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71.
Core histones of the amitochondriate protist, Giardia lamblia 总被引:3,自引:0,他引:3
Wu G McArthur AG Fiser A Sali A Sogin ML Mllerm M 《Molecular biology and evolution》2000,17(8):1156-1163
Genes coding for the core histones H2a, H2b, H3, and H4 of Giardia lamblia were sequenced. A conserved organism- and gene-specific element, GRGCGCAGATTTVGG, was found upstream of the coding region in all core histone genes. The derived amino acid sequences of all four histones were similar to their homologs in other eukaryotes, although they were among the most divergent members of this protein family. Comparative protein structure modeling combined with energy evaluation of the resulting models indicated that the G. lamblia core histones individually and together can assume the same three-dimensional structures that were established by X-ray crystallography for Xenopus laevis histones and the nucleosome core particle. Since G. lamblia represents one of the earliest-diverging eukaryotes in many different molecular trees, the structure of its histones is potentially of relevance to understanding histone evolution. The G. lamblia proteins do not represent an intermediate stage between archaeal and eukaryotic histones. 相似文献
72.
Bonanno JB Almo SC Bresnick A Chance MR Fiser A Swaminathan S Jiang J Studier FW Shapiro L Lima CD Gaasterland TM Sali A Bain K Feil I Gao X Lorimer D Ramos A Sauder JM Wasserman SR Emtage S D'Amico KL Burley SK 《Journal of structural and functional genomics》2005,6(2-3):225-232
Structural GenomiX, Inc. (SGX), four New York area institutions, and two University of California schools have formed the
New York Structural GenomiX Research Consortium (NYSGXRC), an industrial/academic Research Consortium that exploits individual
core competencies to support all aspects of the NIH-NIGMS funded Protein Structure Initiative (PSI), including protein family
classification and target selection, generation of protein for biophysical analyses, sample preparation for structural studies,
structure determination and analyses, and dissemination of results. At the end of the PSI Pilot Study Phase (PSI-1), the NYSGXRC
will be capable of producing 100–200 experimentally determined protein structures annually. All Consortium activities can
be scaled to increase production capacity significantly during the Production Phase of the PSI (PSI-2). The Consortium utilizes
both centralized and de-centralized production teams with clearly defined deliverables and hand-off procedures that are supported
by a web-based target/sample tracking system (SGX Laboratory Information Data Management System, LIMS, and NYSGXRC Internal
Consortium Experimental Database, ICE-DB). Consortium management is provided by an Executive Committee, which is composed
of the PI and all Co-PIs. Progress to date is tracked on a publicly available Consortium web site (http://www.nysgxrc.org)
and all DNA/protein reagents and experimental protocols are distributed freely from the New York City Area institutions. In
addition to meeting the requirements of the Pilot Study Phase and preparing for the Production Phase of the PSI, the NYSGXRC
aims to develop modular technologies that are transferable to structural biology laboratories in both academe and industry.
The NYSGXRC PI and Co-PIs intend the PSI to have a transforming effect on the disciplines of X-ray crystallography and NMR
spectroscopy of biological macromolecules. Working with other PSI-funded Centers, the NYSGXRC seeks to create the structural
biology laboratory of the future. Herein, we present an overview of the organization of the NYSGXRC and describe progress
toward development of a high-throughput Gene→Structure platform. An analysis of current and projected consortium metrics reflects
progress to date and delineates opportunities for further technology development. 相似文献
73.
Characterization of a di-leucine-based signal in the cytoplasmic tail of the nucleotide-pyrophosphatase NPP1 that mediates basolateral targeting but not endocytosis
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Bello V Goding JW Greengrass V Sali A Dubljevic V Lenoir C Trugnan G Maurice M 《Molecular biology of the cell》2001,12(10):3004-3015
Enzymes of the nucleotide pyrophosphatase/phosphodiesterase (NPPase) family are expressed at opposite surfaces in polarized epithelial cells. We investigated the targeting signal of NPP1, which is exclusively expressed at the basolateral surface. Full-length NPP1 and different constructs and mutants were transfected into the polarized MDCK cell line. Expression of the proteins was analyzed by confocal microscopy and surface biotinylation. The basolateral signal of NPP1 was identified as a di-leucine motif located in the cytoplasmic tail. Mutation of either or both leucines largely redirected NPP1 to the apical surface. Furthermore, addition of the conserved sequence AAASLLAP redirected the apical nucleotide pyrophosphatase/phosphodiesterase NPP3 to the basolateral surface. Full-length NPP1 was not significantly internalized. However, when the cytoplasmic tail was deleted upstream the di-leucine motif or when the six upstream flanking amino acids were deleted, the protein was mainly found intracellularly. Endocytosis experiments indicated that these mutants were endocytosed from the basolateral surface. These results identify the basolateral signal of NPP1 as a short sequence including a di-leucine motif that is dominant over apical determinants and point to the importance of surrounding amino acids in determining whether the signal will function as a basolateral signal only or as an endocytotic signal as well. 相似文献
74.
Our study was aimed at examinating whether or not the human genome encodes for previously unreported cysteine cathepsins. To this end, we used analyses of the genome sequence and mRNA expression levels. The program TBLASTN was employed to scan the draft sequence of the human genome for the 11 known cysteine cathepsins. The cathepsin-like segments in the genome were inspected, filtered, and annotated. In addition to the known cysteine cathepsins, the scan identified three pseudogenes, closely related to cathepsin L, on chromosome 10, as well as two remote homologs, tubulointerstitial protein antigen and tubulointerstitial protein antigen-related protein. No new members of the family were identified. mRNA expression profiles for 10 known human cysteine cathepsins showed varying expression levels in 46 different human tissues and cell lines. No expression of any of the three cathepsin L-like pseudogenes was found. Based on these results, it is likely that to date all human cysteine cathepsins are known. 相似文献
75.
We have developed a variable gap penalty function for use in the comparison program COMPARER which aligns protein sequences on the basis of their 3-D structures. For deletions and insertions, components are a function of structural features of individual amino acid residues (e.g. secondary structure and accessibility). We have also obtained relative weights for different features used in the comparison by examining the equivalent residues in weight matrices and in alignments for pairs of 3-D structures where the equivalencies are relatively unambiguous. We have used the new parameters and the variable gap penalty function in COMPARER to align protein structures in the Brookhaven Data Bank. The variable gap penalty function is useful especially in avoiding gaps in secondary structure elements and the new feature weights give improved alignments. The alignments for both azurins and plastocyanins and N- and C-terminal lobes for aspartic proteinases are discussed. 相似文献
76.
77.
Peng Hou Jian Ni Sali Cao Haimin Lei Zhengjun Cai Tao Zhang Fang Yu Qingzhong Tan 《AAPS PharmSciTech》2013,14(2):629-638
Ensuring sufficient drug solubility is a crucial problem in pharmaceutical-related research. For water-insoluble drugs, various formulation approaches are employed to enhance the solubility and bioavailability of lead compounds. The goal of this study was to enhance the dissolution and absorption of a new antitumor lead compound, T-OA. Early-stage preparation discovery concept was employed in this study. Based on this concept, a solid dispersion system was chosen as the method of improving drug solubility and bioavailability. Solid dispersions of T-OA in polyvinylpyrrolidone (PVP) K30 were prepared by the solvent evaporation method. Dissolution testing determined that the ideal drug-to-PVP ratio was 1:5. X-ray diffraction, Fourier transform infrared spectroscopy, and differential scanning calorimetry were employed to confirm the formation of solid dispersions. Scanning electron microscopy demonstrated that T-OA was converted into an amorphous form. Both in vitro dissolution testing and the in vivo studies demonstrated that the solubility and bioavailability of T-OA were significantly improved when formulated in a solid dispersion with PVP. The dissolution rate of the T-OA/PVP solid dispersion was greatly enhanced relative to the pure drug, and the relative bioavailability of T-OA solid dispersions was found to be 392.0%, which is 4-fold higher than the pure drug. 相似文献
78.
Wang Q Sun J Zhou M Yang H Li Y Li X Lv S Li X Li Y 《Bioinformatics (Oxford, England)》2011,27(11):1521-1528
MOTIVATION: In the functional genomic era, a large number of gene sets have been identified via high-throughput genomic and proteomic technologies. These gene sets of interest are often related to the same or similar disorders or phenotypes, and are commonly presented as differentially expressed gene lists, co-expressed gene modules, protein complexes or signaling pathways. However, biologists are still faced by the challenge of comparing gene sets and interpreting the functional relationships between gene sets into an understanding of the underlying biological mechanisms. RESULTS: We introduce a novel network-based method, designated corrected cumulative rank score (CCRS), which analyzes the functional communication and physical interaction between genes, and presents an easy-to-use web-based toolkit called GsNetCom to quantify the functional relationship between two gene sets. To evaluate the performance of our method in assessing the functional similarity between two gene sets, we analyzed the functional coherence of complexes in functional catalog and identified protein complexes in the same functional catalog. The results suggested that CCRS can offer a significant advance in addressing the functional relationship between different gene sets compared with several other available tools or algorithms with similar functionality. We also conducted the case study based on our method, and succeeded in prioritizing candidate leukemia-associated protein complexes and expanding the prioritization and analysis of cancer-related complexes to other cancer types. In addition, GsNetCom provides a new insight into the communication between gene modules, such as exploring gene sets from the perspective of well-annotated protein complexes. Availability and Implementation: GsNetCom is a freely available web accessible toolkit at http://bioinfo.hrbmu.edu.cn/GsNetCom. 相似文献
79.
Self-renewing cancer cells are the only cell types within a tumor that have an unlimited ability to promote tumor growth, and are thus known as tumor-propagating cells, or tumor-initiating cells. It is thought that targeting these self-renewing cells for destruction will block tumor progression and stop relapse, greatly improving patient prognosis. The most common way to determine the frequency of self-renewing cells within a tumor is a limiting dilution cell transplantation assay, in which tumor cells are transplanted into recipient animals at increasing doses; the proportion of animals that develop tumors is used the calculate the number of self-renewing cells within the original tumor sample. Ideally, a large number of animals would be used in each limiting dilution experiment to accurately determine the frequency of tumor-propagating cells. However, large scale experiments involving mice are costly, and most limiting dilution assays use only 10-15 mice per experiment. Zebrafish have gained prominence as a cancer model, in large part due to their ease of genetic manipulation and the economy by which large scale experiments can be performed. Additionally, the cancer types modeled in zebrafish have been found to closely mimic their counterpart human disease. While it is possible to transplant tumor cells from one fish to another by sub-lethal irradiation of recipient animals, the regeneration of the immune system after 21 days often causes tumor regression. The recent creation of syngeneic zebrafish has greatly facilitated tumor transplantation studies. Because these animals are genetically identical, transplanted tumor cells engraft robustly into recipient fish, and tumor growth can be monitored over long periods of time. Syngeneic zebrafish are ideal for limiting dilution transplantation assays in that tumor cells do not have to adapt to growth in a foreign microenvironment, which may underestimate self-renewing cell frequency. Additionally, one-cell transplants have been successfully completed using syngeneic zebrafish and several hundred animals can be easily and economically transplanted at one time, both of which serve to provide a more accurate estimate of self-renewing cell frequency. Here, a method is presented for creating primary, fluorescently-labeled T-cell acute lymphoblastic leukemia (T-ALL) in syngeneic zebrafish, and transplanting these tumors at limiting dilution into adult fish to determine self-renewing cell frequency. While leukemia is provided as an example, this protocol is suitable to determine the frequency of tumor-propagating cells using any cancer model in the zebrafish. 相似文献
80.