National Doctoral Programme in
Informational and Structural Biology

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Publications 2002

• Baker MD, Papageorgiou AC, Titball RW, Miller J, White S, Lingard B, Lee JJ, Cavanagh D, Kehoe MA, Robinson JH & Acharya KR. (2002) Structural and functional role of threonine-112 in a superantigen Staphylococcus aureus enterotoxin-B. J Bio. Chem. 277:2756-2762.
• Bamford D & Butcher S. (2002) Menetelmien yhdistäminen paljasti virusten sukulaisuuden Kemia-Kemi 29:42-43
• Belogurov GA & Lahti R. (2002) A Lysine Substitute for K+. A460K mutation elilminates K+ dependence in H+ -pyrophosphatase of Carboxydothermus hydrogenoformans. J Biol Chem 277:49651-49654.
• Belogurov GA, Turkina MV, Penttinen A, Vanhatalo S, Baykov AA & Lahti R. (2002) H+-pyrophosphatase of Rhodospirillum rubrum: High-yield expression in Escherichia coli and identification of the cys residues responsible for inactivation by mersalyl. J Biol Chem. 277: 22209-22214.
• Benevides JM, Juuti JT, Tuma R, Bamford DH & Thomas GJ Jr. (2002) Characterization of subunit-specific interactions in a double-stranded RNA virus: Raman difference spectroscopy of the f 6 procapsid. Biochemistry 41:11946-53.
• Bengoechea JA, Pinta E, Salminen T, Oertel C, Holst O, Radziejewska-Lebrecht J, Piotrowska-Seget Z, Venho R & Skurnik MN. (2002) Functional characterization of Gne (UDP-N-acetylglucosamine-4-epimerase), Wzz (chain length determinant), and Wzy (O-antigen polymerase) of Yersinia enterocolitica serotype O:8. Journal of Bacteriology. 184:4277-87.
• Castrén M, Lampinen KE, Miettinen R, Koponen E, Sipola I, Bakker CE, Oostra BA. & Castrén E. (2002) BDNF regulates the expression of fragile X mental retardation protein in the hippocampus. Neurobiol Disease. 11:221-229.
• Chen Z, Ahonen M, Hämäläinen H, Bergelson JM, Kähäri V-M & Lahesmaa R. (2002)High-efficiency gene transfer to primary T lymphocytes by recombinant adenovirus vectors. J Immunol Methods. 260:79-89.
• Coffey ET, Smiciene G, Hongisto V, Cao J, Brecht S, Herdegen T&Courtney MJ. (2002) JNK2/3 is specifically activated by stress, mediating c-jun activation, in the presence of constitutive JNK1 activity in cerebellar neurons. J Neurosci. 22:4335-4345.
• Denesyuk AI, Denessiouk KA, Korpela T & Johnson MS. (2002) Functional attributes of the phosphate group binding "cup" of pyridoxal phosphate - dependent enzymes. J Mol Biol, 316:155-172.
• Fernández M, Keyriläinen J, Serimaa R, Torkkeli M, Karjalainen-Lindsberg M.-L, Tenhunen M, Thomlinson W, Urban V & Suortti P. (2002) Small-angle x-ray scattering studies of human breast tissue samples. Physics in medicine & biology. 47:577-592.
• Haapasalo A, Sipola I, Larsson K, Åkerman KEO, Stoilov P, Stamm S, Wong G & Castrén E. (2002) Regulation of TrkB Surface Expression by Brain-Derived Neurotrophic Factor and Truncated TrkB Isoforms. J Biol Chem. 277: 43160-43167.
• Haataja S, Penttinen A., Pulliainen A., Tikkanen K., Finne J. & Papageorgiou AC. (2002). Expression, purification and crystallisation of Dpr, a ferritin-like protein from the Gram-positive meningitis-associated bacterium Streptococcus suis. Acta Cryst. D 58:1851-1853.
• Hakulinen N, Kiiskinen LL, Kruus K, Saloheimo M, Koivula A & Rouvinen J. (2002) Crystal structure of a laccase from Melanocarpus albomyces with an intact trinuclear copper site. Nature Struct Biol. 9:601-605.
• Halonen P, Baykov AA, Goldman A, Lahti R & Cooperman BS. (2002) Single-turnover kinetics of Saccharomyces cerevisiae inorganic pyrophosphatase. Biochemistry. 41:12025-12031.
• Hernberg M, Virkkunen P, Maasilta P, Keyriläinen J, Blomqvist C, Bergh J & Wiklund T. (2002) Pulmonary toxicity after radiotherapy in primary breast cancer patients: results from a randomized chemotherapy study. International Journal of Radiation Oncology*Biology*Physics. 52:128-136.
• Hendriks JHM, Jasaitis AA, Saraste M & Verkhovsky MI. (2002) Proton and electron pathways in the bacterial nitric oxide reductase. Biochemistry 41:2331-2340.
• Hirvonen M, & Papageorgiou, AC. (2002) Crystallisation and preliminary crystallographic analysis of a family 45 endoglucanase from the thermophilic fungus Melanocarpus albomyces. Acta Cryst. D 58: 336-338.
• Hyytinen E-R, Haapala K, Thompson J, Lappalainen I, Roiha M, Rantala I, Helin HJ, Jänne OA, Vihinen M, Palvimo JJ & Koivisto PA.. (2002) Pattern of Somatic Androgen Receptor Gene Mutations in Patients with Hormone-Refractory Prostate Cancer Lab Invest. 82:1591-98.
• Hänninen P. (2002) Light microscopy - Beyond the diffraction limit. Nature 419:802-802.
• Ivaska J, Nissinen L, Immonen N, Eriksson JE, Kähäri VM & Heino J. (2002) Integrin a2b1 promotes activation of protein phosphatase 2A and dephosphorylation of Akt and GSK3b. Mol Cell Biol 22:1352-1359
• Jouppila A, Pentikäinen OT, Settimo L, Nyrönen T, Haapalahti JP, Lampinen M, Mottershead DG, Johnson MS & Keinänen K (2002) Determinants of antagonist binding at the a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit GluR-D: Role of the conserved Arg-507 and Glu-727 residues. Eur J Biochem. 269: 6261-6270
• Kajander T, Merckel MC, Thompson A, Deacon AM, Mazur P, Kozarich JW & Goldman A. (2002) The structure of Neurospora crassa 3-carboxy-cis, cis-muconate lactonizing enzyme, a beta propeller cycloisomerase. Structure (Camb). 10:483-92.
• Merckel MC, Kajander T, Deacon AM, Thompson A, Grossmann JG, Kalkkinen N & Goldman A. (2002) 3-Carboxy-cis, cis-muconate lactonizing enzyme from Neurospora crassa: MAD phasing with 80 selenomethionines. Acta Crystallogr D58:727-34.
• Kankaanpää HT, Vuorensola KM, Sipiä VO & Meriluoto JAO. (2002) Chromatographic and spectral behaviour and detection of hepatotoxic nodularin in fish, clam, mussel and mouse tissues using HPLC analysis. Chromatographia 55:157-162.
• Karisola P, Alenius H, Mikkola J, Kalkkinen N, Helin J, Pentikäinen OT, Repo S, Reunala T, Turjanmaa K, Johnson MS, Palosuo T, Kulomaa MS.(2002) The major conformational IgE-binding epitopes of hevein (Hev b6.02) are identified by a novel chimera-based allergen epitope mapping. J Biol Chem. 277:22656-61.
• Keyriläinen J, Fernández M & Suortti P. (2002) Refraction contrast in X-ray imaging. Nuclear instruments & methods in physics research. 488: 419-427.
• Kollman PA, Kuhn B & Peräkylä M. (2002) Computational studies of enzyme-catalyzed reactions: Where are we in predicting mechanisms and in understanding the nature of enzyme catalysis? J Phys Chem B. 106:1537-1542.
• Kontkanen O, Lakso M, Wong G & Castrén E. (2002) Chronic antipsychotic drug treatment induces long-lasting expression of fos and jun family genes and activator protein 1 complex in the rat prefrontal cortex. Neuropsychopharmacology, 27:152-162.
• Kontkanen O & Castrén E. (2002) Functional genomics in neuropsychiatric disorders and in neuropharmacology. Exp Opin Ther Targets 6: 363-374.
• Kontkanen O, Törönen P, Lakso M, Wong G & Castrén E. (2002) Antipsychotic drug clozapine differentially regulates genes related to presynaptic function in the rat prefrontal cortex. J Neurochem. 83:1043-1053.
• Koskelin MM, Soini AE, Meltola NJ & Ponomarev GV. (2002) Phosphorescent labeling reagents of platinum(II) and palladium(II) coproporphyrin-II. Preparation and performance characteristics. Journal of Porphyrins and Phthalocyanines 6:533-543.
• Laitinen OH, Hytönen VP, Ahlroth MK, Pentikäinen OT, Gallagher C, Nordlund HR, Ovod V, Marttila AT, Porkka E, Heino S, Johnson MS, Airenne KJ & Kulomaa MJ. (2002) Chicken avidin-related proteins show altered immunological and physico-chemical properties as compared to avidin. Biochem J. 363: 609-617.
• Lampinen M, Settimo L, Pentikäinen OT, Jouppila A, Mottershead DG, Johnson MS & Keinänen K. (2002). Discrimination between agonists and antagonists by the a-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid - selective glutamate receptor. A mutation analysis of the ligand-binding domain of GluR-D subunit . J Biol Chem. 277:41940-41947.
• Lappalainen I & M. Vihinen. (2002) Structural Basis of ICF Causing Mutations in the Methyltransferase Domain of DNMT3B. Prot. Eng. 15, 1005-1014.
• Larramendy ML, Niini T, Elonen E, Nagy B, Ollila J, Vihinen M & Knuutila S. (2002) Overexpression of translocation-associated fusion genes of FGFRI, MYC, NPMI, and DEK, but absence of the translocations in acute myeloid leukemia. A microarray analysis. Haematologica. 87(6):569-77.
• Lehtiö L, Leppänen VM, Kozarich JW & Goldman A. (2002) Structure of Escherichia coli Pyruvate formate lyase with pyruvate Acta Cryst. D58:2209-2212
• Lehtolainen P, Taskinen A, Laukkanen J, Airenne KJ, Heino S, Lappalainen M, Ojala K, Marjomäki V, Martin JF, Kulomaa MS & Ylä-Herttuala S. (2002) Cloning and characterisation of scavidin, a fusion protein for the targeted delivery of biotinylated molecules, J Biol Chem. 277: 8545-8550.
• Lindholm T, Degerlund M, Spoof L Meriluoto J. (2002) A century of water quality changes in a coastal lake with toxic Planktothrix - Verhandlungen der Internationalen Vereinigung für Theoretische und Angewandte Limnologie 28:984-987.
• Lähteinen S, Pitkänen A., Saarelainen T, Nissinen J, Koponen E & Castrén E. (2002) Epileptogenesis is delayed in mice overexpressing truncated trkB reseptors. Eur J Neurosci. 15: 721-734.
• Marjomäki V, Pietiäinen V, Upla P, Matilainen H, Ivaska J, Nissinen L, Reunanen H, Huttunen P, Hyypiä T & Heino J. (2002) Endocytosis of echovirus 1 in caveolae. J Virol. 76:1856-1865.
• Marvanová M, Törönen P, Storvik M, Lakso M, Castrén E & Wong G. (2002) Synexpression Analysis of ests in the Rat Brain Reveals Distinct Patterns and Potential Drug Targets. Mol Brain Res. 104:176-186.
• Mattinen M-L, Pääkkönen K, Ikonen T, Laakso T, Craven J, Drakenberg T, Serimaa R, Waltho J & Annila A. (2002) Quaternary structure built from subunits combining NMR and SAXS data. Biophysical Journal 83:1177-1183.
• Nikkilä J, Törönen P, Kaski S, Venna J, Castrén E & Wong G.(2002) Analysis and visualization of gene expression data using self-organizing maps. Neural Networks. 15: 953-966.
• Nousiainen M, Derrick PJ, Kaartinen MT, Mäenpää PH, Rouvinen J & Vainiotalo P. (2002) A mass spectrometric study of metal binding to osteocalcin. Chem. Biol. 9:195-202
• Nummelin H, El Tahir Y, Ollikka P, Skurnik M & Goldman A.(2002). Expression, purification and crystallization of a collagen-binding fragment of Yersinia adhesin YadA. Acta Cryst. D58:1042-1044.
• Nymalm Y, Kravchuk Z, Salminen T, Chumanevich A, Dubnovitsky A, Kankare J, Pentikäinen O, Lehtonen J, Arosio P, Martsev S & Johnson M. (2002) Antiferritin VL homodimer binds human spleen ferritin with high specificity. J Struct Biol. 138:171-186.
• Ohvo-Rekilä H, Ramstedt B, Leppimäki P & Slotte JP. (2002) Cholesterol interactions with phospholipid in membranes. Prog Lipid Res. 41:66-97.
• Oja M, Nikkilä J, Törönen P, Wong G, Castrén E & Kaski S. (2002) Exploratory clustering on gene expression profiles of mutated yeast strains. In: Computational and statistical approaches to genomics, eds. Wei Zhang and Ilya Schmulevich. Kluwer Academic Publishers.
• Oja M, Nikkilä J, Törönen P, Castrén E & Kaski S. (2002) Learning Metrics for Visualizing gene functional similarities. STeP 2002 - Intelligenece, The Art of Natural and Artificial, the 10th Finnish Artificial Intelligence Conference, Edited by Pekka Ala-Siuru and Samuel Kaski, pp. 31-40.
• Ojala PJ, Paavilainen VO, Vartiainen MK, Tuma R, Weeds AG & Lappalainen P. (2002) The two ADF-H domains of twinfilin play functionally distinct roles in interactions with actin monomers. Mol. Biol. Cell 13:3811-3821.
• Okoh MP. (2002) Molecular and Biophysical Analysis of the Non-Catalytic PH, TH, SH3 and SH2 Domain of Bruton Tyrosine Kinase (Btk) Protein. Dissertationes Biocentri Viikki Universitatis Helsingiensis. University of Helsinki (Dissertation)
• Ollila J & Vihinen M. (2002) Microarray analysis of B-cell stimulation. Vitam Horm. 64:77-99.
• Ollila F. (2002) Charactrizing the Interactions of small Molecules with Lipid Membranes and Cyclodextrins. Department of Biochemistry and Pharmacy. Åbo Akademi University (Dissertation)
• Ollila F, Halling K, Vuorela P, Vuorela H & Slotte JP. (2002) Characterization of lavonoid/biomembrane interactions. Arch. Biochem. Biophys. 399:103-108.
• Ollila F & Slotte JP. (2002) Partitioning of Triton X-100, deoxycholate and C10EO8 into bilayers composed of native and hydrogenated egg yolk sphingomyelin. Biochem. Biophys. Acta. 1564:281-288.  
• O'Riordan TC, Soini AE, Soini JT & Papkovsky DB. (2002) Performance evaluation of the phosphorescent porphyrin label: Solid-phase immunoassay of alpha-fetoprotein. Analytical Chemistry 74:5845-5850.
• O'Sullivan PJ, Burke M, Soini AE & Papkovsky DB. (2002) Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays. Nucleic Acid Res. 30:e144.
• Pasternack A, Coleman SK, Jouppila A, Mottershead DG, Lindfors M, Pasternack M and Keinänen K. (2002) a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor channels lacking the N-terminal domain. J Biol Chem. 277: 49662-49667.
• Päivärinta J, Poso A, Hotokka M & Muttonen E. ( 2002 ) Molecular Dynamics of Steroid Structures in Different Solvents. Crystal Growth & Design 2:121-126.
• Ramstedt B and Slotte JP. (2002) Membrane properties of sphingomyelins. FEBS Lett 531:33-37.
• Rantanen V-V, Gyllenberg M, Koski T, & Johnson MS. (2002). A dissimilarity matrix between protein atom clases based on Gaussian mixtures. Bioinformatics. 18:9:1257-1263
• Reinikainen M, Lindvall F, Meriluoto JAO, Repka S, Sivonen K, Spoof L & Wahlsten M. (2002) Effects of dissolved cyanobacterial toxins on the survival and egg-hatching of estuarine calanoid copepods - Marine Biology. 140:577-583.
• Saarela JA, Tuppurainen K, Peräkylä M, Santa H & Laatikainen R. (2002) Correlative motions and memory effects in molecular dynamics simulations of molecules: Principal components and rescaled range analysis suggest that the motions of native BPTI are more correlated than those of its mutants. Biophys. Chem. 95:49-57.
• Salmi J, Aittokallio T, Westerholm J, Griese M, Rosengren A, Nyman TA, Lahesmaa R & Nevalainen O. (2002)Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels. Proteomics 2:1504-15.
• Salminen A. (2002) Discovery of a new family of soluble pyrophosphatases and the functional role of quaternary structure in pyrophosphatases. Department of Biochemistry and Food Chemistry, University of Turku. (Dissertation)
• Salminen A, Parfenyev AN, Salli K, Efimova IS, Magretova NN, Goldman A, Baykov AA & Lahti R. (2002) Modulation of dimer stability in yeast pyrophosphatase by mutation at the subunit interface and ligand binding to the active site. J Biol Chem. 277:15465-15471.
• San Martin C, Huiskonen J, Bamford JKH, Butcher SJ, Fuller SD, Bamford DH & Burnett R. (2002) Minor proteins, mobile arms and membrane-capsid interactions in bacteriophage PRD1 capsid. Nature Structural Biology. 9:756-763.
• Santa H, Ylisirniö M, Hassinen T, Laatikainen R & Peräkylä M. (2002) Stability and Amino Acid Preferences of Type VIII Reverse Turn: The Most Common Turn in Peptides? Protein Eng. 15:651-657.
• Sipiä VO, Lahti K, Kankaanpää HT, Vuorinen PJ & Meriluoro JAO. (2002) Screening for cyanobacterial hepatotoxins in herring and salmon from the Baltic Sea. Aquatic Ecosystem Health & Management 5:451-456.
• Soini AE, Seveus L, Meltola NJ, Papkovsky DB & Soini E. (2002) Phosphorescent metalloporphyrins as labels in time-resolved luminescence microscopy: Effect of mounting on emission intensity. Microscopy Research and Technique 58:125-131.
• Soini JT, Soukka JM, Soini E & Hänninen PE. (2002) Two-photon excitation microfluorometer for multiplexed single-step bioaffinity assays. Review of Scientific Instruments 73:2680-2685.
• Solovyan V, Bezvenyuk Z, Salminen A, Austin CA & Courtney MJ. (2002) The role of topoisomerase II beta in the excision of DNA loop domains during apoptosis J Biol Chem., 277: 21458-21467.
• Spoof L & Meriluoto J. (2002) Rapid separation of microcystins and nodularin using a monolithic silica C18 column - J of Chromatography. A 947:237-245.
• Stoilov P, Castrén E. & Stamm S. (2002) Analysis of the human TrkB gene Ggnomic organization reveals novel TrkB isoforms, unusual gene length, and splicing mechanism. Biochem. Biophys Res Commun. 290:1054-1065.
• Tiirola MA, Männistö MK, Puhakka JA & Kulomaa MS. (2002) Isolation and Characterization of Sphingomonas sp. MT1, A Dominant olychlorophenol Degrading Strain in a Groundwater Bioremediation System. Appl Env Microb. 68:173-180
• Tiirola MA, Wang H, Paulin L & Kulomaa MS. (2002) Evidence for Natural Horizontal Transfer of the pcpB Gene Evolution of Polychlorophenol-Degrading in Sphingomonads. Appl Env Microb 68:4495-4501.
• Tiirola M, Valtonen TE, Rintamäki-Kinnunen & Kulomaa. (2002) Diagnosis of flavobacteriosi by direct amplification of rRNA genes, Diss Aquatic Organ. 51:93-100.
• Tuma R & Thomas GJ, Jr. (2002) Raman spectroscopy of viruses. In Handbook of Vibrational Spectroscopy, Chalmers, J. M. and Griffith, P. R. Eds., John Wiley & Sons, Chichester, UK.
• Tuppurainen K, Viisas M, Laatikainen R & Peräkylä M. (2002) Evaluation of a novel electronic eigenvalue (EEVA) molecular descriptor for QSAR/QSPR studies: validation using a benchmark steroid dataset J. Chem. Inf. Comput. Sci. 42:607-613.
• Törönen P, Storvik M, Lindén A-M, Kontkanen O, Marvanova M, Lakso M, Castrén E & Wong G. (2002) Expression Profiling to Understand Actions of NMDA/Glutamate Receptor Antagonists in Rat Brain. Neurochem. Res. 27:1205-1216.
• Valjakka J, Takkinen K, Söderlund H & Rouvinen J. (2002) Structural insights to steroid hormone recognition and binding: Crystal structure of a recombinant anti-testosterone Fab-fragment in native and ligand bound form. J. Biol. Chem. 277:4183-4190.
• Valjakka J, Hemminki A, Niemi S, Söderlund H, Takkinen K & Rouvinen J. (2002) Crystal structure of an vitro affinity and specificity matured anti-testosterone Fab in complelx with testosterone: Improved affinity results from small structural changes within variable domains. J. Biol. Chem. 277:44021-44027
• Wang H, Marjomäki V, Ovod V & Kulomaa MS. (2002) Subcellular Localization of Pentachlorophenol 4-monooxygenase in Sphingomonas chlorophenolica ATCC39723, Biochem Biophys Res Commun. 299:703-709.
• Waris ME, Meltola NJ, SOini JT, Soini E, Peltola OJ & Hänninen PE. (2002) Two-photon excitation fluorometric measurement of homogeneous microparticle immunoassay for C-reactive protein. Analytical Biochemistry 309:67-74.
• Venäläinen JI, Juvonen RO, Forsberg MM, Garcia-Horsman A, Poso A, Wallen EAA, Gynther J & Männistö PT. (2002) Substrate-Dependent, Nonhyperbolic Kinetics of Pig Brain Prolyl Oligopeptidase and its Tight Binding Inhibition by JTP-4819. Biochem Pharmacol. 64:463-471.
• Väisänen S, Peräkylä M, Kärkkäinen JI, Steinmeyer A & Carlberg C. (2002) Critical role of helix 12 of the vitamin D3 receptor for the partial agonism of carboxylic ester antagonists. J Mol Biol. 315:229-238.  
• Väisänen S, Ryhänen S, Saarela JTA, Peräkylä M, Andersin T, Mäenpää PH. (2002) Structurally and Functionally Important Amino Acids of the Agonistic Conformation of the Human Vitamin D Receptor. Mol Pharmacol. 62:788-794.
• Zyryanov AB, Shestakov AS, Lahti R & Baykov AA. (2002) Mechanism by which metal cofactors control substrate specificity in pyrophosphatase. Biochem J. 376:901-906