{"entity": "publications", "timestamp": "2026-04-13T04:22:27.669Z", "year": "2007", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publications/2007.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publications/2007"}}, "publications_count": 13, "full": true, "publications": [{"entity": "publication", "iuid": "39f59d7fe3334278817ec7ef27092ea1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/39f59d7fe3334278817ec7ef27092ea1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/39f59d7fe3334278817ec7ef27092ea1"}}, "title": "The Schistosoma mansoni protein Sm16/SmSLP/SmSPO-1 is a membrane-binding protein that lacks the proposed microtubule-regulatory activity.", "authors": [{"family": "Holmfeldt", "given": "Per", "initials": "P"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Kristoffer", "initials": "K"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME"}, {"family": "Segerman", "given": "Bo", "initials": "B"}, {"family": "Carlsson", "given": "Sven R", "initials": "SR"}, {"family": "Gullberg", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2007-12-00", "journal": {"title": "Molecular and biochemical parasitology", "issn": "0166-6851", "volume": "156", "issue": "2", "pages": "225-234", "issn-l": null}, "abstract": "Sm16/SmSLP/SPO-1 (Sm16) has been identified as a developmentally regulated protein that is released from specific glands of the Schistosoma mansoni parasite during skin penetration. Sm16 has been ascribed both anti-inflammatory activities and a functional similarity with the conserved cytosolic tubulin-binding protein stathmin/Op18. Here we used a cell line to confirm signal peptide-dependent secretion and to define the secreted form of Sm16 for production in E. coli. We present evidence from both in vitro experiments and studies on transfected human cells that refute any functional similarity with stathmin/Op18. Instead of an Op18-like activity, we found that targeting of Sm16 to the cytosol of human cells, which was achieved by ectopic expression of Sm16 lacking the signal peptide, results in a caspase-dependent apoptotic response. Interestingly, by analysis of recombinant preparations we found that the secreted form of Sm16 is a lipid bilayer-binding protein that efficiently binds to the surface of diverse cell types by a polyanion-independent mechanism, which results in uptake by endocytosis. While the significance of the pro-apoptotic activity exerted by cytosolic Sm16 remains unclear, the present findings on cell-surface-binding properties of Sm16 seems likely to be of functional relevance during skin penetration of the parasite.", "doi": "10.1016/j.molbiopara.2007.08.006", "pmid": "17913257", "labels": {"Mikael Sellin": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0166-6851(07)00247-2"}], "notes": [], "created": "2020-10-05T15:23:24.034Z", "modified": "2022-11-07T11:35:38.162Z"}, {"entity": "publication", "iuid": "1e4d2e431a054a92a31372e17b75acd7", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1e4d2e431a054a92a31372e17b75acd7.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1e4d2e431a054a92a31372e17b75acd7"}}, "title": "Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies.", "authors": [{"family": "Alml\u00f6f", "given": "Martin", "initials": "M"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "\u00c5qvist", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2007-11-00", "journal": {"title": "J. Chem. Theory Comput.", "issn": "1549-9618", "volume": "3", "issue": "6", "pages": "2162-2175", "issn-l": "1549-9618"}, "abstract": "A linear response method for estimating the free energy of solvation is presented and validated using explicit solvent molecular dynamics, thermodynamic perturbation calculations, and experimental data. The electrostatic contribution to the solvation free energy is calculated using a linear response estimate, which is obtained by comparison to the free energy calculated using thermodynamic perturbation. Systematic deviations from the value of (1)/2 in the potential energy scaling factor are observed for some types of compounds, and these are taken into account by introducing specific coefficients for different chemical groups. The derived model reduces the rms error of the linear response estimate significantly from 1.6 to 0.3 kcal/mol on a training set of 221 molecules used to parametrize the model and from 3.7 to 1.3 kcal/mol on a test set of 355 molecules that were not used in the derivation of the model. The total solvation free energy is estimated by combining the derived model with an empirical size dependent term for predicting the nonpolar contribution. Using this model, the experimental hydration free energies for 192 molecules are reproduced with an rms error of 1.1 kcal/mol. The use of LIE in simplified binding free energy calculations to predict protein-ligand binding free energies is also discussed.", "doi": "10.1021/ct700106b", "pmid": "26636209", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-29T13:51:21.385Z", "modified": "2022-11-07T11:33:17.763Z"}, {"entity": "publication", "iuid": "8a1c5e88ef964b8ebe996080f6f8c2a1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a1c5e88ef964b8ebe996080f6f8c2a1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a1c5e88ef964b8ebe996080f6f8c2a1"}}, "title": "Positron emission tomography: a real-time tool to quantify early islet engraftment in a preclinical large animal model.", "authors": [{"family": "Eich", "given": "Torsten", "initials": "T"}, {"family": "Eriksson", "given": "Olof", "initials": "O"}, {"family": "Sundin", "given": "Anders", "initials": "A"}, {"family": "Estrada", "given": "Sergio", "initials": "S"}, {"family": "Brandhorst", "given": "Daniel", "initials": "D"}, {"family": "Brandhorst", "given": "Heide", "initials": "H"}, {"family": "Langstrom", "given": "Bengt", "initials": "B"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Lundgren", "given": "Torbjorn", "initials": "T"}], "type": "journal article", "published": "2007-10-15", "journal": {"title": "Transplantation", "issn": "0041-1337", "volume": "84", "issue": "7", "pages": "893-898", "issn-l": null}, "abstract": "Clinical islet transplantation is currently being explored as a therapeutic option for persons with type I diabetes and hypoglycemic unawareness. Techniques to monitor graft survival are urgently needed to optimize the procedure. Therefore, the objective of the present study was to develop a technique for imaging survival of transplanted islets in the peritransplant and early posttransplant phase.\n\nIsolated porcine islets were labeled in vitro with 2-deoxy-2[F]fluoro-D-glucose ([F]FDG) and infused intraportally into anesthetized pigs (n=10). Dynamic examination was performed on a positron emission tomography/computed tomography hybrid system.\n\nMore than 95% of the radioactivity was confined to the islets at the time of transplantation. The peak percentage of infused radioactivity within the liver, quantified at the end of the islet infusion, was only 54+/-5.1%. The distribution of the radioactivity in the liver was found to be heterogeneous. A whole-body examination showed no accumulation in the lungs or brain; extrahepatic radioactivity was, except urinary excretion, evenly distributed in the pig body.\n\nOur results imply that almost 50% of the islets were damaged to the extent that the FDG contained was release within minutes after intraportal transplantation. The distribution of radioactivity without accumulation in the brain indicates that the activity is released from lysed islet cells in the form of [F]FDG-6P rather than native [F]FDG. The presented technique shows promise to become a powerful and quantitative tool, readily available in the clinic, to evaluate initial islet engraftment and survival.", "doi": "10.1097/01.tp.0000284730.86567.9f", "pmid": "17984843", "labels": {"Olof Eriksson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "00007890-200710150-00014"}], "notes": [], "created": "2020-10-06T14:11:52.328Z", "modified": "2022-11-07T11:35:51.940Z"}, {"entity": "publication", "iuid": "1f3c395a70394b609efe127bc8709b9d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3c395a70394b609efe127bc8709b9d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1f3c395a70394b609efe127bc8709b9d"}}, "title": "Blue-light (488nm)-irradiation-induced photoactivation of the photoactivatable green fluorescent protein", "authors": [{"family": "Testa", "given": "Ilaria", "initials": "I"}, {"family": "Mazza", "given": "Davide", "initials": "D"}, {"family": "Barozzi", "given": "Sara", "initials": "S"}, {"family": "Faretta", "given": "Mario", "initials": "M"}, {"family": "Diaspro", "given": "Alberto", "initials": "A"}], "type": "journal-article", "published": "2007-09-24", "journal": {"title": "Appl. Phys. Lett.", "issn": "0003-6951", "volume": "91", "issue": "13", "pages": "133902", "issn-l": null}, "abstract": null, "doi": "10.1063/1.2790847", "pmid": null, "labels": {"Ilaria Testa": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-29T13:04:25.384Z", "modified": "2025-12-04T17:04:30.538Z"}, {"entity": "publication", "iuid": "8cf01fd79fdd4a76b9945fcd44631681", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8cf01fd79fdd4a76b9945fcd44631681.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8cf01fd79fdd4a76b9945fcd44631681"}}, "title": "Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "Holm", "given": "Karl", "initials": "K"}, {"family": "McIntyre", "given": "Lauren M", "initials": "LM"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2007-09-00", "journal": {"title": "PLANT PHYSIOLOGY", "issn": "0032-0889", "volume": "145", "issue": "1", "pages": "160-173", "issn-l": "0032-0889"}, "abstract": "Understanding the genetic basis of natural variation is of primary interest for evolutionary studies of adaptation. In Capsella bursa-pastoris, a close relative of Arabidopsis (Arabidopsis thaliana), variation in flowering time is correlated with latitude, suggestive of an adaptation to photoperiod. To identify pathways regulating natural flowering time variation in C. bursa-pastoris, we have studied gene expression differences between two pairs of early- and late-flowering C. bursa-pastoris accessions and compared their response to vernalization. Using Arabidopsis microarrays, we found a large number of significant differences in gene expression between flowering ecotypes. The key flowering time gene FLOWERING LOCUS C (FLC) was not differentially expressed prior to vernalization. This result is in contrast to those in Arabidopsis, where most natural flowering time variation acts through FLC. However, the gibberellin and photoperiodic flowering pathways were significantly enriched for gene expression differences between early- and late-flowering C. bursa-pastoris. Gibberellin biosynthesis genes were down-regulated in late-flowering accessions, whereas circadian core genes in the photoperiodic pathway were differentially expressed between early- and late-flowering accessions. Detailed time-series experiments clearly demonstrated that the diurnal rhythm of CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1) expression differed between flowering ecotypes, both under constant light and long-day conditions. Differential expression of flowering time genes was biologically validated in an independent pair of flowering ecotypes, suggesting a shared genetic basis or parallel evolution of similar regulatory differences. We conclude that genes involved in regulation of the circadian clock, such as CCA1 and TOC1, are strong candidates for the evolution of adaptive flowering time variation in C. bursa-pastoris.", "doi": "10.1104/pp.107.102632", "pmid": "17631524", "labels": {"Tanja Slotte": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "pp.107.102632"}, {"db": "pmc", "key": "PMC1976575"}], "notes": [], "created": "2020-10-09T13:58:28.754Z", "modified": "2022-11-07T11:38:19.961Z"}, {"entity": "publication", "iuid": "bf0832354e654a2cb89440410f24041a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bf0832354e654a2cb89440410f24041a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bf0832354e654a2cb89440410f24041a"}}, "title": "Phylogenomics reshuffles the eukaryotic supergroups.", "authors": [{"family": "Burki", "given": "Fabien", "initials": "F"}, {"family": "Shalchian-Tabrizi", "given": "Kamran", "initials": "K"}, {"family": "Minge", "given": "Marianne", "initials": "M"}, {"family": "Skjaeveland", "given": "Asmund", "initials": "A"}, {"family": "Nikolaev", "given": "Sergey I", "initials": "SI"}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS"}, {"family": "Pawlowski", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2007-08-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "2", "issue": "8", "pages": "e790", "issn-l": "1932-6203"}, "abstract": "Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial.\n\nHere, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history.\n\nThis well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name 'SAR' (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.", "doi": "10.1371/journal.pone.0000790", "pmid": "17726520", "labels": {"Fabien Burki": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC1949142"}], "notes": [], "created": "2020-09-28T12:16:46.791Z", "modified": "2022-11-07T11:31:56.933Z"}, {"entity": "publication", "iuid": "45a595e0e5494a21866c10cbb8671998", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/45a595e0e5494a21866c10cbb8671998.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/45a595e0e5494a21866c10cbb8671998"}}, "title": "MicroRNA-mediated regulation of stomatal development in Arabidopsis.", "authors": [{"family": "Kutter", "given": "Claudia", "initials": "C"}, {"family": "Sch\u00f6b", "given": "Hanspeter", "initials": "H"}, {"family": "Stadler", "given": "Michael", "initials": "M"}, {"family": "Meins", "given": "Frederick", "initials": "F"}, {"family": "Si-Ammour", "given": "Azeddine", "initials": "A"}], "type": "journal article", "published": "2007-08-00", "journal": {"title": "Plant Cell", "issn": "1040-4651", "volume": "19", "issue": "8", "pages": "2417-2429", "issn-l": null}, "abstract": "The proper number and distribution of stomata are essential for the efficient exchange of gases between the atmosphere and the aerial parts of plants. We show that the density and development of stomatal complexes on the epidermis of Arabidopsis thaliana leaves depend, in part, on the microRNA-mediated regulation of Agamous-like16 (AGL16), which is a member of the MADS box protein family. AGL16 mRNA is targeted for sequence-specific degradation by miR824, a recently evolved microRNA conserved in the Brassicaceae and encoded at a single genetic locus. Primary stomatal complexes can give rise to higher-order complexes derived from satellite meristemoids. Expression of a miR824-resistant AGL16 mRNA, but not the wild-type AGL16 mRNA, in transgenic plants increased the incidence of stomata in higher-order complexes. By contrast, reduced expression of AGL16 mRNA in the agl16-1 deficiency mutant and in transgenic lines overexpressing miR824 decreased the incidence of stomata in higher-order complexes. These findings and the nonoverlapping patterns of AGL16 mRNA and miR824 localization led us to propose that the miR824/AGL16 pathway functions in the satellite meristemoid lineage of stomatal development.", "doi": "10.1105/tpc.107.050377", "pmid": "17704216", "labels": {"Claudia Kutter": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "tpc.107.050377"}, {"db": "pmc", "key": "PMC2002609"}, {"db": "GENBANK", "key": "AF389288"}, {"db": "GENBANK", "key": "AK226543"}], "notes": [], "created": "2020-09-25T14:36:54.528Z", "modified": "2022-11-07T11:30:38.615Z"}, {"entity": "publication", "iuid": "cfa2f554ee9b4db09388de8f21a6f4e8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cfa2f554ee9b4db09388de8f21a6f4e8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cfa2f554ee9b4db09388de8f21a6f4e8"}}, "title": "Roles of curli, cellulose and BapA in Salmonella biofilm morphology studied by atomic force microscopy.", "authors": [{"family": "Jonas", "given": "Kristina", "initials": "K"}, {"family": "Tomenius", "given": "Henrik", "initials": "H"}, {"family": "Kader", "given": "Abdul", "initials": "A"}, {"family": "Normark", "given": "Staffan", "initials": "S"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}, {"family": "Belova", "given": "Lyubov M", "initials": "LM"}, {"family": "Melefors", "given": "Ojar", "initials": "O"}], "type": "journal article", "published": "2007-07-24", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "7", "issue": null, "pages": "70", "issn-l": "1471-2180"}, "abstract": "Curli, cellulose and the cell surface protein BapA are matrix components in Salmonella biofilms. In this study we have investigated the roles of these components for the morphology of bacteria grown as colonies on agar plates and within a biofilm on submerged mica surfaces by applying atomic force microscopy (AFM) and light microscopy.\n\nAFM imaging was performed on colonies of Salmonella Typhimurium grown on agar plates for 24 h and on biofilms grown for 4, 8, 16 or 24 h on mica slides submerged in standing cultures. Our data show that in the wild type curli were visible as extracellular material on and between the cells and as fimbrial structures at the edges of biofilms grown for 16 h and 24 h. In contrast to the wild type, which formed a three-dimensional biofilm within 24 h, a curli mutant and a strain mutated in the global regulator CsgD were severely impaired in biofilm formation. A mutant in cellulose production retained some capability to form cell aggregates, but not a confluent biofilm. Extracellular matrix was observed in this mutant to almost the same extent as in the wild type. Overexpression of CsgD led to a much thicker and a more rapidly growing biofilm. Disruption of BapA altered neither colony and biofilm morphology nor the ability to form a biofilm within 24 h on the submerged surfaces. Besides curli, the expression of flagella and pili as well as changes in cell shape and cell size could be monitored in the growing biofilms.\n\nOur work demonstrates that atomic force microscopy can efficiently be used as a tool to monitor the morphology of bacteria grown as colonies on agar plates or within biofilms formed in a liquid at high resolution.", "doi": "10.1186/1471-2180-7-70", "pmid": "17650335", "labels": {"Kristina Jonas": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "1471-2180-7-70"}, {"db": "pmc", "key": "PMC1949822"}], "notes": [], "created": "2020-11-30T14:48:59.924Z", "modified": "2022-11-07T11:33:47.310Z"}, {"entity": "publication", "iuid": "cc997f56522f4928a18b568fda0a8697", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cc997f56522f4928a18b568fda0a8697.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cc997f56522f4928a18b568fda0a8697"}}, "title": "Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis.", "authors": [{"family": "Henriksson", "given": "Lena M", "initials": "LM"}, {"family": "Unge", "given": "Torsten", "initials": "T"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Aqvist", "given": "Johan", "initials": "J"}, {"family": "Mowbray", "given": "Sherry L", "initials": "SL"}, {"family": "Jones", "given": "T Alwyn", "initials": "TA"}], "type": "journal article", "published": "2007-07-06", "journal": {"title": "J. Biol. Chem.", "issn": "0021-9258", "volume": "282", "issue": "27", "pages": "19905-19916", "issn-l": null}, "abstract": "Isopentenyl diphosphate is the precursor of various isoprenoids that are essential to all living organisms. It is produced by the mevalonate pathway in humans but by an alternate route in plants, protozoa, and many bacteria. 1-deoxy-D-xylulose-5-phosphate reductoisomerase catalyzes the second step of this non-mevalonate pathway, which involves an NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose 5-phosphate to form 2-C-methyl-D-erythritol 4-phosphate. The use of different pathways, combined with the reported essentiality of the enzyme makes the reductoisomerase a highly promising target for drug design. Here we present several high resolution structures of the Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase, representing both wild type and mutant enzyme in various complexes with Mn(2+), NADPH, and the known inhibitor fosmidomycin. The asymmetric unit corresponds to the biological homodimer. Although crystal contacts stabilize an open active site in the B molecule, the A molecule displays a closed conformation, with some differences depending on the ligands bound. An inhibition study with fosmidomycin resulted in an estimated IC(50) value of 80 nm. The double mutant enzyme (D151N/E222Q) has lost its ability to bind the metal and, thereby, also its activity. Our structural information complemented with molecular dynamics simulations and free energy calculations provides the framework for the design of new inhibitors and gives new insights into the reaction mechanism. The conformation of fosmidomycin bound to the metal ion is different from that reported in a previously published structure and indicates that a rearrangement of the intermediate is not required during catalysis.", "doi": "10.1074/jbc.M701935200", "pmid": "17491006", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "M701935200"}, {"db": "PDB", "key": "2JCV"}, {"db": "PDB", "key": "2JCX"}, {"db": "PDB", "key": "2JCY"}, {"db": "PDB", "key": "2JCZ"}, {"db": "PDB", "key": "2JD0"}, {"db": "PDB", "key": "2JD1"}, {"db": "PDB", "key": "2JD2"}], "notes": [], "created": "2020-09-29T13:51:22.461Z", "modified": "2022-11-07T11:33:17.774Z"}, {"entity": "publication", "iuid": "1a511588334f4355a49e54291d6f0e08", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a511588334f4355a49e54291d6f0e08.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a511588334f4355a49e54291d6f0e08"}}, "title": "Visualization of early engraftment in clinical islet transplantation by positron-emission tomography.", "authors": [{"family": "Eich", "given": "Torsten", "initials": "T"}, {"family": "Eriksson", "given": "Olof", "initials": "O"}, {"family": "Lundgren", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Nordic Network for Clinical Islet Transplantation", "given": "", "initials": ""}], "type": "letter", "published": "2007-06-28", "journal": {"title": "N. Engl. J. Med.", "issn": "1533-4406", "volume": "356", "issue": "26", "pages": "2754-2755", "issn-l": "0028-4793"}, "abstract": null, "doi": "10.1056/NEJMc070201", "pmid": "17596618", "labels": {"Olof Eriksson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "356/26/2754"}], "notes": [], "created": "2020-10-06T14:11:33.027Z", "modified": "2022-11-07T11:35:51.952Z"}, {"entity": "publication", "iuid": "d2bf357928a048d687cc6a87e19ef31c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2bf357928a048d687cc6a87e19ef31c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2bf357928a048d687cc6a87e19ef31c"}}, "title": "Structural basis for the inhibition of tyrosine kinase activity of ZAP-70.", "authors": [{"family": "Deindl", "given": "Sebastian", "initials": "S"}, {"family": "Kadlecek", "given": "Theresa A", "initials": "TA"}, {"family": "Brdicka", "given": "Tomas", "initials": "T"}, {"family": "Cao", "given": "Xiaoxian", "initials": "X"}, {"family": "Weiss", "given": "Arthur", "initials": "A"}, {"family": "Kuriyan", "given": "John", "initials": "J"}], "type": "journal article", "published": "2007-05-18", "journal": {"title": "Cell", "issn": "0092-8674", "volume": "129", "issue": "4", "pages": "735-746", "issn-l": null}, "abstract": "ZAP-70, a cytoplasmic tyrosine kinase required for T cell antigen receptor signaling, is controlled by a regulatory segment that includes a tandem SH2 unit responsible for binding to immunoreceptor tyrosine-based activation motifs (ITAMs). The crystal structure of autoinhibited ZAP-70 reveals that the inactive kinase domain adopts a conformation similar to that of cyclin-dependent kinases and Src kinases. The autoinhibitory mechanism of ZAP-70 is, however, distinct and involves interactions between the regulatory segment and the hinge region of the kinase domain that reduce its flexibility. Two tyrosine residues in the SH2-kinase linker that activate ZAP-70 when phosphorylated are involved in aromatic-aromatic interactions that connect the linker to the kinase domain. These interactions are inconsistent with ITAM binding, suggesting that destabilization of this autoinhibited ZAP-70 conformation is the first step in kinase activation.", "doi": "10.1016/j.cell.2007.03.039", "pmid": "17512407", "labels": {"Sebastian Deindl": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S0092-8674(07)00455-2"}], "notes": [], "created": "2020-10-09T09:53:54.796Z", "modified": "2022-11-07T11:37:50.965Z"}, {"entity": "publication", "iuid": "7bfc9df96bd549fd9b480c6e917c0731", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7bfc9df96bd549fd9b480c6e917c0731.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7bfc9df96bd549fd9b480c6e917c0731"}}, "title": "The structure of a plant photosystem I supercomplex at 3.4 A resolution.", "authors": [{"family": "Amunts", "given": "Alexey", "initials": "A"}, {"family": "Drory", "given": "Omri", "initials": "O"}, {"family": "Nelson", "given": "Nathan", "initials": "N"}], "type": "journal article", "published": "2007-05-03", "journal": {"title": "Nature", "issn": "0028-0836", "volume": "447", "issue": "7140", "pages": "58-63", "issn-l": null}, "abstract": "All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems. We report the structure of plant PSI at 3.4 A resolution, revealing 17 protein subunits. PsaN was identified in the luminal side of the supercomplex, and most of the amino acids in the reaction centre were traced. The crystal structure of PSI provides a picture at near atomic detail of 11 out of 12 protein subunits of the reaction centre. At this level, 168 chlorophylls (65 assigned with orientations for Q(x) and Q(y) transition dipole moments), 2 phylloquinones, 3 Fe(4)S(4) clusters and 5 carotenoids are described. This structural information extends the understanding of the most efficient nano-photochemical machine in nature.", "doi": "10.1038/nature05687", "pmid": "17476261", "labels": {"Alexey Amunts": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "nature05687"}, {"db": "PDB", "key": "2O01"}], "notes": [], "created": "2020-09-25T14:25:05.909Z", "modified": "2022-11-07T11:30:20.547Z"}, {"entity": "publication", "iuid": "d8f63839c27e4d89896b3ad47e2757f8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d8f63839c27e4d89896b3ad47e2757f8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d8f63839c27e4d89896b3ad47e2757f8"}}, "title": "Active site of epoxide hydrolases revisited: a noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate.", "authors": [{"family": "Thomaeus", "given": "Ann", "initials": "A"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Aqvist", "given": "Johan", "initials": "J"}, {"family": "Widersten", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2007-03-06", "journal": {"title": "Biochemistry", "issn": "0006-2960", "volume": "46", "issue": "9", "pages": "2466-2479", "issn-l": null}, "abstract": "The carboxylate of Glu35 in the active site of potato epoxide hydrolase StEH1 interacts with the catalytic water molecule and is the first link in a chain of hydrogen bonds connecting the active site with bulk solvent. To probe its importance to catalysis, the carboxylate was replaced with an amide through an E35Q mutation. Comparing enzyme activities using the two trans-stilbene oxide (TSO) enantiomers as substrates revealed the reaction with R,R-TSO to be the one more severely affected by the E35Q mutation, as judged by determined kinetic parameters describing the pre-steady states or the steady states of the catalyzed reactions. The hydrolysis of S,S-TSO afforded by the E35Q mutant was comparable with that of the wild-type enzyme, with only a minor decrease in activity, or a change in pH dependencies of kcat, and the rate of alkylenzyme hydrolysis, k3. The pH dependence of E35Q-catalyzed hydrolysis of R,R-TSO, however, exhibited an inverted titration curve as compared to that of the wild-type enzyme, with a minimal catalytic rate at pH values where the wild-type enzyme exhibited maximum rates. To simulate the pH dependence of the E35Q mutant, a shift in the acidity of the alkylenzyme had to be invoked. The proposed decrease in the pKa of His300 in the E35Q mutant was supported by computer simulations of the active site electrostatics. Hence, Glu35 participates in activation of the Asp nucleophile, presumably by facilitating channeling of protons out of the active site, and during the hydrolysis half-reaction by orienting the catalytic water for optimal hydrogen bonding, to fine-tune the acid-base characteristics of the general base His300.", "doi": "10.1021/bi062052s", "pmid": "17284015", "labels": {"Jens Carlsson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-09-29T13:52:12.508Z", "modified": "2022-11-07T11:33:17.786Z"}]}