National Doctoral Programme in
Informational and Structural Biology

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Publications 2006

• Ahola V, Aittokallio T, Vihinen M, Uusipaikka E. (2006) A statistical score for assessing the quality of multiple sequence alignments. BMC Bioinformatics. 7:484.
• Airenne TT*, Kidron H*, Nymalm Y, Nylund M, West G, Mattjus P & Salminen TA. (2006) Structural evidence for adaptive ligand binding of glycolipid transfer protein. J Mol Biol. 355:224-36.
• Alanen HI, Salo KEH, Pirneskoski A & Ruddock LW. (2006) pH dependence of the peptide thiol-disulphide oxidase activity of six members of the human protein disulphide isomerase family. Antioxid Redox Signal. 8:283-91.
• Alanen HI, Williamson RA, Howard MJ, Hatahet FS, Salo KEH, Kauppila A, Kellokumpu S & Ruddock LW. (2006) ERp27,a new non-catalytic endoplasmic reticulum located human PDI-family member, interacts with ERp57. J Biol Chem. 281:33727-33738.
• Alvesalo JKO, Siiskonen A, Vainio, MJ, Tammela PSM, Vuorela PM. (2006) Similarity based virtual screening: A tool for targeted library design. J Med Chem. 49:2353-2356.
• Amundsen LK & Sirén H. (2006) Partial-filling MEKC technique for analysis of testosterone. J Chromatogr A. 1131:267-274.
• Anckar J, Hietakangas V, Denessiouk K, Thiele DJ, Johnson MS & Sistonen L. (2006) Inhibition of DNA binding by differential sumoylation of heat shock factors. Mol Cell Biol. 26:955-64.
• Askolin S, Linder M, Scholtmeijer K, Tenkanen M, Penttila M, de Vocht ML & Wösten HAB. (2006) Interaction and comparison of a class I hydrophobin from Schizophyllum commune and class II hydrophobins from Trichoderma reesei. Biomacromolecules. 7:1295-301.
• Barton WA, Tzvetkova-Robev D, Miranda EP, Kolev MV, Rajashankar KR, Himanen JP & Nikolov DB. (2006) Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex. Nat Struct Mol Biol. 13:524-532.
• Belevich I, Tuukkanen A, Wikstrom M & Verkhovsky MI. (2006) Electron coupled proton reequilibration in the soluble and membrane bound cytochrome c oxidase from Paracoccus denitrificans. Biochemistry. 45:4000-4006.
• Belevich I, Verkhovsky MI & Wikstrom M. (2006) Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Nature. 440:829-832.
• Bicskei Z, Ylander P & Hänninen P. (2006) Calibration of bioaffinity assays using kinetic data. Journal of Biochemical and Biophysical Methods. 67:75-85.
• Blom T, Bergelin N, Slotte JP & Törnquist K. (2006) Sphingosine kinase regulates voltage operated calcium channels in GH4C1 rat pituitary cells. Cell Signal. 18:1366-75.
• Bogachev AV, Bertsova YV, Bloch DA & Verkhovsky MI. (2006) Thermodynamic properties of the redox centers of Na+-translocating NADH:quinone oxidoreductase. Biochemistry. 45:3421-3428.
• Cai C, Li H, Rivera C & Keinänen K. (2006) Interaction between SAP97 and PSD-95, two Maguk proteins involved in synaptic trafficking of AMPA receptors. J Biol Chem 281:4267-4273.
• Collado M.C, Jalonen L, Meriluoto J & Salminen S. (2006) Protection mechanism of probiotic combination against human pathogens: in vitro adhesion to human intestinal mucus. Asia Pacific Journal of Clinical Nutrition. 15:570-575.
• Denessiouk K & Johnson MS. (2006) Novel structural motifs within contiguous segments of protein structure. In Peptide Sci 2005 (T Wakamiya, Ed.), pp. 509-512.
• Dudich E, Semenkova L, Dudich I, Denesyuk A, Tatulov E & Korpela T. (2006) Alpha-fetoprotein antagonizes X-linked inhibitor of apoptosis protein anticaspase activity and disrupts XIAP-caspase interaction. FEBS Journal. 273:3837-3849.
• D'yakova EV, Rakitin AL, Kamionskaya AM, Baikov AA, Lahti, R, Ravin NV & Skryabin,KG. (2006) A study of the effect of expression of the gene encoding the membrane H⁺ -pyrophosphatase of Rhodospirillum rubrum on salt resistance of transgenic tobacco plants. Doklady Biological Sciences 409:346-348.
• Elo L, Katajamaa M, Lund R, Oresic M, Lahesmaa R & Aittokallio T. (2006) Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays. OMICS A Journal of Integrative Biology. 10:369-80.
• Fortelius M & Mattjus P. (2006) Galactose oxidase action on galactose containing glycolipids - a fluorescence method. Chem Phys Lipids. 142:103-10.
• Gopalacharyulu PV , Lindfors E, Bounsaythip C & Oresic M. (2006) Context dependent visualization of protein function, Proceedings of Probabilistic Modelling and Machine Learning in Structural and Systems Biology Workshop (Rousu, J., Kaski, S., and Ukkonen, E. eds.), June 17-18:26-31.
• Gorbikova E, Vuorilehto K, Wikstrom M & Verkhovsky MI. (2006) Redox titration of all electron carriers of cytochrome c oxidase by FTIR spectroscopy. Biochemistry. 45:5641-5649.
• Grahn AM, Butcher S, Bamford JKH & Bamford DH. (2006) PRD1 - dissecting the genome, structure and entry. In "The Bacteriophage" Ed. R. Calendar. Oxford University Press, New York. p.161-170.
• Hahtola S, Tuomela S, Elo L, Hakkinen T, Karenko L, Nedoszytko B, Heikkila H, Saarialho-Kere U, Roszkiewicz J, Aittokallio T, Lahesmaa R & Ranki A. (2006) Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma. Clin Cancer Res. 12:4812-21.
• Hakanpää J. (2006) Structural studies of Trichoderma reesei hydrophobins HFBI and HFBII - the molecular basis for the function of fungal amphiphiles. Department of Chemistry, University of Joensuu, Joensuu. (Dissertation)
• Hakanpää J, Linder M, Popov A, Schmidt A & Rouvinen J. (2006) Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75Å. Acta Crystallogr. D 62:356-367.
• Hakanpää J, Szilvay G, Kaljunen H, Maksimainen M, Linder M & Rouvinen J. (2006) Two crystal structures of Trichoderma reesei hydrophobin HFBI - The structure of a protein amphiphile with and without detergent. Protein Sci. 15:2129-40.
• Hakulinen N, Kruus K, Koivula A & Rouvinen J. (2006) A crystallographic and spectroscopic study on the effect of X-ray radiation on the crystal structure of Melanocarpus albomyces laccase. Biochem Biophys Res Comm. 350:929-934.
• Halak S*, Lehtio L*, Basta T, Burger S, Contzen M, Stolz A, Goldman A. (2006 )Structure and function of the 3-carboxy-cis,cis-muconate lactonizing enzyme from the protocatechuate degradative pathway of Agrobacterium radiobacter S2. FEBS J. 273:5169-82.
• Heczková B. (2006) Effect of structure on phospholipid membrane behavior and interaction with cholesterol. Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku. (Dissertation)
• Heczková B & Slotte JP. (2006) Effect of anti-tumor ether lipids on ordered domains in model membranes. FEBS Lett. 580:2471-2476.
• Hellman M, Paavilainen VO, Annila A, Lappalainen P & Permi P. (2006) NMR assignment of the C-terminal ADF-H domain of an actin monomer binding protein, twinfilin. J Biomol NMR. 36 Suppl 1:66.
• Huhtiniemi T, Wittekindt C, Laitinen T, Leppänen J, Salminen A, Poso A & Lahtela-Kakkonen M. (2006) Comparative and pharmacophore model for deacetylase SIRT1. J Comp-Aid Mol Design. 20:589-599.
• Huiskonen JT, de Haas F, Bubeck D, Bamford DH, Fuller SD & Butcher SJ. (2006) Structure of the bacteriophage phi6 nucleocapsid suggests a mechanism for sequential RNA packaging. Structure. 14:1039-48.
• Hytönen VP, Hörhä J, Airenne TT, Niskanen EA, Helttunen K, Johnson MS, Salminen TA, Kulomaa M & Nordlund HR. (2006) Controlling the quaternary structure assembly - Subunit interface engineering and crystal structure of dual chain avidin. J Mol Biol. 359:1352-63.
• Imanishi SY, Kochin V, Eriksson JE. (2006) Optimization of phosphopeptide elution conditions in immobilized Fe(III) affinity chromatography. Proteomics. 7:174-176.
• Jantaro S*, Kidron H*, Chesnel D, Incharoensakdi A, Mulo P, Salminen T* & Mäenpää P*. (2006) Structural modeling and environmental regulation of arginine decarboxylase in Synechocystis sp. PCC 6803. Archives of Microbiology. 84:397-406.
• Kainov DE, Tuma R & Mancini E. (2006) Hexameric molecular motors: P4 packaging ATPase unravels the mechanism. Cell Mol Life Sci 63:1095-1105.
• Kallio P, Sultana A, Niemi J, Mantsala P & Schneider G. (2006) Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. J Mol Biol. 357:210-20.
• Kankaanpää P, Pahajoki K, Marjomäki V, Heino J & White D. (2006) BioImageXD - New open source free software for the processing, analysis and visualization of multidimensional microscopic images. Microscopy Today 3: 12-16. (not peer reviewed)
• Kapetaniou EG, Thanassoulas A, Dubnovitsky AP, Nounesis G & Papageorgiou AC. (2006) Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: thermodynamic and crystallographic studies. Proteins. 63:742-53.
• Karihtala P, Winqvist R, Syväoja JE, Kinnula VL & Soini Y. (2006) Increasing oxidative damage and loss of mismatch repair enzymes during breast carcinogenesis. Eur J Cancer. 42:2653-9.
• Karppinen S-M, Erkko H, Reini K, Pospiech H, Heikkinen K, Rapakko K, Syväoja JE & Winqvist R. (2006) Identification of a common polymorphism in the TOPBP1 gene associated with hereditary susceptibility to breast and ovarian cancer. Eur J cancer. 42:2647-52.
• Katajamaa M, Miettinen J & Oresic M. (2006) MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics. 22:634-6.
• Kauko A, Pulliainen AT, Haataja S, Meyer-Klaucke W, Finne J & Papageorgiou AC. (2006) Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase centre and leads to the formation of a ferrihydrite-like core. J Mol Biol. 364:97-109.
• Kidron H. (2006) Structure-based predictions of enzyme function. Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku. (Dissertation)
• Kiema T, Lad Y, Jiang P, Oxley CL, Baldassarre M, Wegener KL, Campbell ID, Ylänne J, & Calderwood DA. (2006) Structure of a filamin-integrin complex reveals the molecular basis of binding and competition with talin. Mol. Cell. 21:337-347.
• Kiviranta PH, Leppänen J, Kyrylenko S, Salo HS, Lahtela-Kakkonen M, Tervo AJ, Wittekindt C, Suuronen T, Kuusisto E, Järvinen T, Salminen A, Poso A & Wallén EA. (2006) N,N'-Bisbenzylidenebenzene-1,4-diamines and N,N'-Bisbenzylidenenaphthalene-1,4-diamines as Sirtuin Type 2 (SIRT2) Inhibitors. J Med Chem. 49:7907-11.
• Klaavuniemi T & Ylänne J. (2006) Zasp/Cypher Internal ZM-Motif Containing Fragments Are Sufficient To Co-Localize With a-Actinin - Analysis Of Patient Mutations. Exp Cell Res. 312:1299-311.
• Kochin V, Imanishi SY, Eriksson JE. (2006) Fast track to a phosphoprotein sketch - MALDI-ToF characterization of TLC-based tryptic phosphopeptide maps at femtomolar detection sensitivity. Proteomics. 6:5676-82.
• Koskinen JO, Vaarno J, Vainionpää R, Meltola NJ & Soini AE. (2006) A Novel separation-free assay technique for serum antibodies using antibody bridging assay principle and two-photon excitation fluorometry. J Immunol Methods. 309:11-24.
• Kostiainen MA, Szilvay GR, Smith DK, Linder MB & Ikkala O. (2006) Multivalent dendrons for high-affinity adhesion of proteins to DNA. Angewandte Chem. 45:3538-3542.
• Kull TP, Sjovall OT, Tammenkoski MK, Backlund PH & Meriluoto JA. (2006) Oxidation of the cyanobacterial hepatotoxin microcystin-LR by chlorine dioxide: influence of natural organic matter. Environ Sci Technol. 40:1504-10.
• Laaksonen R, Katajamaa M, Päivä H, Sysi-Aho M, Saarinen L, Junni P, Lütjohann D, Smet J, Van Coster R, Seppänen-Laakso T, Lehtimäki T, Soini J, Oresic M. (2006) A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin induced changes in muscle. PLoS ONE 1:e97.
• Laitinen OH, Nordlund HR, Hytönen VP & Kulomaa MS (2006) Genetically engineered avidins and streptavidins (invited review). Cell Mol Life Sci. 63:2992-3017.
• Lankoff A, Wojcik A, Fessard V & Meriluoto J. (2006) Nodularin-induced genotoxicity following oxidative DNA damage and aneuploidy in HepG2 cells. Toxicol Lett. 164:239-48.
• Lehtiö L. (2006) Enzymes with radical tendencies: the PFL family. Institute of Biotechnology, University of Helsinki, Helsinki. (Dissertation)
• Lehtiö L, Grossmann JG, Kokona B, Fairman R & Goldman A. (2006) Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus. J Mol Biol. 357:221-35.
• Lehtovuori PT & Nyrönen TH. (2006) SOMA - Workflow for Small Molecule Property Calculations on a Multiplatform Computing Grid. Journal of Cheminformatics and Modeling. 46:620-625.
• Leiros I, Wang E, Rasmussen T, Oksanen E, Repo H, Petersen SB, Heikinheimo P & Hough E. (2006) The 2.1Å structure of Aerococcus viridans L-lactate oxidase (LOX). Acta Crystallographica section F. 62:1185-1190.
• Leskela HV, Olkku A, Lehtonen S, Mahonen A, Koivunen J, Turpeinen M, Uusitalo J, Pelkonen O, Kangas L, Selander K & Lehenkari P. (2006) Estrogen receptor alpha genotype confers interindividual variability of response to estrogen and testosterone in mesenchymal-stem-cell-derived osteoblasts. Bone. 39:1026-34.
• Lisal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG & Tuma R. (2006) Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology. 351:73-9.
• Louhivuori M, Otten R, Lindorff-Larsen K & Annila A. (2006) Conformational fluctuations affect protein alignment in dilute liquid crystal media. J Am Chem Soc. 128:4371-6.
• Lännenpää M & Syväoja JE. (2006) Device for handling electron microscopy grids. BioTechniques. 40:450-452.
• Marttila-Ichihara F, Smith DJ, Stolen C, Yegutkin G, Elima K, Mercier N, Merinen M, Kiviranta R, Pihlavisto M, Alaranta S, Pentikainen U, Pentikainen OT, Fulop F, Jalkanen S & Salmi M. (2006) Vascular amine oxidases are needed for leukocyte extravasation into inflamed joints in vivo. Arthritis & Rheumatism. 54:2852-2862.
• Matero S, Lahtela-Kakkonen M, Korhonen O, Ketolainen J, Lappalainen R & Poso A. (2006) Chemical Space of Orally Active Compounds. Chemometr. Intell. Lab. 84:134-141.
• Matilainen H, Mäkelä AR, Riikonen R, Saloniemi T, Korhonen E, Hyypiä T, Heino J, Grabherr R & Oker-Blom C. (2006) RGD motifs on the surface of baculovirus enhance transduction of human lung carcinoma cells. J Biotechnol. 125:114-126.
• Mattinen ML, Hellman M, Permi P, Autio K, Kalkkinen N & Buchert J. (2006) Effect of protein structure on laccase-catalyzed protein oligomerization. J Agric Food Chem. 54:8883-90.
• Mazur-Marzec H, Meriluoto J & Plinski M. (2006) The degradation of the cyanobacterial hepatotoxin nodularin (NOD) by UV radiation. Chemosphere. 65:1388-95.
• Mazur-Marzec H, Meriluoto J, Plinski M & Szafranek J. (2006) Characterization of nodularin variants in Nodularia spumigena from the Baltic Sea using liquid chromatography/mass spectrometry/mass spectrometry. Rapid Commun Mass Spectrom. 20:2023-32.
• Messinger J, Hirvela L, Husen B, Kangas L, Koskimies P, Pentikainen O, Saarenketo P & Thole H. (2006) New inhibitors of 17beta-hydroxysteroid dehydrogenase type 1. Mol Cell Endocrinol. 248:192-8.
• Metcalf JS, Meriluoto JA & Codd GA. (2006) Legal and security requirements for the air transportation of cyanotoxins and toxigenic cyanobacterial cells for legitimate research and analytical purposes. Toxicol Lett. 163:85-90.
• Mirtti T, Nylund C, Lehtonen J, Hiekkanen H, Nissinen L, Kallajoki M, Alanen K, Gullberg D, & Heino J. (2006) Regulation of prostate cell collagen receptors by malignant transformation. Int J Cancer. 118:889-98.
• Molnar F, Peräkylä M & Carlberg C. (2006) Vitamin D receptor agonists specifically modulate the volume of the ligand-binding pocket. J Biol Chem. 281:10516-10526.
• Mononen N, Seppala EH, Duggal P, Autio V, Ikonen T, Ellonen P, Saharinen J, Saarela J,Vihinen M, Tammela TL, Kallioniemi O, Bailey-Wilson JE & Schleutker J. (2006) Profiling genetic variation along the androgen biosynthesis and metabolism pathways implicates several single nucleotide polymorphisms and their combinations as prostate cancer risk factors. Cancer Res. 66:743-7.
• Nakamura F, Pudas R, Heikkinen O, Permi P, Kilpeläinen I, Munday AD, Hartwig JH, Stossel TP & Ylänne J. (2006) The structure of the GPIb-filamin A complex. Blood. 107:1925-1932.
• Nasheuer H-P, Pospiech H & Syväoja JE. (2006) DNA Polymerases. Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine.
• Nasheuer H-P, Pospiech H & Syväoja JE. (2006) Progress Towards the Anatomy of DNA Replication Fork. Genome Dynamics and Stability, Springer Verlag. D.H. Lankenau, Ed. pp.27-68.
• Nylund M, Kjellberg MA, Molotkovsky JG, Byun HS, Bittman R & Mattjus P. (2006) Molecular features of phospholipids that affect glycolipid transfer protein-mediated galactosylceramide transfer between vesicles. Biochim Biophys Acta. 1758:807-12.
• Nyrönen T, Kinnunen T & Lehtovuori P. (2006) Seamless Computing Across Versatile IT Infrastructures - The SOMA Drug Discovery Environment. CSC News. 2:36-37
• Oksanen EJ, Jaakola V-P, Tolonen T, Valkonen K, Åkerström B, Kalkkinen N, Virtanen V & Goldman A. (2006) Reindeer β−lactoglobulin crystal structure with pseudo-body centered non-crystallographic symmetry, Acta Crystallographica section D. 62:1369-1374.
• Olivari S, Cali T, Salo KEH, Pahanetti P, Ruddock LW & Molinari M. (2006) EDEM1 regulates ER-associated degradation by accelerating de-mannosylation of folding-defective polypeptides and by inhibiting their covalent aggregation. Biochem Biophys Res Com. 349:1278-1284.
• Ortutay C & Vihinen M. (2006) Immunome: a reference set of genes and proteins for systems biology of the human immune system. Cell Immunol. 244:87-9.
• von Ossowski I, Oksanen E, von Ossowski L, Cai C, Sundberg M, Goldman A & Keinänen, K. (2006) Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptide. FEBS Journal. 273:5219-5229.
• von Ossowski L, Tossavainen H, von Ossowski I, Cai C, Aitio O, Fredriksson K, Permi P, Annila A & Keinanen K. (2006) Peptide binding and NMR analysis of the interaction between SAP97 PDZ2 and GluR-A: potential involvement of a disulfide bond. Biochemistry. 45:5567-75.
• Papageorgiou AC, Saarinen S, Ramirez-Bartutis R, Kato H, Uchiyama T, Kirikae T & Miyoshi-Akiyama T. (2006) Expression, purification and crystallization of Streptococcus dysgalactiae-derived mitogen. Acta Crystallogr F.62:242-4.
• Parikka M, Nissinen L, Kainulainen T, Bruckner-Tuderman L, Salo T, Heino J & Tasanen K. (2006) The cell adhesion domain of collagen XVII promotes squamocellular carcinoma cell transmigration. Exp Cell Res. 312:1431-1438.
• Parkkari T, Salo OMH, Huttunen KM, Savinainen JR, Laitinen JT, Poso A, Nevalainen T & Jarvinen T. (2006) Synthesis and CB1 receptor activities of dimethylheptyl derivatives of 2-arachidonoyl glycerol (2-AG) and 2-arachidonyl glyceryl ether (2-AGE). Bioorg. Med. Chem. 14:2850-8.
• Parkkinen T, Nevanen T, Koivula A & Rouvinen J. (2006) Crystal structures of an enantioselective Fab and its complex with Finrozole. J Mol Biol. 357:471-480.
• Peltoniemi MH, Karala A-R, Jurvansuu JK, Kinnula VL & Ruddock LW. (2006) Insights into deglutathionylation reactions: different intermediates in the glutaredoxin and protein disulphide isomerase catalysed reactions are defined by the gamma-linkage present in glutathione. J Biol Chem. 281:33107-33114.
• Peltoniemi MJ, Karala A-R, Jurvansuu JK, Kinnula VL & Ruddock LW. (2006) Insights into deglutathionylation reactions: different intermediates in the glutaredoxin and protein disulphide isomerase catalysed reactions are defined by the gamma-linkage present in glutathione. J Biol Chem. 281:33107-33114.
• Peltoniemi MJ, Rytila PH, Harju TH, Soini YM, Salmenkivi KM, Ruddock LW & Kinnula VL. (2006) Modulation of glutaredoxin in the lung and sputum of cigarette smokers and chronic obstructive pulmonary disease. Respiratory Research. 7:133.
• Pentikainen U, Settimo L, Johnson MS & Pentikainen OT. (2006) Subtype selectivity and flexibility of ionotropic Glutamate Receptors upon antagonist ligand binding. Organic & Biomolecular Chemistry. 4:1058-1070.
• Peura M, Grotkopp I, Lemke H, Vikkula A, Laine J, Muller M & Serimaa R. (2006) Negative Poisson ratio of crystalline cellulose in sulphate cooked Norway spruce. Biomacromolecules. 7:1521-1528.
• Piirila H, Valiaho J & Vihinen M. (2006) Immunodeficiency mutation databases (IDbases). Hum Mutat. 27:1200-8.
• Poso A, Honkakoski P. (2006) Ligand recognition by drug-activated nuclear receptors PXR and CAR: structural, site-directed mutagenesis and molecular modeling studies. Mini Rev Med Chem. 6:937-47.
• Prizant M, Eisenberg-Domovich Y, Hytönen VP, Kulomaa MS, Wilchek M, Bayer EA & Livnah O. (2006) Factors dictating the pseudocatalytic efficiency of avidins. J Mol Biol. 358:754-763.
• Psencik J, Arellano JB, Ikonen TP, Borrego CM, Laurinmäki PA, Butcher SJ, Serimaa RE & Tuma R. (2006) Internal structure of chlorosomes from brown-coloured Chlorobium species and the role of carotenoids in their assembly. Biophys J. 91:1433-1440.
• Puttonen E, Tossavainen H & Permi P. (2006) Simultaneous determination of one- and two-bond scalar and residual dipolar couplings between (13)C', (13)C(alpha) and (15)N spins in proteins. Magn Reson Chem. 44:168-176.
• Raitio KH, Savinainen JR, Vepsalainen J, Laitinen JT, Poso A, Jarvinen T & Nevalainen T. (2006) Synthesis and SAR studies of 2-oxoquinoline derivatives as CB2 receptor inverse agonists. J Med Chem. 49:2022-7.
• Rantanen MK, Lehtio L, Rajagopal L, Rubens CE, Goldman A. (2006) Crystallization and preliminary crystallographic analysis of two Streptococcus agalactiae proteins: the family II inorganic pyrophosphatase and the serine/threonine phosphatase. Acta Crystallograph Sect F Struct Biol Cryst Commun. 62(Pt9):891-4.
• Rauhamäki V, Baumann M, Soliymani R, Puustinen A, Wikström M. (2006) Free in PMC Identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from Rhodobacter sphaeroides. Proc Natl Acad Sci U S A. 103:16135-40.
• Repo S, Paldanius TA, Hytönen VP, Nyholm TKM, Halling KK, Huuskonen J, Pentikäinen OT, Rissanen K, Slotte JP, Airenne TT, Salminen TA, Kulomaa MS & Johnson MS. (2006) Binding properties of HABA-type azo derivatives to avidin and avidin-related protein 4. Chem Biol. 13:1029-39.
• Rischer H, Oresic M, Seppänen-Laakso T, Katajamaa M, Lammertyn F, Ardiles-Diaz W, Van Montagu MC, Inze D, Oksman-Caldentey KM & Goossens A. (2006) Gene-to-metabolite networks for terpenoid indole alkaloid biosynthesis in Catharanthus roseus cells. Proc Natl Acad Sci U S A. 103:5614-9.
• Ruddock LW. (2006) Gaining access to ERp57 function. Structure. 14:1209-1210.
• Ruddock LW & Molinari M. (2006) N-glycan processing in ER quality control. J Cell Sci. 119:4373-4380.
• Rytkönen A, Vaara M, Nethanel T, Kauffman G, Sormunen R, Läärä E, Nasheuer H-P, Rahmeh A, Lee MYWT, Syväoja JE & Pospiech H. (2006) Distinctive activities of DNA polymerases during human DNA replication. FEBS J. 273:2984-3001.
• Rytkönen AK, Hillukkala T, Vaara M, Sokka M, Jokela M, Sormunen R, Nethanel T, Kaufmann G, Pospiech H, and Syväoja JE. (2006) DNA polymerase epsilon associates with the elongating form of RNA polymerase II and nascent transcripts. FEBS J. 273:5535-5549
• Räty J, Liimatainen T, Wirth T. Airenne KJ, Huhtala T, Ihalainen TO, Hamerlynck E, Vihinen-Ranta M, Närvänen A, Ylä-Herttuala S, and Hakumäki J. (2006) Magnetic resonance imaging of viral particle biodistribution in vivo. Gene Therapy 13:1440-1446.
• Rönkko T, Tervo AJ, Parkkinen J & Poso A. (2006) BRUTUS: Optimization of a Grid-Based Similarity Function for Rigid-Body Molecular Superposition. II. Description and Characterization. J Comp-Aid Mol Design. 20:227-36.
• Saario SM, Poso A, Juvonen RO, Jarvinen T & Salo-Ahen OM. (2006) Fatty acid amide hydrolase inhibitors from virtual screening of the endocannabinoid system. J Med Chem. 49:4650-6.
• Salmi J, Moulder R, Filen JJ, Nevalainen OS, Nyman TA, Lahesmaa R & Aittokallio T. (2006) Quality classification of tandem mass spectrometry data. Bioinformatics. 22:400-6.
• Salminen A, Ilias,M, Belogurov G, Baykov AA, Lahti R & Young T. (2006) Two soluble pyrophosphatases in Vibrio cholerae: transient redundancy or enduring cooperation? Biochemistry (Moscow) 71:978-982.
• Salo OMH. (2006) Molecular modeling of the endogenous cannabinoid system. Department of Pharmaceutical Chemistry, University of Kuopio, Kuopio. (Dissertation)
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• * = equal contribution