National Doctoral Programme in
Informational and Structural Biology

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Publications 2004

• Abrescia NGA, Cockburn JJB, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martin C, Burnett R, Stuart DI, Bamford DH & Bamford JKH. (2004) The X-ray structure of bacteriophage PRD1 provides clues to the assembly of large complexes and reveals a viral integral membrane protein. Nature 432:68-74.
• Ahola V, Aittokallio T, Uusipaikka E & Vihinen M. (2004) Statistical methods for identifying conserved residues in multiple sequence alignment. Stat Appl Genet Mol Biol. 3:Article28.
• Amundsen LK, Kokkonen JT, Rovio S & Sirén H. (2004) Analysis of anabolic steroids by partial filling micellar electrokinetic capillary chromatography and electrospray mass spectrometry. Journal of chromatography A 1040:123-31.
• Annila A & Permi P. (2004) Weakly aligned macromolecules in dilute liquid crystals. Concepts in Magnetic Resonance.
• Bass R, Ruddock LW, Klappa P & Freedman RB. (2004). A major fraction of ER-located glutathione is present as mixed disulphides with protein. J Biol Chem 279: 5257-5262
• Belogurov G. (2004) Pyrophosphate-energized proton pumps: identification of the residues determining K+ requirements and discovery of a Na+-dependent enzyme. Department of Biochemistry and Food Chemistry, University of Turku. (Dissertation)
• Bloch D, Belevich I, Jasaitis A., Ribacka C., Puustenen A.,Verkhovsky MI & WikstrÖm M. (2004) The catalytic cycle of cytochrome c oxidase is not the sum of its two halves. Proc. Natl. Acad. Sci. 101:529-533.
• Cao J, Semenova MM, Solovyan VT, Han J, Coffey ET, Courtney MJ. (2004) Distinct requirements for p38-alpha and JNK stress-activated protein kinases in different forms of apoptotic neuronal death. J Biol Chem. 279(34):35903-35913.
• Cheesman C, Freedman RB & Ruddock LW. (2004) The disassembly and reassembly of mutants of E.coli heat-labile enterotoxin: Replacement of proline 93 does not abolish the reassembly-competent and reassembly-incompetent states. Biochemistry 43: 1618-1625.
• Cheesman C, Ruddock LW & Freedman RB. (2004) The kinetics of refolding of E.coli heat labile enterotoxin B-subunit: Analysis of reassembly-competent and reassembly-incompetent unfolded states. Biochemistry 43: 1609-1617.
• Chen D, Roberts R, Pohl M, Nigam S, Kreidberg J, Wang Z, Heino J, Ivaska J, Coffa S, Harris RC, Pozzi A & Zent R. (2004). Differential expression of collagen and laminin binding integrins mediate ureteric bud and inner medullary collecting duct cell tubulogenesis. Am J Physiol Renal Physiol. 287: F602-611.
• Dionisio Pires L M, Karlsson KM, Meriluoto JAO, Kardinaal E, Visser PM, Siewertsen K, Van Donk E & Ibelings BW. (2004) Assimilation and depuration of microcystin-LR by the zebra mussel, Dreissena polymorpha - Aquatic Toxicology 69: 385-396.
• Edqvist J, Ronnberg E, Rosenquist S, Blomqvist K, Viitanen L, Salminen TA, Nylund M, Tuuf J & Mattjus P. (2004) Plants express a lipid transfer protein with high similarity to mammalian sterol carrier protein-2. J Biol Chem 279:53544-53.
• Fabrichniy IP, Lehtiö L, Salminen A, Zyryanov AB, Baykov AA, Lahti R & Goldman A. (2004) Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus ion. Biochemistry 43:14403-11.
• Ferrer A, Ollila J, Tobin C, Nagy B, Thunberg U, Aalto Y, Vihinen M, Vilpo J, Rosenquist R, & Knuutila S. (2004). Different gene expression in immunoglobulin-mutated and immunoglobulin-unmutated forms of chronic lymphocytic leukemia. Cancer Genet. Cytogenet. 153:69.
• Fredriksson K,  Louhivuori M,  Permi P & Annila A. (2004) On the Interpretation of Residual Dipolar Couplings as Reporters of Molecular Dynamics. J Am Chem Soc.
• Gergov M, Weinmann W, Meriluoto J, Uusitalo J & Ojanperä I. (2004) Comparison of product ion spectra obtained by liquid chromatography/triple-quadrupole mass spectrometry for library search - Rapid Communications in Mass Spectrometry 18: 1039-1046.
• Giurcaneanu CD, Tabus I, Astola J, Ollila J & Vihinen M. (2004). Fast iterative gene clustering based on information theoretic criteria for selecting the cluster structure. J. Comput. Biol. 11:660.
• Hakanpää J, Linder M, Askolin S, Nakari-Setälä T, Parkkinen T, Penttilä M & Rouvinen  J. (2004) Atomic resolution structure of the HFBII hydrophobin: a self-assembling  amphihile. J Biol Chem 279:527-533.
• Hakanpää J, Paananen A, Askolin S, Nakari-Setälä T, Parkkinen T, Penttilä M,  Linder M and Rouvinen J. (2004) Atomic resolution structure of the HFBII hydrophobin: a self-assembling amphiphile. J. Biol. Chem. 279, 534-539.
• Hakanpää J,  Parkkinen T, Hakulinen N, Linder M & Rouvinen J. (2004) Crystallization  and preliminary X-ray characterization of Trichoderma reesei hydrophobin  HFBII. Acta Cryst D 60:163-165.
• Halling K and Slotte JP. (2004) Membrane properties of plant sterols in phospholipid bilayers as determined by differential scanning calorimetry, resonance energy transfer and detergent-induced solubilization. Biochim Biophys Acta 1664:161-171.
• Halonen M, Kangas H, Rüppel T, Ilmarinen T, Ollila J, Kolmer M, Vihinen M, Palvimo J, Saarela J, Ulmanen I & Eskelin P. (2004) APECED-causing mutations in AIRE reveal the functional domains of the protein. Hum. Mutat 23:245-257.
• Huiskonen JT, Kivelä HM, Bamford DH & Butcher SJ. (2004) The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes. Nat. Struct. Mol. Biol. 11:850-856.
• Hytönen VP, Nyholm TKM, Pentikäinen OT, Vaarno J, Porkka EJ, Nordlund HR, Johnson MS, Slotte JP, Laitinen OH & Kulomaa MS. (2004) Chicken avidin-related protein 4/5 shows superior thermal stability when compared to avidin retaining high affinity to biotin. J Biol Chem 279:9337-9343.
• Hytönen VP, Laitinen OH, Airenne TT, Kidron H, Meltola NJ, Porkka E, Hörhä J, Paldanius T, Määttä JA, Nordlund HR, Johnson MS, Salminen TA, Airenne KJ, Ylä-Herttuala S & Kulomaa MS. (2004) Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli. Biochemical Journal 384(Pt 2):385-390.
• Häkkinen L, Koivisto L, Gardner H, Saarialho-Kere U, Carroll J, Lakso M, Rauvala H, Laato M, Heino J & Larjava H. (2004) Increased expression of beta-6 integrin in skin leads to spontaneous development of chronic wounds. Am J Pathol. 164: 229-242.
• Ikeno S, Szilvay GR, Linder M, Aritomi H, Ajimi M & Haruyama T. (2004) Protein dot stamp using hydrophobin as immobilization carrier. Sensors and Materials. 16:413-420.
• Jansson A, Koskiniemi H, Mäntsälä P, Niemi J & Schneider GH. (2004) Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products. J. Biol. Chem. 279:41149-56.
• Jokela M, Eskelinen A, Pospiech H, Rouvinen J & Syväoja JE. (2004) Characterization of the 3´exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucl Acids Res 32:2430-2440.
• Jokinen J, Dadu E, Nykvist P, Käpylä J, White DJ, Ivaska J, Vehviläinen P,. Reunanen H, Larjava H, Häkkinen L & Heino J. (2004). Integrin-mediated cell adhesion to type I collagen fibrils. J Biol Chem. 279: 31956-31963
• Jurczak T, Tarczynska M, Karlsson K & Meriluoto J. (2004) Characterization and diversity of cyanobacterial hepatotoxins (microcystins) in blooms from Polish freshwaters identified by liquid chromatography-electrospray ionisation mass spectrometry - Chromatographia 59: 571-578.
• Jänis J, Turunen O, Leisola M, Derrick PJ, Rouvinen J & Vainiotalo P. (2004) Characterization  of mutant xylanases using Fourier tranform ion cyclotron resonance  mass spectrometry: stabilizing contributions of disulphide bridges  and N-erminal extensions. Biochemistry 43:9556-9566.
• Kainov DE, Lísal J, Bamford DH & Tuma R. (2004) Packaging motor from double-stranded RNA bacteriophage phi12 acts as an obligatory passive conduit during transcription. Nucl Acid Res  32:3515-21.
• Kankainen M & Holm L. (2004) POBO: transcription factor binding site verification with bootstrapping. Nucl Acids Res 32:W222-W229.
• Kankainen M, Laitinen T & Peräkylä M. (2004) "Recognition of Reactive High- Energy Conformations by Shape Complementarity and Specific Enzyme-Substrate Interactions in Family 10 and 11 Xylanases." Phys. Chem. Chem. Phys. (in press).
• Karimäki J, Parkkinen T, Santa S, Pastinen O, Leisola M, Rouvinen J & Turunen O. (2004) Engineering the substrate specificity of xylose isomerase. Prot. Eng. Des. Select. 17:861-869.
• Karisola P. (2004) Immunological characterization and engineering of the major latex allergen, hevein (Hev b 6.02) Department of Biological and Environmental Science, University of Jyväskylä. (Dissertation)
• Karisola P, Mikkola J, Kalkkinen N, Airenne KJ, Laitinen OH, Repo S, Pentikäinen OT, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, KulomaaMS & Alenius H. (2004) Construction of Hevein (Hev b 6.02) with Reduced Allergenicity for Immunotherapy of Latex Allergy by Comutation of Six Amino Acid Residues on the Conformational IgE Epitopes. J. Immunol. 172:2621-2628.
• Kaukinen U, Lönnberg H & Peräkylä M. (2004) "Stabilisation of the Transition State of Phosphodiester Bond Cleavage within Linear Single-Stranded Oligoribonucleotides." Org. Biomol. Chem. 2:66-73.
• Kauko A, Haataja S, Pulliainen AT, Finne J & Papageorgiou AC. (2004) Crystal structure of Streptococcus suis Dps-like peroxide resistance protein Dpr: Implications for iron incorporation. J Mol Biol 338:547-558.
• Keyriläinen J. (2004) Diffraction-enhanced X-ray imaging of in vitro breast tumours. Division of X-ray Physics, Department of Physical Sciences, Faculty of Science, University of Helsinki and Department of Oncology, Helsinki University Central Hospital, Helsinki. (Dissertation)
• Khorram O, Garthwaite M, Johnson MS, Denessiouk KA, Han G, Guo T, McPhaul LW, Magee TR, Westerman B, Golos TG. (2004) Identification and characterization of a novel luciferase-like protein in the human female reproductive tract. J Clin Endocrinol Metab. 89:5837-46.
• Kiiskinen L-L, Palonen H, Linder M, Viikari L & Kruus K. (2004) Laccase from Melanocarpus albomyces binds effectively to cellulose. FEBS Lett. 576:251-255.
• Koistinen P, Ahonen M, Kähäri VM & Heino J. (2004) aV Integrin promotes in vitro and in vivo survival of cells in metastatic melanoma. Int J Cancer 112:61-70.
• Koskinen JO, Vaarno J, Meltola NJ, Soini JT, Hänninen PE, Luotola J, Waris ME & Soini AE. (2004) Fluorescent nanoparticles as labels for immunometric assay of C-reactive protein using two-photon excitation assay technology. Analytical Biochemistry 328:210-218.
• Kriikku P, Grass B, Hokkanen A, Stuns I & Sirén H. (2004) Isotachophoresis of beta-blockers in a capillary and on a poly(methyl methacrylate) chip. Electrophoresis 25: 1687-94.
• Kukkonen A, Peräkylä M, Åkerman KEO & Näsman J. (2004) Muscarinic Toxin 7 Selectivity is Dictated by Extracellular Receptor Loops. J. Biol. Chem 279:50923-50929.
• Kull TPJ, Backlund PH, Karlsson KM & Meriluoto JAO. (2004) Oxidation of the cyanobacterial hepatotoxin microcystin-LR by chlorine dioxide - reaction kinetics, characterization and toxicity of reaction products. Environmental Science & Technology 38:6025-31.
• Käpylä J, Jaalinoja J, Tulla M, Ylöstalo J, Nissinen L, Viitasalo T, Vehviläinen P, Marjomäki V, Nykvist P, Saamanen AM, Farndale RW, Birk DE, Ala-Kokko L & Heino J. (2004) The fibril-associated collagen IX provides a novel mechanism for cell adhesion to cartilaginous matrix. J Biol Chem 279:51677-87.
• Laitinen T, Kankare JA & Peräkylä M. (2004) Free Energy Simulations and MM-PBSA Analyses on the Affinity and Spesificity of Steroid Binding to Anti-Estradiol Antibody. Proteins 55:34-43.
• Lappalainen I. (2004) Human Pathogenic Mutations in Protein Domains. Department of Biological and Environmental Sciences, Division of Biochemistry, University of Helsinki. (Dissertation)
• Lappalainen I & M. Vihinen. (2004) Structural Basis of ICF-causing Mutations in the Methyltransferase Domain of DNMT3B. Prot. Eng. 15:1005-14.
• Lappe M & Holm L. (2004) Unraveling protein interaction networks with near-optimal efficiency. Nature Biotechnology 22:98-103.
• Lappi AK, Lensink M, Alanen HI, Salo KEH, Lobell M, Juffer A & Ruddock, LW. (2004) A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases. J Mol Biol 335: 283-295.
• Lehtiö L & Goldman A. (2004) The pyruvate formate lyase family: sequences, structures and activation. Prot Eng Des Sel 17:545-52.
• Lehtonen JV. (2004) Development of computational methods for analysis and visualization of biomolecules and their complexes. Department of Biochemistry and Pharmacy, Åbo Akademi University. (Dissertation)
• Lehtonen JV, Still D-J, Rantanen V-V, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M & Johnson MS. (2004) BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comp. Aided Molec. Des. 18:401-19.
• Lehtonen P, Sirén H, Ojanperä I & Kostiainen R. (2004) Migration behaviour and separation of tramadol metabolites and diastereomeric separation of tramadol glucuronides by capillary electrophoresis. Journal of chromatography. A 1041:227-34.
• Leppänen V-M, Bespalov M, Runeberg-Roos P, Puurand Ü, Merits A, Saarma M, & Goldman A. (2004) The structure of GFR alpha-1 domain 3 reveals a novel fold and new insights into GDNF binding and RET activation. EMBO J. 23:1452-1462.
• Linder MB, Qiao M, Laumen F, Selber K, Hyytiä T, Nakari-Setälä T & Penttilä ME. (2004) Efficient purification of recombinant proteins using hydrophobins as tags in surfactant-based two-phase systems. Biochemistry, 43:11873-82.
• Lisal J, Kainov DE, Bamford DH, Thomas GJ, Jr. & Tuma R. (2004) Enzymatic mechanism of RNA translocation in dsRNA bacteriophages. J Biol Chem 279:1343-1350.
• Louhivuori M, Fredriksson K, Pääkkönen K, Permi P & Annila A. (2004) Alignment of chain-like molecules. J Biomol NMR 29(4):517-524.
• Lund R., Chen Z., Scheinin J & Lahesmaa R.(2004) Early target genes of IL-12/STAT4 signaling in T helper cells. J. Immunol. 172:6775-82
• Malinen AM, Belogurov GA, Salminen M, Baykov AA. & Lahti R. (2004) Elucidating the role of conserved glutamates in H+-pyrophosphatase of Rhodospirillum rubrum. J. Biol. Chem. 279: 26811-26816.
• Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH & Stuart DI. (2004) Atomic Snapshots of an RNA Packaging Motor Reveal Conformational Changes Linking ATP Hydrolysis to RNA Translocation. Cell 118:743-755.
• Mancini EJ, Kainov DE, Hui W, Gottlieb P, Tuma R, Bamford DH, Stuart DI & Grimes JM. (2004)  Production, crystallization and preliminary X-ray crystallographic studies of the bacteriophage phi12 packaging motor. Acta Cryst D 60:588-590.
• Meltola NJ, Soini AE & Hänninen PE. (2004) Syntheses of Novel Dipyrrylmethene-BF2 Dyes and Their Performance as Labels in Two-Photon Excited Fluoroimmunoassay. Journal of Fluorescence 14:129-138.
• Meltola NJ, Wahlroos R & Soini AE. (2004) Hydrophilic labeling reagents of dipyrrylmethene-BF2 dyes for two-photon excited fluorometry: Syntheses and photophysical characterization. Journal of Fluorescence 14:635-647.
• Meriluoto J, Karlsson K & Spoof L. (2004) High-throughput screening of ten microcystins and nodularins, cyanobacterial peptide hepatotoxins, by reversed-phase liquid chromatography-electrospray ionisation mass spectrometry - Chromatographia 59: 291-298.
• Mikhailov A, Härmälä-Brasken AS, Hellman J, Polosukhina E, Meriluoto J & Eriksson JE. (2004) Immunochemical analysis and determination of cellular targets of microcystins and nodularin. Lakes and Reservoirs: Research and Management.(in press)
• Moretti L, Pentikäinen OT, Settimo L & Johnson MS. (2004) Model structures of the N-methyl-d-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands. J. Struc. Biol. 145:205-215.
• Nigmatullin R, Lovitt R, Wright C, Linder M, Nakari-Setälä T & Gama M. (2004) Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains. Colloids Surfaces B Biointerfaces 35:125-135.
• Nikkola-Paakkarinen J, Vihinen P, Vlaykova T, Hahka-Kemppinen M, Heino J & PyrhÖnen S. (2004) Integrin chains b1 and aV as prognostic markers in human metastatic melanoma. Melanoma Research 14:29-37
• Nummelin H. (2004) The structure of Yersinia adhesin A collagen-binding domain. Department of Biochemistry and Food Chemistry, University of Turku; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University; and Institute of Biotechnology, Research Program for Structural Biology and Biophysics, University of Helsinki.(Dissertation)
• Nummelin H, Merckel MC, Leo JC, Lankinen H, Skurnik M & Goldman A. (2004) The structure of Yersinia adhesin YadA collagen-binding domain reveals a novel left-handed parallel beta-roll. EMBO J 23:701-711.
• Nymalm Y. (2004) Structural basis of protein function: Integrin alpha-1I, vascular adhesion protein-1 and the VL domain of the antiferritin antibody. Department of Biochemistry and Pharmacy, Åbo Akademi University. (Dissertation)
• Nymalm Y, Puranen SJ, Nyholm TKM, Käpylä J, Kidron H, Pentikäinen OT, Airenne TT, Heino J, Slotte JP, Johnson MS & Salminen T. (2004) Jararhagin-derived "RKKH"-peptides induce structural changes in alpha I-Domain of Human Integrin alpha1-beta1. J Biol. Chem. 279:7962-7970.
• Nyrönen T. (2004) Lääkkeen ominaisuudet ovat kirjoitettuna lääkemolekyylin rakenteeseen, Lääkkeen Tie, Lääketietokeskus 1-4.
• Palviainen J, Rouvinen  J & Silvennoinen R. (2004) Analysis of microfibril angle of wood fibers  by use of laser microscope polarimetry. Opt Eng 43:186-191.
• Papageorgiou AC, Baker MD, Mcleod JD, Goda S, Manzotti CN, Sansom DM, Tranter HS & Acharya KR. (2004). Identification of a secondary zinc-binding site in staphylococcal enterotoxin C2: Implications for superantigen recognition. J. Biol. Chem. J. Biol. Chem. 279, 1297-1303
• Papageorgiou AC & Wikman LE (2004). Is JAK3 a new drug target in immunomodulation-based therapies? Trends Pharmacol Sci 25:558-62. Review.
• Parkkinen T, Hakulinen  N, Tenkanen M, Siika-aho M & Rouvinen J. (2004)  Crystallization and preliminary X-ray analysis of a novel Trichoderma  reesei xylanase IV belonging to glycoside hydrolase family 5. Acta Cryst D. 60:542-544.
• Perera D, Pérez-Hidalgo L, Moens PB, Reini K, Lakin N, Syväoja JE, San-Segundo PA & Freire R. (2004) TopBP1 and ATR co-localization at meiotic chromosomes: role of TopBP1/Cut5 in the meiotic recombination checkpoint. Mol Biol Cell 15: 1568-1579.
• Permi P& Annila. (2004) Coherence transfer in proteins. Prog. Nucl Magn Res Spectr 44:97-137.
• Peräkylä M, Molnar F & Carlberg C. (2004) "A Structural Basis for the Species- Spesific Antagonism of 26,23-Lactones on Vitamin D Signaling." Chem. Biol. 11:1147-1156.
• Pirneskoski A, Klappa P, Lobell M, Williamson RA, Byrne L, Alanen HI, Salo KEH, Kivirikko KI, Freedman RB & Ruddock LW. (2004) Molecular characterisation of the principal substrate binding site of the ubiquitous folding catalyst protein disulphide isomerase. J Biol Chem 279: 10374-10381.
• Poranen MM & Tuma R. (2004). Self-assembly of double-stranded RNA bacteriophages. Virus Res. 101:93-100.
• Psencik L, Ikonen TP, Laurinmäki P, Merckel MC, Butcher SJ, Serimaa RE & Tuma R. (2004) Lamellar organization of pigments in chlorosomes, the light harvesting complexes of green photosynthetic bacteria. Biophysical J. 87: 1165-1172
• Rautajoki K*, Nyman T* & Lahesmaa R. (2004) Identification of novel proteins differentially expressed by human Th1 and Th2 CD4+ T lymphocytes. (*Equal contribution). Proteomics 4:84-92.
• Reini K, Uitto L, Perera M., Moens PB, Freire R & Syväoja JE. (2004) TopBP1 Localizes to Centrosomes in Mitosis and to chromosome cores in Meiosis. Chromosoma 112:323-330.
• Rosengren AT, Nyman TA, Syyrakki S, Matikainen S & Lahesmaa R. (2004) Proteomic and transcriptomic characterization of IFN-a-induced human primary T helper cells. Proteomics. 5:371-379.
• Russell SJ, Ruddock LW, Salo KEH, Oliver JD, Roebuck QP, Llewellyn DH, Roderick HL, Koivunen P, Myllyharju J, High, S. 2004. The primary substrate binding site in the b' domain of ERp57 is adapted for ER lectin association. J Biol Chem 279: 18861-18869.
• Ruuskanen J, Xhaard H, Marjamäki A, Salaneck E, Salminen T, Yan Y-L, Postlethwait JH, Johnson MS, Larhammar D & Scheinin M. (2004) Identification of duplicated fourth alpha-2-adrenergic receptor subtype by cloning and mapping of five receptor genes in zebrafish. Mol. Biol. Evol. 21:14-28.
• Saarela J, Oinonen  C, Jalanko A, Rouvinen J & Peltonen L. (2004) Autoproteolytic processing  of aspartylglucosaminidase. Biochem J 378:363-371.
• Salgado PS, Makeyev EV, Butcher SJ, Bamford DH, Stuart DI & Grimes JM. (2004) The structural basis for RNA specificity and calcium inhibition of an RNA-dependent RNA polymerase. Structure.12:307-316.
• Salo OMH, Lahtela-Kakkonen M, Gynther J, Järvinen T & PosoA. (2004) Development of a 3D Model for the Human Cannabinoid CB1 Receptor, J. Med. Chem. 47:3048-3057.
• Sillanpää N, Magureanu CG, Murumägi A, Reinikainen A, West A, Manninen A, Heino M, Ranki A, Saksela K, Krohn K, Lahesmaa R & Peterson P. (2004) Autoimmune regulator induced changes in the gene expression profile of human monocyte-dendritic cell -lineage. Mol Immunol. 41:1185-98.
• Simonaho S-P, Tolonen Y, Rouvinen J & Silvennoinen R. (2004) Laser light scattering  from wood samples soaked in water and in benzyl bentsoate. Optik 114:445-448.
• Sipiä, VO, Karlsson KM, Meriluoto JAO & Kankaanpää HT. (2004) Eiders (Somateria mollissima) obtain nodularin, a cyanobacterial hepatotoxin, in Baltic Sea food web - Environmental Toxicology and Chemistry 23: 1256-1260.
• Sirén H, Luomanperä K, Työppönen T, Rovio S, Vastamäki P & Savolahti P. (2004) Process control and drug analysis with an on-line capillary electrophoresis system.Journal of biochemical and biophysical methods. 60:295-307.
• Sirén H, Mielonen M & Herlevi M. (2004) Capillary electrophoresis in the determination of anionic catecholamine metabolites from patients' urine. Journal of chromatography. A 1032(1-2): 289-97.
• Soini JT, Waris ME & Hänninen PE. (2004) Detection methods of microsphere based single-step bioaffinity and in vitro diagnostic assays. Journal of Pharmaceutical and Biomedical Analysis 34:753-760.
• Soukka JM, Virkki A, Hänninen PE & Soini JT. (2004) Optimization of multi-photon event discrimination levels using Poisson statistics. Optics Express 12:84-89.
• Spoof Lisa (2004) High-performance liquid chromatography of microcystins and nodularins, cyanobacterial peptide toxins. Department of Biochemistry and Pharmacy, The Faculty of Mathematics and Sciences, Åbo Akademi University. (Dissertation)
• Stenholm TJ, Soini JT & Hänninen PE. (2004) A long-arm autocorrelator for measurement of pico- to nanosecond laser pulse widths. Meas Sci Technol 15:2001-2004.
• Sultana A, Kallio P, Jansson A, Wang J-S, Niemi J, Mäntsälä P & Schneider G. (2004) Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 60(Pt 6):1118-2000.
• Sultana A, Kallio P, Jansson A, Wang J-S, Niemi J, Mäntsälä P & Schneider G. (2004) Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation EMBO J. 5;23(9):1911-21.
• Tammela P, Laitinen L, Galkin A, Wennberg T, Heczko R, Vuorela H, Slotte JP & Vuorela P. (2004) Permeability characteristics and membrane affinity of flavonoids and alkyl gallates in Caco-2 cells and in phospholipid vesicles. Arch Biochem Biophys 425:193-199.
• Terova B, Slotte JP & Nyholm T. (2004) Miscibility of acyl-chain defined phosphatidylcholines with N-palmitoyl sphingomyelin in bilayer membranes. Biochim Biophys Acta 1667:182-189
• Tervo A, Nyrönen TH, Rönkkö T & Poso A. (2004) Comparing The Quality and Predictiveness Between 3D QSAR Models Obtained from Manual and Automated Alignment. J. Chem. Inf. Comput. Sci. 44:807-816.
• Tichelaar W, Safferling M, Keinänen K, Stark H & Madden DR (2004) The three-dimensional structure of an ionotropic glutamate receptor reveals a dimer-of-dimers assembly. J. Mol. Biol. 344:435-42.
• Tuma R. (2004) Quality control for biopharmaceuticals. European Pharmaceutical Review 9/4, 24-27.
• Tuominen V, Myles D, Dauvergne M-T, Lahti R, Heikinheimo P & Goldman A. (2004) Production and preliminary analysis of perdeuterated yeast inorganic pyrophosphatase crystals suitable for neutron diffraction. Acta Crystallogr D 60:606-609.
• Tuovinen L,Peltonen S,Liikola M, Hotakainen M, Lahtela-Kakkonen M, Poso A & Järvinen K. (2004) Drug release from starch-acetatemicroparticles and films with and without incorporated a-amylase. Biomaterials 25:4355-4362.
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