Publications in international journals 2005
  • Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B.
    The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation.
    Biochem J, Sep 1;390(Pt 2):529-540., 2005 , PDF


  • Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ.
    Genome-Wide Detection and Analysis of Cell Waal-Bound Proteins with LPxTG-Like Sorting Motifs.
    J. Bacteriol, Jul;187(14):4928-4934., 2005 , PDF


  • Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, Gabaldón T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, Tielens AG, Friedrich T, Veenhuis M, Huynen MA, Hackstein JH.
    An anaerobic mitochondrion that produces hydrogen.
    Nature, Mar 3;434(7029):74-79., 2005 , PDF


  • Dolk E, van der Vaart M, Lutje Hulsik D, Vriend G, de Haard H, Spinelli S, Cambillau C, Frenken L, Verrips T.
    Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.
    Appl Environ Microbiol, Jan;71(1):442-450., 2005 , PDF


  • Dolk E, van Vliet C, Perez JM, Vriend G, Darbon H, Ferrat G, Cambillau C, Frenken LG, Verrips T.
    Induced refolding of a temperature denatured llama heavy-chain antibody fragment by its antigen.
    Proteins, May 15;59(3):555-564., 2005 , PDF


  • van Driel MA, Cuelenaere K, Kemmeren PP, Leunissen JA, Brunner HG, Vriend G.
    GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.
    Nucleic Acids Res, Jul 1;33(Web Server issue):W758-761., 2005 , PDF


  • Duquesne AE, Ruijter M, Brouwer J, Drijfhout JW, Nabuurs SB, Spronk CA, Vuister GW, Ubbink M, Canters GW.
    Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase.
    J Biomol NMR, Jul;32(3):209-218., 2005 , PDF


  • Ettema TJ, de Vos WM, van der Oost J.
    Discovering novel biology by in silico archaeology.
    Nat Rev Microbiol, Nov;3(11):859-869., 2005 , PDF


  • Folkertsma S, van Noort PI, Brandt RF, Bettler E, Vriend G, de Vlieg J.
    The nuclear receptor ligand-binding domain: a family-based structure analysis.
    Curr Med Chem, 12(9):1001-1016., 2005 , PDF


  • Francke C, Siezen RJ, Teusink B.
    Reconstructing the metabolic network of a bacterium from its genome.
    Trends Microbiol, Nov;13(11):550-558., 2005 , PDF


  • Gabaldón T, Huynen MA.
    Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
    Bioinformatics, Sep 1;21 Suppl 2:ii144-150., 2005 , PDF


  • Gabaldón T, Rainey D, Huynen MA.
    Tracing the evolution of a large protein complex in the eukaryotes, NADH: ubiquinone oxidoreductase (Complex I).
    J Mol Biol, May 13;348(4):857-870., 2005 , PDF


  • Hekkelman ML, Vriend G.
    MRS: a fast and compact retrieval system for biological data.
    Nucleic Acids Res, Jul 1;33(Web Server issue):W766-9., 2005 , PDF


  • Huynen MA, Gabaldón T, Snel B.
    Variation and evolution of biomolecular systems: searching for functional relevance.
    FEBS Lett, Mar 21;579(8):1839-1845. , 2005 , PDF


  • Huynen MA, Spronk CA, Gabaldon T, Snel B.
    Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin.
    FEBS Lett, Jan 31;579(3):591-596., 2005 , PDF


  • Kalay E, de Brouwer AP, Caylan R, Nabuurs SB, Wollnik B, Karaguzel A, Heister JG, Erdol H, Cremers FP, Cremers CW, Brunner HG, Kremer H.
    A novel D458V mutation in the SANS PDZ binding motif causes atypical Usher syndrome.
    J Mol Med, Dec;83(12):1025-1032., 2005 , PDF


  • Kantardzhieva A, Gosens I, Alexeeva S, Punte IM, Versteeg I, Krieger E, Neefjes-Mol CA, den Hollander AI, Letteboer SJ, Klooster J, Cremers FP, Roepman R, Wijnholds J.
    MPP5 recruits MPP4 to the CRB1 complex in photoreceptors.
    Invest Ophthalmol Vis Sci, Jun;46(6):2192-2201., 2005 , PDF


  • Kaper T, Talik B, Ettema TJ, Bos H, van der Maarel MJ, Dijkhuizen L.
    Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels.
    Appl Environ Microbiol, Sep;71(9):5098-5106., 2005 , PDF


  • van Kranenburg R, Golic N, Bongers R, Leer RJ, de Vos WM, Siezen RJ, Kleerebezem M.
    Functional Analysis of Three Plasmids from Lactobacillus plantarum.
    Appl Environ Microbiol, Mar;71(3):1223-1230., 2005 , PDF


  • Kunin V, Teichmann SA, Huynen MA, Ouzounis CA.
    The properties of protein family space depend on experimental design.
    Bioinformatics, Jun 1;21(11):2618-2622., 2005 , PDF


  • Liu M, van Enckevort FH, Siezen RJ.
    Genome update: lactic acid bacteria genome sequencing is booming.
    Microbiology, Dec;151(Pt 12):3811-3814., 2005 , PDF


  • von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P.
    STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
    Nucleic Acids Res, Jan 1;33(Database issue):D433-437., 2005 , PDF


  • Molenaar D, Bringel F, Schuren FH, de Vos WM, Siezen RJ, Kleerebezem M.
    Exploring Lactobacillus Plantarum genome diversity by using microarrays.
    J Bacteriol, Sep;187(17):6119-6127., 2005 , PDF


  • Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CA, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AM.
    RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank.
    Proteins, Jun 1;59(4):662-672., 2005 , PDF


  • Nabuurs SB, Krieger E, Spronk CA, Nederveen AJ, Vriend G, Vuister GW.
    Definition of a new information-based per-residue quality parameter.
    J Biomol NMR, Oct;33(2):123-134., 2005 , PDF


  • Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.
    Correlation between sequence conservation and the genomic context after gene duplication .
    Nucleic Acids Res, Oct 27;33(19):6164-6171., 2005 , PDF


  • de Pont J, Qui LY, Krieger E, Schaftenaar G, Swarts HGP, Willems P, Koenderink JB.
    Elucidation of the ouabain-binding site in Na-KATPase by chimeric approaches.
    Journal of General Physiology, 126(1):9-10., 2005


  • Qiu LY, Krieger E, Schaftenaar G, Swarts HG, Willems PH, De Pont JJ, Koenderink JB.
    Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acids.
    Journal of Biological Chemistry, Sep 16;280(37):32349-32355., 2005 , PDF


  • van Reeuwijk J, Janssen M, van den Elzen C, Beltran-Valero de Bernabé D, Sabatelli P, Merlini L, Boon M, Scheffer H, Brockington M, Muntoni F, Huynen MA, Verrips A, Walsh CA, Barth PG, Brunner HG, van Bokhoven H.
    POMT2 mutations cause {alpha}-dystroglycan hypoglycosylation and Walker-Warburg syndrome.
    J Med Genet, Dec;42(12):907-912., 2005 , PDF


  • Schaftenaar G, de Wijs GA, Sanchez-Portal D, Vlieg E.
    Quantum mechanics calculations on the diastereomeric salts of cyclic phosphoric acids with ephedrine.
    Journal of Molecular Structure-Theochem, 717:205-214, 2005 , PDF


  • Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM.
    Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.
    Appl Environ Microbiol, Dec;71(12):8371-8382., 2005 , PDF


  • Smid EJ, van Enckevort FJ, Wegkamp A, Boekhorst J, Molenaar D, Hugenholtz J, Siezen RJ, Teusink B.
    Metabolic models for rational improvement of lactic acid bacteria as cell factories.
    J Appl Microbiol, 98(6):1326-1331., 2005 , PDF


  • Smid EJ, Molenaar D, Hugenholtz J, de Vos WM, Teusink B.
    Functional ingredients production: application of global metabolic models.
    Curr Opin Biotechnol, Apr;16(2):190-197., 2005 , PDF


  • Snel B, Huynen MA, Dutilh BE.
    Genome trees and the nature of genome evolution.
    Annu Rev Microbiol, 59:191-209., 2005 , PDF


  • Swarts HG, Koenderink JB, Willems PH, Krieger E, De Pont JJ.
    Asn792 participates in the hydrogen bond network around the K+-binding pocket of gastric H,K-ATPase.
    J Biol Chem, Mar 25;280(12):11488-11494., 2005 , PDF


  • Teusink B, van Enckevort FH, Francke C, Wiersma A, Wegkamp A, Smid EJ, Siezen RJ.
    In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
    Appl Environ Microbiol, Nov;71(11):7253-7262., 2005 , PDF


  • Wessels E, Duijsings D, Notebaart RA, Melchers WJ, van Kuppeveld FJ.
    A proline-rich region in the coxsackievirus 3A protein is required for the protein to inhibit endoplasmic reticulum-to-golgi transport.
    J Virol, Apr;79(8):5163-5173., 2005 , PDF


  • Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.
    Correlation between sequence conservation and the genomic context after gene duplication.
    Nucleic Acids Res, Oct 27;33(19):6164-6171., 2005 , PDF