Despite the differences in intrinsic compositional characteristics
between the proteins from the different genomes we have also identified certain common characteristics. We have carried out
exploratory Principal Component Analysis of the multivariate data on the proteins of each organism in an effort to classify
the proteins into clusters. Interestingly, we found that most of the proteins in each organism cluster closely together, but
there are a few ‘outliers’. We focus on the outliers for the functional investigations, which may aid in revealing any unique
features of the biology of the respective organisms. 相似文献
40.
Hypocrea jecorina (formerly Trichoderma reesei) Cel7A has a catalytic domain (CD) and a cellulose-binding domain (CBD) separated by a highly glycosylated linker. Very little is known of how the 2 domains interact to degrade crystalline cellulose. Based on the interaction energies and forces on cello-oligosaccharides computationally docked to the CD and CBD, we propose a molecular machine model, where the CBD wedges itself under a free chain end on the crystalline cellulose surface and feeds it to the CD active site tunnel. Enzyme-substrate interactions produce the forces required to pull cellulose chains from the surface and also to help the enzyme move on the cellulose chain for processive hydrolysis. The energy to generate these forces is ultimately derived from the chemical energy of glycosidic bond breakage. 相似文献