| 1. |
- Meyer, Peter A., et al.
(författare)
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Data publication with the structural biology data grid supports live analysis
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data. sbgrid. org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
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| 2. |
- Ghavami, Saeid, et al.
(författare)
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S100A8/A9 induces autophagy and apoptosis via ROS-mediated cross-talk between mitochondria and lysosomes that involves BNIP3
- 2010
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Ingår i: Cell Research. - : Springer Science and Business Media LLC. - 1001-0602 .- 1748-7838. ; 20:3, s. 314-331
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Tidskriftsartikel (refereegranskat)abstract
- The complex formed by two members of the S100 calcium-binding protein family, S100A8/A9, exerts apoptosis-inducing activity in various cells of different origins. Here, we present evidence that the underlying molecular mechanisms involve both programmed cell death I (PCD I, apoptosis) and PCD II (autophagy)-like death. Treatment of cells with S100A8/A9 caused the increase of Beclin-1 expression as well as Atg12-Atg5 formation. S100A8/A9-induced cell death was partially inhibited by the specific PI3-kinase class III inhibitor, 3-methyladenine (3-MA), and by the vacuole H+-ATPase inhibitor, bafilomycin-A1 (Baf-A1). S100A8/A9 provoked the translocation of BNIP3, a BH3 only pro-apoptotic Bcl2 family member, to mitochondria. Consistent with this finding, ΔTM-BNIP3 overexpression partially inhibited S100A8/A9-induced cell death, decreased reactive oxygen species (ROS) generation, and partially protected against the decrease in mitochondrial transmembrane potential in S100A8/A9-treated cells. In addition, either ΔTM-BNIP3 overexpression or N-acetyl-L-cysteine co-treatment decreased lysosomal activation in cells treated with S100A8/A9. Our data indicate that S100A8/A9-promoted cell death occurs through the cross-talk of mitochondria and lysosomes via ROS and the process involves BNIP3.
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| 3. |
- Akke, Mikael, et al.
(författare)
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An open and shut case
- 2001
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Ingår i: Nature Structural Biology. - : Springer Science and Business Media LLC. - 1072-8368. ; 8:11, s. 910-912
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Tidskriftsartikel (refereegranskat)abstract
- A powerful new NMR technique applied to the ubiquitous Ca2+ sensor, calmodulin, reveals significant conformational flexibility within each globular domain, which contributes to its ability to bind a wide range of targets. These measurements of residual dipolar couplings between nuclear spins demonstrate a fast and accurate method for pinpointing structural features that cannot be delineated reliably by traditional NOE analysis.
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| 4. |
- Carlström, Göran, et al.
(författare)
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[7] NMR studies of complex DNA structures : The holliday junction intermediate in genetic recombination
- 1995
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Ingår i: Methods in Enzymology : Nuclear Magnetic Resonance and Nucleic Acids - Nuclear Magnetic Resonance and Nucleic Acids. - 0076-6879. - 9780121821623 ; 261, s. 163-182
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Bokkapitel (refereegranskat)abstract
- Publisher Summary This chapter discusses the current status, of using nuclear magnetic resonance (NMR), to study the structure and dynamics of the holliday junction (HJ). Complex deoxyribonucleic acid (DNA) structures (e.g., triplexes, quadruplexes, junctions) pose difficult problems for study, by NMR, relative to the typical DNA duplexes, because they have nonstandard or distorted local conformations and higher molecular weights that give rise to large resonance linewidths and severe 1H spectral overlap. With more atoms in the system, both assignment and structure calculation become more challenging. The HJ, a four-arm DNA crossover structure, is a transient intermediate formed in the course of genetic recombination as well as during other cellular processes, such as replication and telomere resolution. A significant body of evidence has accumulated, indicating that the structure at the junction has a central role, in determining the outcome of these cellular events. For NMR studies, the titration of the four component 16-mer strands to create an equimolar mixture is critical. Gel electrophoresis has shown that titrations based on the standard ultraviolet (UV) estimates of strand concentrations result in significant amounts of residual single-strand, half-complementary duplex, and three-arm structures.
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| 5. |
- Ghavami, Saeid, et al.
(författare)
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S100A8/9 induces cell death via a novel, RAGE-independent pathway that involves selective release of Smac/DIABLO and Omi/HtrA2
- 2008
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Ingår i: Biochimica et Biophysica Acta. Molecular Cell Research. - : Elsevier. - 0167-4889 .- 1879-2596. ; 1783:2, s. 297-311
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Tidskriftsartikel (refereegranskat)abstract
- A complex of two S100 EF-hand calcium-binding proteins S100A8/A9 induces apoptosis in various cells, especially tumor cells. Using several cell lines, we have shown that S100A8/A9-induced cell death is not mediated by the receptor for advanced glycation endproducts (RAGE), a receptor previously demonstrated to engage S100 proteins. Investigation of cell lines either deficient in, or over-expressing components of the death signaling machinery provided insight into the S100A8/A9-mediated cell death pathway. Treatment of cells with S100A8/A9 caused a rapid decrease in the mitochondrial membrane potential (ΔΨm) and activated Bak, but did not cause release of apoptosis-inducing factor (AIF), endonuclease G (Endo G) or cytochrome c. However, both Smac/DIABLO and Omi/HtrA2 were selectively released into the cytoplasm concomitantly with a decrease in Drp1 expression, which inhibits mitochondrial fission machinery. S100A8/A9 treatment also resulted in decreased expression of the anti-apoptotic proteins Bcl2 and Bcl-XL, whereas expression of the pro-apoptotic proteins Bax, Bad and BNIP3 was not altered. Over-expression of Bcl2 partially reversed the cytotoxicity of S100A8/A9. Together, these data indicate that S100A8/A9-induced cell death involves Bak, selective release of Smac/DIABLO and Omi/HtrA2 from mitochondria, and modulation of the balance between pro- and anti-apoptotic proteins.
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| 6. |
- Ghavami, Saeid, et al.
(författare)
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S100A8/A9 at low concentration promotes tumor cell growth via RAGE ligation and MAP kinase-dependent pathway
- 2008
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Ingår i: Journal of Leukocyte Biology. - : eration of American Societies for Experimental Biology. - 0741-5400 .- 1938-3673. ; 83:6, s. 1484-1492
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Tidskriftsartikel (refereegranskat)abstract
- The complex formed by two members of the S100 calcium-binding protein family, S100A8/A9, exerts apoptosis-inducing activity against various cells, especially tumor cells. Here, we present evidence that S100A8/A9 also has cell growth-promoting activity at low concentrations. Receptor of advanced glycation end product (RAGE) gene silencing and cotreatment with a RAGE-specific blocking antibody revealed that this activity was mediated via RAGE ligation. To investigate the signaling pathways, MAPK phosphorylation and NF-κB activation were characterized in S100A8/A9-treated cells. S100A8/A9 caused a significant increase in p38 MAPK and p44/42 kinase phosphorylation, and the status of stress-activated protein kinase/JNK phosphorylation remained unchanged. Treatment of cells with S100A8/A9 also enhanced NF-κB activation. RAGE small interfering RNA pretreatment abrogated the S100A8/A9-induced NF-κB activation. Our data indicate that S100A8/A9-promoted cell growth occurs through RAGE signaling and activation of NF-κB.
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| 7. |
- Potts, Barbara C.M., et al.
(författare)
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1H NMR assignments of apo calcyclin and comparative structural analysis with calbindin d(9k) and s 100β
- 1996
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Ingår i: Protein Science. - : Wiley. - 0961-8368 .- 1469-896X. ; 5:11, s. 2162-2174
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Tidskriftsartikel (refereegranskat)abstract
- The homodimeric S100 protein calcyclin has been studied in the apo state by two-dimensional 1H NMR spectroscopy. Using a combination of scalar correlation and NOE experiments, sequence-specific 1H NMR assignments were obtained for all but one backbone and >90% of the side-chain resonances. To our knowledge, the 2 x 90 residue (20 kDa) calcyclin dimer is the largest protein system for which such complete assignments have been made by purely homonuclear methods. Sequential and medium-range NOEs and slowly exchanging backbone amide protons identified directly the four helices and the short antiparallel β-type interaction between the two binding loops that comprise each subunit of the dimer. Further analysis of NOEs enabled the unambiguous assignment of 556 intrasubunit distance constraints, 24 intrasubunit hydrogen bonding constraints, and 2 x 26 intersubunit distance constraints. The conformation of the monomer subunit was refined by distance geometry and restrained molecular dynamics calculations using the intrasubunit constraints only. Calculation of the dimer structure starting from this conformational ensemble has been reported elsewhere. The extent of structural homology among the apo calcyclin subunit, the monomer subunit of apo S100β, and monomeric apo calbindin D(9k) has been examined in detail by comparing 1H NMR chemical shifts and secondary structures. This analysis was extended to a comprehensive comparison of the three-dimensional structures of the calcyclin monomer subunit and calbindin D(9k), which revealed greater similarity in the packing of their hydrophobic cores than was anticipated previously. Together, these results support the hypothesis that all members of the S100 family have similar core structures and similar modes of dimerization. Analysis of the amphiphilicity of Helix IV is used to explain why calbindin D(9k) is monomeric, but full-length S100 proteins form homodimers.
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