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161.
Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications 总被引:1,自引:0,他引:1
Rao KN Kumaran D Seetharaman J Bonanno JB Burley SK Swaminathan S 《Protein science : a publication of the Protein Society》2006,15(7):1735-1744
We report here the crystal structure of a trehalose-6-phosphate phosphatase-related protein (T6PP) from Thermoplasma acidophilum, TA1209, determined by the dual-wavelength anomalous diffraction (DAD) method. T6PP is a member of the haloacid dehalogenase (HAD) superfamily with significant sequence homology with trehalose-6-phosphate phosphatase, phosphoserine phosphatase, P-type ATPases and other members of the family. T6PP possesses a core domain of known alpha/beta-hydrolase fold, characteristic of the HAD family, and a cap domain, with a tertiary fold consisting of a four-stranded beta-sheet with two alpha-helices on one side of the sheet. An active-site magnesium ion and a glycerol molecule bound at the interface between the two domains provide insight into the mode of substrate binding by T6PP. A trehalose-6-phosphate molecule modeled into a cage formed by the two domains makes favorable interactions with the protein molecule. We have confirmed that T6PP is a trehalose phosphatase from amino acid sequence, three-dimensional structure, and biochemical assays. 相似文献
162.
163.
Nagampalli S. A. Krushna Chandanpurath Shiny Srinivasan Dharanya Arivazhagan Sindhu Sridharan Aishwarya Rangarajan B. Narayanan 《Microbiology and immunology》2009,53(3):173-183
cDNA coding for Brugia malayi pepsin inhibitor homolog (Bm-33) from the human filarial parasite was cloned in pRSET for large-scale expression and functional characterization. The pRSET-B cloned gene did not yield recombinant protein expression and the reason was attributed to the presence of an N-terminal signal peptide. The gene was subcloned in pRSET-A without a signal peptide and the 33 kDa histidine-tagged recombinant protein was purified by IMAC. All individuals from an endemic area generated IgG responses against Bm-33 in the order MF>CP>EN. Isotype analysis indicated an elevated IgG4 reactivity in the order MF>EN>CP. Bm-33-specific IgE levels were elevated in MF, CP and EN compared to non-endemic normals with no significant differences among the groups. Paraffin-embedded sections of Setaria digitata (cattle filarial parasite) stained with mouse anti-Bm-33 antibodies exhibited the hypodermal nature of Bm-33. These findings suggest that Bm-33 is an immunodominant antigen and contributes to filarial pathogenesis. 相似文献
164.
Graphiumputredinis, Trichodermaharzianum and fusant were used in the present study to produce extracellular xylanases, an important industrial enzyme used in pulp and paper industry produced in a minimal medium supplemented with oat spelt xylan (1%, w/v) pH 7.0 at 27+/-2 degrees C. The enzyme was purified to homogeneity by DEAE-Cellulose and Superdex 75 FPLC column, respectively. The enzyme was found to be a monomer as determined by SDS gel electrophoresis. The optimum pH and temperature for purified G. putredinis, T. harzianum and fusant xylanases were 5.0-6.0 and 50-70 degrees C, respectively. Pretreatment of paper pulp with G. putredinis, T. harzianum and fusant xylanases decreased pulp kappa number. Xylanases particularly that of fusant at 5 IU/g pulp concentration and 1.5% pulp consistency at 60 degrees C for 18 h followed by EDED process yielded good quality paper from waste paper pulp. A significant increase in pulp brightness and improvement in various pulp properties, viz. burst capacity, thickness and bulkness of the treated pulp were observed in comparison to the conventional chemical bleaching. Easy purification and high stability of these enzymes makes it amicable for industrial applications. 相似文献
165.
Rajaraman Swaminathan Ramanujam Selvakumaran Pulikattil Okkuru Esmy P. Sampath Jacques Ferlay Vinoda Jissa Viswanathan Shanta Mary Cherian Rengaswamy Sankaranarayanan 《Cancer epidemiology》2009,33(5):325-331
Background: Cancer pattern data are rare and survival data are none from rural districts of India. Methods: The Dindigul Ambilikkai Cancer Registry (DACR) covering rural population of 2 millions in Dindigul district, Tamil Nadu state, South India, registered 4516 incident cancers during 2003–2006 by active case finding from 102 data sources for studying incidence pattern, of which, 1045 incident cancers registered in 2003 were followed up for estimating survival. House visits were undertaken annually for each registered case for data completion. Cancer pattern was described using average annual incidence rates and survival experience was expressed by computing observed survival by actuarial method and age-standardized relative survival (ASRS). Results: The average annual age-standardized rate per 100,000 of all cancers together was higher among women (62.6) than men (51.9) in DACR. The most common cancers among men were stomach (5.6), mouth (4.2) and esophagus (3.7). Cervical cancer (22.1) was ranked at the top among women followed by breast (10.9) and ovary (3.3). DACR incidence rates were lesser by at least two folds and 5-year survival were on par or lower than Chennai metropolitan registry for most cancers. Five-year age-standardized relative survival (%) in DACR was as follows: all cancers (29%), larynx (48), mouth (42), breast/tongue (38) and cervix (37). Conclusion: Cancer incidence was significantly lower, cancer patterns were markedly different and population-based cancer survival was lower in rural areas than urban areas thus providing valuable leads in estimating realistic cancer burden and instituting cancer control programs in India. 相似文献
166.
Basirudeen Syed Ahamed Kabeer Rajasekaran Sikhamani Sowmya Swaminathan Venkatesan Perumal Paulkumaran Paramasivam Alamelu Raja 《PloS one》2009,4(5)
Background
A rapid and specific test is urgently needed for tuberculosis (TB) diagnosis especially among human immunodeficiency virus (HIV) infected individuals. In this study, we assessed the sensitivity of Interferon gamma release assay (IGRA) in active tuberculosis patients who were positive for HIV infection and compared it with that of tuberculin skin test (TST).Methodology/Principal Findings
A total of 105 HIV-TB patients who were naïve for anti tuberculosis and anti retroviral therapy were included for this study out of which 53 (50%) were culture positive. Of 105 tested, QuantiFERON-TB Gold in-tube (QFT-G) was positive in 65% (95% CI: 56% to 74%), negative in 18% (95% CI: 11% to 25%) and indeterminate in 17% (95% CI: 10% to 24%) of patients. The sensitivity of QFT-G remained similar in pulmonary TB and extra-pulmonary TB patients. The QFT-G positivity was not affected by low CD4 count, but it often gave indeterminate results especially in individuals with CD4 count <200 cells/µl. All of the QFT-G indeterminate patients whose sputum culture were positive, showed ≤0.25 IU/ml of IFN-γ response to phytohemagglutinin (PHA). TST was performed in all the 105 patients and yielded the sensitivity of 31% (95% CI: 40% to 22%). All the TST positives were QFT-G positives. The sensitivity of TST was decreased, when CD4 cell counts declined.Conclusions/Significance
Our study shows neither QFT-G alone or in combination with TST can be used to exclude the suspicion of active TB disease. However, unlike TST, QFT-G yielded fewer false negative results even in individuals with low CD4 count. The low PHA cut-off point for indeterminate results suggested in this study (≤0.25 IU/ml) may improve the proportion of valid QFT-G results. 相似文献167.
Parthasarathy Sampathkumar Frances Lu Xun Zhao Zhenzhen Li Jeremiah Gilmore Kevin Bain Marc E. Rutter Tarun Gheyi Kenneth D. Schwinn Jeffrey B. Bonanno Ursula Pieper J. Eduardo Fajardo Andras Fiser Steven C. Almo Subramanyam Swaminathan Mark R. Chance David Baker Shane Atwell Devon A. Thompson J. Spencer Emtage Stephen R. Wasserman Andrej Sali J. Michael Sauder Stephen K. Burley 《Proteins》2010,78(14):3056-3062
168.
The loops which connect or flank helices/sheets in protein structures are known to be functionally important. However, ironically they also belong to the part of protein whose structure is least accurately predicted. Here, a new method to isolate and analyze loop regions in protein structure is proposed using the spatial coordinates of the solved three‐dimensional structure. The extent of dispersion among points of successive amino acid residues in the Ramachandran map of protein region is utilized to calculate the Mean Separation between these points in the Ramachandran Plot (MSRP). Based on analysis of 2935 protein secondary structure regions obtained using DSSP software, spanning a range from 2 to 64 residues, taken from a set of 170 proteins, it is shown that helices (MSRP < 17) and strands (MSRP < 64) stand effectively demarcated from the loop regions (MSRP > 130). Analysis of 43 DNA binding and 98 ligand binding proteins revealed several loop regions with clear change in MSRP subsequent to binding. The population of such loops correlated with the magnitude of backbone displacement in the protein subsequent to binding. Can changes in MSRP quantify the temporal oscillations in dihedral angles among structured/unstructured regions in proteins? Molecular dynamics simulations (10 ns) revealed that deviations in MSRP among different snapshots in the trajectory were at least twofold higher for unstructured proteins in comparison with ordered proteins. The above results validate the use of MSRP parameter as a tool to identify and investigate functionally active loops and unstructured regions in protein structures. Proteins 2010. © 2009 Wiley‐Liss, Inc. 相似文献
169.
Christopher J. Penkett Glen van Ginkel Sameer Velankar Jawahar Swaminathan Eldon L. Ulrich Steve Mading Tim J. Stevens Rasmus H. Fogh Aleksandras Gutmanas Gerard J. Kleywegt Kim Henrick Wim F. Vranken 《Journal of biomolecular NMR》2010,48(2):85-92
We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html. 相似文献