National Doctoral Programme in
Informational and Structural Biology

• School
  • Front page
  • Background
  • Board
  • Funding decisions
  • Networks
  • Contact
• Members
  • Students
  • Supervisors
• Graduates
• Publications
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • 2003
  • 2002
  • 2001
  • 2000
  • 1999
  • 1998
• Instructions
  • Applying
  • Handbook
  • Ministry Recom- mendations
  • Forms
  • Logo
• Events
  • Upcoming
  • Past
  • Reports
• Links
  • Scientific practice
  • Funding and careers

Publications 2005

• Acero JL, Rodriguez E & Meriluoto J. (2005). Kinetics of reactions between chlorine and the cyanobacterial toxins microcystins. Wat Res. 39:1628-1638.
• Aho TL, Lund RJ, Ylikoski EK, Matikainen S, Lahesmaa R & Koskinen PJ. (2005) Expression of human pim family genes is selectively up-regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation. Immunology. 116:82-8.
• Airenne TT, Nymalm Y, Kidron H, Smith DJ, Pihlavisto M, Salmi M, Jalkanen S, Johnson MS & Salminen TA. (2005) Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications. Protein Sci. 14:1964-1974.
• Alanko S, Halling K, Maunula S, Slotte JP & Ramstedt B. (2005) Displacement of sterol from sterol/sphingomyelin rich domains in fluid bilayers by membrane intercalators. Biochim Biophys Acta. 1715:111-121.
• Andersson S, Serimaa R, Väänänen T, Paakkari T, Jämsä S & Viitaniemi P. (2005) X-ray scattering studies on thermally modified Scots pine (Pinus sylvestris). Holzforchung. 59:422-427.
• Battchikova N, Zhang P, Rudd S, Ogawa T & Aro EM. (2005) Identification of NdhL and Ssl1690 (NdhO) in NDH-1L and NDH-1M complexes of Synechocystis sp. PCC 6803. J Biol Chem. 280:2587-95.
• Belevich I, Borisov VB, Konstantinov AA & Verkhovsky MI. (2005) Oxygenated complex of cytochrome bd from Escherichia coli: Stability and photolability. FEBS Lett. 579:4567-4570.
• Belevich I, Borisov VB, Zhang J, Yang K, Konstantinov AA, Gennis RB & Verkhovsky MI. (2005) Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc Natl Acad Sci USA. 102:3657-3662.
• Belogurov G, Malinen A, Turkina MV, Jalonen U, Rytkönen K, Baykov AA. & Lahti R. (2005) Membrane-bound pyrophosphatase of Thermotoga maritima requires sodium for activity. Biochemistry. 44:2088-2096.
• Bjorkblom B, Ostman N, Hongisto V, Komarovski V, Filen JJ, Nyman TA, Kallunki T, Courtney MJ & Coffey ET. (2005) Constitutively active cytoplasmic c-Jun N-terminal kinase 1 is a dominant regulator of dendritic architecture: role of microtubule-associated protein 2 as an effector. J Neurosci. 25:6350-61.
• Björkqvist J, Nyholm T, Slotte JP & Ramstedt B. (2005) Domain formation and stability in complex lipid bilayers as reported by cholestatrienol. Biophys J. 88:4054-63.
• Blom T, Slotte JP, Pitson SM & Törnquist K. (2005) Enhancement of intracellular sphingosine-1-phosphate production by inositol 1,4,5-trisphosphate-evoked calcium mobilisation in HEK-293 cells: endogenous sphingosine-1-phosphate as a modulator of the calciumresponse. Cell Signal. 17:827-36.
• Bogachev AV & Verkhovsky MI. (2005) Na+-Translocating NADH:Quinone Oxidoreductase: Progress Achieved and Prospects of Investigations. Biochemistry (Moscow). 70:143-149.
• Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, Richard MW & Coruzzi GM. (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics. 6:143.
• Briggs JAG, Huiskonen JT, Fernando KV, Gilbert RJC, Scott P, Butcher SJ & Fuller SD. (2005) Classification and three-dimensional reconstruction of unevenly distributed or symmetry mismatched features of icosahedral particles. J Struct Biol. 150:332-339.
• Brosché M, Vinocur B, Alatalo E, Lamminmäki A, Teichmann T, Ottow EA, Djilianov D, Afif A, Bogeat-Triboulot M-B, Altman A, Polle A, Dreyer E, Rudd S, Paulin L, Auvinen P & Kangasjärvi J. (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol. 6:R101.
• Cao J. (2005) The regulation and role of stress-activated protein kinases (p38 and JNK) in neuronal cell death. Department of Neurobiology, Faculty of Medicine, University of Kuopio, Kuopio (Dissertation).
• Cao J, Viholainen JI, Dart C, Warwick HK, Leyland ML & Courtney MJ. (2005) The PSD95-nNOS interface: a target for inhibition of excitotoxic p38 stress-activated protein kinase activation and cell death. J Cell Biol. 168:117-26.
• Connors WL & Heino J. (2005) A Duplexed Microsphere-Based Cellular Adhesion Assay. Analytical Biochem 337:246-255.
• Curtis K, Oresic M & Vidal-Puig A. (2005) Pathways to analysis of microarray data, Trends Biotechnol. 8:429-435.
• Denessiouk KA, Johnson MS & Denesyuk AI. (2005) Novel CalphaNN structural motif for protein recognition of phosphate ions. J Mol Biol. 345:611-629.
• Dubnovitsky AP, Kapetaniou EG & Papageorgiou AC. (2005) Enzyme adaptation to alkaline pH: Atomic resolution (1.08 Å) structure of phosphoserine aminotransferase from Bacillus alkalophilus. Protein Sci. 14:97-110.
• Dubnovitsky AP, Ravelli RBG, Popov AN & Papageorgiou AC. (2005) Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci. 14:1498-1507.
• Eisenberg-Domovich Y, Hytonen VP, Wilchek M, Bayer EA, Kulomaa MS & Livnah O. (2005) High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability. Acta Crystallogr D. 61:528-538.
• Ellgaard L & Ruddock LW. (2005) The human protein disulphide isomerase family: substrate interactions and functional properties. EMBO Reports. 6:28-32.
• Elo L, Lahti L, Skottman H, Kyläniemi M, Lahesmaa R & Aittokallio T. (2005) Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acid Res. 33:e193.
• Fernández M, Keyriläinen J, Serimaa R, Torkkeli M, Karjalainen-Lindsberg M-L, Leidenius M, von Smitten K, Tenhunen M, Fiedler S, Bravin A, Weiss TM & Suortti P. (2005) Human breast cancer in vitro: matching histo-pathology with small-angle X-ray scattering and diffraction enhanced X-Ray imaging. Phys Med Biol. 50:2991-3006.
• Filén J-J*, Nyman T*, Korhonen J, Goodlett DR & Lahesmaa R. (2005) Characterization of microsomal fraction proteome in human lymphoblasts reveals the down-regulation of galectin-1 by interleukin-12. Proteomics. 5:4719-32.
• Friedel CC, Jahn KH, Sommer S, Rudd S, Mewes HW & Tetko IV. (2005) Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinformatics. 21:1383-1388.
• Germain H, Rudd S, Zotti C, Caron S, O'Brien M, Chantha SC, Lagace M, Major F & Matton DP. (2005) A 6374 unigene set corresponding to low abundance transcripts expressed following fertilization in solanum chacoense bitt, and characterization of 30 receptor-like kinases. Plant Mol Biol. 59:515-32.
• Gong S, Yoon G, Jang I, Bolser D, Dafas P, Schroeder M, Choi H, Cho Y, Han K, Lee S, Choi H, Lappe M, Holm L, Kim S, Oh D & Bhak J. (2005) PSIbase: a Database of Protein Structural Interactome map (PSIMAP). Bioinformatics. 21:2541-2543.
• Gopalacharyulu P, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmen J & Oresic M. (2005) Data integration and visualization system for enabling conceptual biology. Bioinformatics. 21:i177-i185.
• Gotherstrom C, West A, Liden J, Uzunel M, Lahesmaa R & Le Blanc K. (2005) Difference in gene expression between human fetal liver and adult bone marrow mesenchymal stem cells. Haematologica. 90:1017-26.
• Halonen P. (2005) Metal-activated phosphohydrolases: Soluble inorganic pyrophosphatase, a case study. Department of Biochemistry and Food Chemistry, University of Turku, Turku (Dissertation).
• Halonen P, Tammenkoski M, Niiranen L, Huopalahti S, Parfenyev AN, Goldman A, Baykov AA & Lahti R (2005) Effects of active site mutations on the metal binding affinity, catalytic competence, and stability of the family II pyrophosphatase from Bacillus subtilis. Biochemistry. 44:4004-4010.
• Heger A & Holm L. (2005) Towards next generation bioinformatics methods by exhaustive comparison between all protein sequences. In CSC Report on Scientific Computing in Finland 2004-2005, M Laine (Editor). (in press)
• Heger A, Wilton CA, Sivakumar A & Holm L. (2005) ADDA: a domain database with global coverage of the protein universe. Nucl Acids Res 33 Database Issue. D188-D191.
• Holm L. (2005) Protein structure comparison. In ENCYCLOPEDIA OF GENETICS, GENOMICS, PROTEOMICS AND BIOINFORMATICS, Eds. W.R. Taylor et al. John Wiley & Sons. (in press)  
• Huhtala M, Heino J, Casciari D, de Luise A & Johnson MS. (2005) Integrin evolution: insights from ascidian and teleost fish genomes. Matrix Biol. 24:83-95.
• Huiskonen JT. (2005) Structure and assembly of membrane-containing dsDNA bacteriophages. Department of Biological and Environmental Sciences, University of Helsinki, Helsinki. (Dissertation)
• Hytonen VP. (2005) The avidin protein family - properties of family members and engineering of novel biotin-binding protein tools. Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä (Dissertation).
• Hytönen VP, Nordlund HR, Hörhä J, Nyholm TK, Hyre, D, Kulomaa T, Porkka E, Marttila AT, Stayton. P, Slotte JP, Laitinen OH & Kulomaa MS. (2005) Dual-affinity avidin molecules, PROTEINS: Structure, Function, and Bioinformatics. 61:597-607.
• Hytönen VP, Määttä J, Kidron H, Halling K, Hörhä, J, Kulomaa T, Nyholm T, Johnson MS, Salminen TA, Kulomaa MS & Airenne TT. (2005) Adivin related protein 2 shows unique structural and functional features among the avidin protein family. BMC Biotechnology. 5:28.
• Hytonen VP, Maatta JA, Nyholm TK, Livnah O, Eisenberg-Domovich Y, Hyre D, Nordlund HR, Horha J, Niskanen EA, Paldanius T, Kulomaa T, Porkka EJ, Stayton PS, Laitinen OH & Kulomaa MS. (2005) Design and construction of highly stable, proteaseresistant chimeric avidins. J Biol Chem. 280:10228-10233.
• Inkinen K, Lahesmaa R, Brandt A, Katajamaa M, Halme L, Hockerstedt K & Lautenschlager I. (2005) DNA microarray-based gene expression profiles of cytomegalovirus infection and acute rejection in liver transplants. Transplant Proc. 37:1227-9.
• Jaakola V-P, Prilusky J, Sussman JL & Goldman A. (2005) G protein- coupled receptors show unusual patterns of intrinsic unfolding. Prot Eng Des Sel. 18:103-110.
• Jaakola V-P, Rehn M, Alexiev U, Goldman A & Turner GJ. (2005) G- protein-coupled receptor domain over-expression in Halobacterium salinarum: a new tool for structural and functional studies of integral membrane proteins. Proteins: Struct Funct Genet. 60:412-423.
• Jaakola V-P, Vainio M, Sen S, Rehn M, Heimo H, Scheinin M & Goldman A. (2005) Intracellularly truncated human α2B-adrenoceptors: stable and functional GPCRs for structural studies. J Recept Sig Transd. 25:99-124.
• Jansen T*, Kidron H*, Taipaleenmäki H, Salminen T & Mäenpää P. (2005) Transcriptional profiles and structural models of the Synechocystis sp. PCC 6803 Deg proteases. Photosynth Res. 84:57-63.
• Jansson A, Koskiniemi H, Erola A, Wang J Mäntsälä P, Schneider G & Niemi J. (2005). Aclacinomycin 10-hydroxylase is a novel substrate-assisted hydroxylase requiring S-adenosyl-L-methionine as cofactor. J Biol Chem. 280:3636-3644.
• Jarho EM, Wallén EAA, Christiaans JAM, Forsberg MM, Venäläinen JI, Männistö PT, Gynther J & Poso A. (2005) Dicarboxylic Acid Azacycle L-Prolyl-pyrrolidine Amides as Prolyl Oligopeptidase Inhibitors and 3D QSAR of the Enzyme-Inhibitor Interactions. J Med Chem. 48:4772-478.
• Jokela M, Raki M, Heikkinen K, Sepponen K, Eskelinen A & Syväoja JE. (2005) The screening of expression and purification conditions for replicative DNA polymerase associated B-subunits, assignment of the exonuclease activity to the the C-terminus of archaeal pol D DP1 subunit. Protein Expression and Purification. 43:73-84.
• Jurczak T, Tarczynska M, Izydorczyk K, Mankiewicz J, Zalewski M & Meriluoto J. (2005) Elimination of microcystins by water treatment processes - examples from Sulejow Reservoir, Poland. Wat Res. 39:2394-2406.
• Jyrkkärinne J, Windshügel B, Mäkinen J, Ylisirniö M, Peräkylä M, Poso A, Sippl W & Honkakoski P. (2005) Amino Acids Important for Ligand Specificity of the Human Constitutive Androstane Receptor. J Biol Chem. 280:5960-5971.
• Jänis J, Hakanpää J, Hakulinen N, Ibatullin FM, Hoxha A, Derrick PJ, Rouvinen J & Vainiotalo P. (2005) Determination of thioxylooligosaccharide binding to family 11 xylanases using electrospray fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography. FEBS J. 272:2317-2333.
• Kainov D. (2005) Packaging motors of cystoviruses. Department of Biological and Environmental Sciences, University of Helsinki, Helsinki. (Dissertation).
• Kankaanpää H, Turunen AK, Karlsson K, Bylund G, Meriluoto J & Sipiä V. (2005) Heterogeneity of nodularin bioaccumulation in northern Baltic Sea flounders in 2002. Chemosphere. 59:1091-1097.
• Kankainen M & Holm L (2005) POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. Nucl Acids Res. 33:W427-W431.
• Kapetaniou EG. (2005) Crystallographic studies of enzyme stability. Department of Biochemistry and Food Chemistry, University of Turku, Turku (Dissertation).
• Kapetaniou EG, Braaz R, Jendrossek D & Papageorgiou AC. (2005) Crystallization and preliminary X-ray analysis of a novel thermoalkalophilic poly(3-hydroxybutyrate) depolymerase (PhaZ7) from Paucimonas lemoignei. Acta Crystallogr. F61:479-481.
• Karisola P, Kotovuori A, Poikonen S, Niskanen E, Kalkkinen N, Turjanmaa K, Palosuo T, Reunala T, Alenius H & Kulomaa MS. (2005) Isolated hevein-like domains but not intact endochitinases are responsible for IgE-mediated in vitro and in vivo reactions in latex-fruit syndrome, J. Allergy & Clin Immunol. 115:598-605.
• Karjalainen M, Reinikainen M, Spoof L, Meriluoto JAO, Sivonen K & Viitasalo M. (2005) Trophic transfer of cyanobacterial toxins from zooplankton to planktivores: Consequences for pike larvae and mysid shrimps. Environ Toxicol. 20:354-362.
• Karlsson KM. (2005) Liquid chromatography - mass spectrometry in distribution and bioaccumulation studies of toxic cyanopeptides. Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku (Dissertation).
• Karlsson KM, Kankaanpää H, Huttunen M & Meriluoto J. (2005) First observation of microcystin-LR in pelagic cyanobacterial blooms in the northern Baltic Sea. Harmful Algae. 4:163-166.
• Karlsson KM, Spoof LEM & Meriluoto JAO. (2005) Quantitative LC-ESI-MS analyses of microcystins and nodularins in animal tissue - Matrix effects and method validation. Environ Toxicol. 20:381-389.
• Katajamaa M & Oresic M. (2005) Processing methods for differential analysis of LC/MS profile data, BMC Bioinformatics. 6:179.
• Kisko K, Torkkeli M, Vuorimaa E, Lemmetyinen H, Seeck O, Linder M & Serimaa R. (2005) Langmuir-Blodgett films of hydrophobins HFBI and HFBII. Surface Science. 584:35-40.
• Koistinen KM, Soininen P, Venäläinen T, Häyrinen J, Laatikainen R, Peräkylä M, Tervahauta AI & Kärenlampi SO. (2005) Birch PR-10c interacts with several biologically important ligands. Phytochemistry. 66:2524-2533.
• Koivunen P, Salo KEH, Myllyharju J & Ruddock LW. (2005) Three binding sites in protein disulfide isomerase co-operate in collagen prolyl 4-hydroxylase tetramer assembly. J Biol Chem. 280:5227-5235.
• Kokkola T, Salo OMH, Poso A & Laitinen JT. (2005) The functional role of cysteines adjacent to the NRY motif of the human MT1 melatonin receptor, J Pineal Res. 39:1-11.
• Koponen T, Karppinen T, Haeggström E, Saranpää P & Serimaa R. (2005) The stiffness modulus in Norway spruce as a function of year ring. Holzforschung. 59:451-455.
• Korhonen LE, Rahnasto M, Mähönen NJ, Wittekindt C, Poso, A Juvonen RO & Raunio H. (2005) Predictive 3D-QSAR of CYP1A2 Inhibitors. J Med Chem. 48:3808-3815.
• Korhonen S-P, Tuppurainen, K, Laatikainen R & Peräkylä M. (2005) Comparing the performance of FLUFF-BALL to SEAL-CoMFA with a large diverse estrogen dataset: from relevant superpositions to solid predictions J Chem Inf Model. 45:1874-83.
• Korhonen S-P, Tuppurainen K, Laatikainen R & Peräkylä M. (2005) Improving the performance of SOMFA by use of standard multivariate methods. SAR QSAR Environ Res. 16:567-79.
• Laihia JK, Koskinen JO, Waris ME & Jansen CT. (2005) Adaptation of human skin by chronic solar-simulating UV irradiation prevents ultraviolet-B irradiation-induced rise in serum C-reactive protein levels. Photochemistry and Photobiology. 81:654-658.
• Laitinen OH, Airenne KJ, Hytönen VP, Peltomaa E, Mähönen AJ, Wirth T, Lind MM, Mäkelä KA, Toivanen PI, Schenkwein D, Heikura T, Nordlund H, Kulomaa MS & Ylä-Herttuala S. (2005) A multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and in vivo, Nucleic Acid Res. 33(4):e42.
• Laitinen R, Immanen J, Auvinen P, Rudd S, Alatalo A, Paulin L, Ainasoja M, Kotilainen M, Koskela S, Teeri TH & Elomaa P. (2005) Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Research. 15:475-486.
• Lappe M & Holm L (2005) Algorithms for protein interaction networks. Biochem Soc Trans. 33:530-534.
• Laurinmäki PA, Huiskonen JT, Bamford DH & Butcher SJ. (2005) Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35. Structure. 13:1819-28.
• Lehtiö L, Fabrichniy IP, Hansen T, Schönheit P & Goldman A. (2005) Unusual twinning in an acetyl coenzyme A synthetase (ADP forming) from Pyrococcus furiosus. Acta Crystallogr D. 61:350-354.
• Lehtonen A, Veckman V, Nikula T, Lahesmaa R, Kinnunen L, Matikainen S & Julkunen I. (2005) Differential expression of IFN regulatory factor (IRF) 4 gene in human monocyte-derived dendritic cells and macrophages. J Immunol. 175:6570-9.
• Lehtovuori P, Söderholm A & Nyrönen T. (2005) Moderni Lääkesuunnittelu, Dosis. 21:35-41.
• Lempiäinen H, Molnár F, Gonzalez MM, Peräkylä M & Carlberg C. (2005) Antagonist- and inverse agonist-driven interactions of the vitamin D receptor and the constitutive androstane receptor with co-repressor protein. Mol Endocrinol. 19:2258-2272.
• Linder MB, Szilvay G, Nakari-Setala T & Penttilä ME (2005) Hydrophobins: the protein amphiphiles of fungi. FEMS Microbiol Rev. 29:877-896.
• Linn ML, Eble J, Lübken C, Slade RW, Heino J, Davies J & Suhrbier A. (2005) An arthritogenic alphavirus uses the α1β1 integrin collagen receptor. Virology. 336:229-239.
• Lísal J, Lam T, Kainov DE, Emmett MR, Marshall AG & Tuma R. (2005) Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states. Nat Struct Mol Biol. 12:460-466.
• Lísal J & Tuma R. (2005) Cooperative mechanism of RNA packaging motor. J Biol Chem. 280:23157-64.
• Lund R, Ahlfors H, Kainonen E, Lahesmaa AM, Dixon C & Lahesmaa R. (2005) Identification of genes involved in the initiation of human Th1 or Th2 cell commitment. Eur J Immunol. 35:3307-19.
• Malewicz B, Valiyaveettil JT, Jacob K, Byun H-S, Mattjus P, Baumann WJ, Bittman R & Brown RE. (2005) The 3-OH group and 4,5-trans double bond of sphingomyelin are essential for modulation of galactosylceramide transmembrane asymmetry. Biophysical Journal. 88:2670-2780.
• Maula S-M, Salminen T, Kaitaniemi S, Nymalm Y, Smith DJ & Jalkanen S. (2005) Carbohydrates located on the top of the "cap" contribute to the adhesive and enzymatic functions of vascular adhesion protein-1 (VAP-1). Eur J Immunol. 35:2718-2727.
• Medina-Gomez G, Virtue S, Lelliott C, Boiani R, Campbell M, Christodoulides C, Perrin C, Jimenez-Linan M, Blount M, Dixon J, Zhan D, Thresher RR, Aparicio S, Carlton M, Colledge WH, Kettunen MI , Seppänen-Laakso T, Sethi JK, O'Rahilly S, Brindle K, Cinti S, Oresic M, Burcelin R & Vidal-Puig A. (2005) The link between nutritional status and insulin sensitivity is dependent on the adipocyte-specific PPAR gamma 2 isoform. Diabetes. 54:1706-1716.
• Meltola NJ, Kettunen MJ & Soini AE. (2005) Dipyrrylmeheneboron difluorides as labels in two-photon excited fluorometry. Part I - Immunometric assays. Journal of Fluorescence. 15:221-232.
• Meltola NJ, Vaarno J& Soini AE. (2005) Dipyrrylmeheneboron difluorides as labels in two-photon excited fluorometry. Part II- Nucleic acid hybridization assays. Journal of Fluorescence. 15:233-242.
• Merckel MC, Huiskonen JT, Bamford DH, Goldman A & Tuma R. (2005). The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture. Mol Cell. 18:161-70.
• Meriluoto J & Codd GA, Eds. 2005. TOXIC: Cyanobacterial Monitoring and Cyanotoxin Analysis. Turku: Åbo Akademi University Press, 149 pp., ISBN 951-765-259-3.
• Meriluoto J, Gueimonde M, Haskard CA, Spoof L, Sjövall O & Salminen S. (2005) Removal of the cyanobacterial toxin microcystin-LR by human probiotics. Toxicon. 46:111-114.
• Mialon A, Sankinen M, Söderström H, Junttila TT, Holmström T, Koivusalo R, Papageorgiou AC, Johnson RS, Hietanen S, Elenius K & Westermarck J. (2005) DNA topoisomerase I is a co-factor for c-Jun in the regulation of EGFR expression and cancer cell proliferation. Mol Cell Biol. 25:5040-5051.
• Moulder R, Filén J-J, Salmi J, Katajamaa M, Nevalainen OS, Oresic M, Aittokallio T, Lahesmaa R & Nyman T. (2005) A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments, Proteomics. 5:2748-2760.
• Nikula T, West A, Katajamaa M, Lönnberg T, Sara R, Aittokallio T, Nevalainen OS & Lahesmaa R. (2005) A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune response. J Immunol Methods. 303:122-34.
• Niskanen EA, Hytönen VP, Grapputo A, Nordlund HR, Kulomaa MS & Laitinen OH. (2005) Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family. BMD Genomics. 6:41.
• Nordlund HR, Hytönen VP, Hörhä J, Määttä JAE, White DJ, Halling K, Porkka EJ, Slotte JP, Laitinen OH & Kulomaa MS. (2005) Single Chain Avidin - From subunits to protein domains via circularly permuted avidins. Biochem J. 392:485-492.
• Nordlund HR, Hytönen VP, Laitinen OH & Kulomaa MS. (2005) Novel Novel Avidin-like Protein from a Root Nodule Symbiotic Bacterium Bradyrhizobium japonicum. J. Biol. Chem. 280:13250-13255.
• Nordlund HR, Laitinen OH, Uotila STH, Kulmala M, Kalkkinen N & Kulomaa MS. (2005) Production of Hev b5 as a GFP-streptavidin core fusion in insect cells: a novel tripartite fusion protein system that enables easy purification and visualization of the product, Biochim. Biophys. Res. Commun. 336:232-238.
• Nybond S, Björkqvist YJ, Ramstedt B & Slotte JP. (2005) Chain length effects ceramide action on sterol/sphingomyelin-rich domains. Biochim Biophys Acta. 1718:61-6.
• Nylund M & Mattjus P. (2005) Protein mediated glycolipid transfer is inhibited FROM sphingomyelin membranes but enhanced TO sphingomyelin containing raft like membranes. Biochimica et Biophysica Acta - Biomembranes. 1669:87-94.
• Olivari S, Galli C, Alanen H, Ruddock L & Molinari M. (2005) A novel stress-induced EDEM variant regulating endoplasmic reticulum-associated glycoprotein degradation. J Biol Chem. 280:2424-2428.
• Ollila J & Vihinen M. (2005) B cells. Int J Biochem Cell Biol. 37:518-523.
• Oresic M, Katajamaa M & Seppänen-Laakso T. (2005) Lipidomics as a tool for characterizing biological systems, Lipid Technology. 17:59-63.
• Peura M, Müller M, Serimaa R, Vainio U, Sarén M-P, Saranpää P & Burghammer M. (2005) Structural studies of single wood cell walls by synchrotron x-ray microdiffraction and polarised light microscopy. Nucl Inst and Meth B. 238:16-20.
• Peräkylä M, Malinen M, Herzig KH & Carlberg C. (2005) Gene regulatory potential of non-steroidal vitamin D receptor ligands. Mol Endocrinol. 19:2060-2073.
• Pietiäinen V, Marjomäki V, Heino J & Hyypiä T. (2005) Virus entry in caveolae and rafts. Ann Med. 37:394-403.
• Poranen MM, Tuma R & Bamford DH. (2005) Assembly of double-stranded RNA bacteriophages. Adv Virus Res. 64:15-43.
• Poukkula M, Kaunisto A, Hietakangas V, Denessiouk K, Katajamäki T, Johnson MS, Sistonen L & Eriksson JE. (2005) Rapid turnover of c-FLIPS is determined by its unique C-terminal tail. J Biol Chem. 280:27345-55.
• Pulliainen AT, Kauko A, Haataja S, Papageorgiou AC & Finne J. (2005) Dps/Dpr ferritin-like protein: Insights into the mechanism of iron incorporation and evidence for a central role in cellular iron homeostasis. Mol Microbiol. 57:1086-1100.
• Pykäläinen M, Kinos R, Valkonen S, Rydman P, Kilpeläinen M, Laitinen LA, Karjalainen J, Nieminen M, Hurme M, Kere J, Laitinen T & Lahesmaa R. (2005) Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes. J Allergy Clin Immunol. 115:80-7.
• Rahnasto M, Poso A, Raunio H & Juvonen RO.(2005) QSAR Analysis of Inhibitors of the Nicotine Metabolizing CYP2A6 Enzyme. J Med Chem. 48:440-449.
• Raitio K, Salo OMH, Nevalainen T, Poso A & Järvinen T. (2005) Targeting the Cannabinoid CB2 Receptor: Mutations, Modeling and Development of CB2 Selective Ligands. Review Curr Med Chem. 12:1217-1237.
• Rantanen V-V, Gyllenberg M, Koski T & Johnson MS. (2005) A priori contact preferences in molecular recognition. J Bioinf Comp Biol. 3:1-30.
• Ribacka C, Verkhovsky MI, Belevich I, Bloch D, Puustinen A & Wikstrom M. (2005) An elementary reaction step of the proton pump is revealed by mutation of tryptophan 164 to phenylalanine in cytochrome c oxidase from Paracoccus denitrificans. Biochemistry. 44:16502-16512.
• Riikonen R, Matilainen H, Rajala N, Pentikainen O, Johnson M, Heino J & Oker-Blom C. (2005) Functional display of an alpha2 integrin-specific motif (RKK) on the surface of baculovirus particles. Technol Cancer Res Treat. 4:437-445.
• Rosengren AT, Nyman TA & Lahesmaa R. (2005) Proteome profiling of IL-12 treated human T helper cells. Proteomics. 5:3137-41.
• Rosengren AT, Nyman TA, Syyrakki S & Lahesmaa R. (2005) Proteomic and transcriptomic characterization of IFN-a-induced human primary T helper cells. Proteomics. 5:371-379.
• Rudd S. (2005) openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res. 33:D622-7.
• Rudd S, Schoof H & Mayer K. (2005) PlantMarkers--a database of predicted molecular markers from plants. Nucleic Acids Res. 33:D628-32.
• Rudd S & Tetko IV. (2005) Éclair ­ a web service for unravelling species origin of sequences sampled from mixed host interfaces. Nucleic Acids Research. 33:W724-W727.
• Ruuskanen JO, Laurila J, Xhaard H, Rantanen V-V, Vuoriluoto K, Wurster S, Marjamäki A, Vainio M, Johnson MS & Scheinin M. (2005) Conserved structural, pharmacological and functional properties among the three human and five zebrafish alpha-2-adrenergic receptors. Brit J Pharm. 144:165-177.
• Saario MS, Salo OMH, Nevalainen T, Poso A, Laitinen JT, Järvinen T & Niemi R. (2005) Characterization of the sulfhydryl-sensitive site in the enzyme responsible for hydrolysis of 2-arachidonoyl-glycerol in rat cerebellar membranes. Chemistry & Biology. 12:649-656.
• Salminen M, Airenne KJ, Rinnankoski R, Reimari J, Välilehto O, Rinne J, Suikkanen S, Kukkonen S, Ylä-Herttuala S, Kulomaa MS & Vihinen-Ranta M. (2005) Improvement of nuclear entry and transgeneexpression of baculoviruses by disintegration of microtubules in human hepatocytes. J Virol. 79:2720-2728.
• Salo OMH, Raitio KH, Savinainen JR, Nevalainen T, Lahtela-Kakkonen M, Laitinen JT, Järvinen T & Poso A. (2005) Virtual screening of novel CB2 ligands using a comparative model of the CB2 receptor. J Med Chem. 48:7166-71
• Sanders JM, Ito K, Settimo L, Pentikainen OT, Shoji M, Sasaki M, Johnson MS, Sakai R & Swanson GT. (2005) Divergent pharmacological activity of novel marine-derived excitatory amino acids on glutamate receptors. J Pharmacol Exp Ther. 314:1068-78.
• Sarén M-P & Serimaa R. (2005) Determination of microfibril angle distribution by X-ray diffraction. Wood science and Technology. (in press)
• Sarén M-P, Peura M & Serimaa R. (2005) Orientation of cellulose microfibrils in wood cells using synchrotron radiation microdiffraction. X-ray science and Techonology. 13:191-197.
• Sarlin T, Nakari-Setälä, T, Linde, M, Penttilä M & Haikara A. (2005) Fungal hydrophobins as predictors of the gushing activity of malt. J Inst Brew. 111:105-111.
• Savinainen J, Kokkola T, Salo OMH, Poso A, Järvinen T & Laitinen JT. (2005) Identification of WIN55212-3 as a competitive neutral antagonist of the human cannabinoid CB2 receptor. Br J Pharmacol. 145:636-645.
• Sbaragli M, Bibi L, Pittis G, Balducci C, Heikinheimo P, Ricci R, Antuzzi D, Parini R, Spaccini L, Bembi B & Beccari T. (2005) Identification and Characterisation of Novel Mutations in Italian Patients with alfa-Mannosidosis. Human Mutation. 25:320-324.
• Sen S, Jaakola V-P, Pirilä P, Finel M & Goldman A. (2005) Expression of recombinant human alpha 2-adrenergic receptors in Spodoptera frugiperda Sf9 cells: an expression system towards functional and structural studies. Biochim Biophys Acta. 1712:62-70.
• Settimo L. (2005) Structural basis for ligand recognition in the ionotropic glutamate receptors. Department of Biochemistry and Pharmacy, Åbo Akademi University, Turku (Dissertation).
• Sinegina L, Wikstrom M, Verkhovsky MI & Verkhovskaya ML. (2005) Activation of Isolated NADH:Ubiquinone Reductase I (Complex I) from Escherichia coli by Detergent and Phospholipids. Recovery of Ubiquinone Reductase Activity and Changes in EPR Signals of Iron-Sulfur Clusters. Biochemistry. 44:8500-8506.
• Sirén H, Kuldvee R, Karla T, Ekstrom T & Riekkola M-L. (2005) Capillary zone electrophoresis of cationic and anionic drugs in methanol. Journal of chromatography A. 1068:89-97.
• Skottman H, Mikkola M, Lundin K, Olsson C, Strömberg AM, Tuuri T, Otonkoski T, Hovatta O & Lahesmaa R. (2005) Gene expression signatures of seven individual human embryonic stem cell lines. Stem Cells. 23:1343-56.
• Soilu-Hänninen M, Koskinen JO, Laaksonen M, Hänninen A, Lilius E & Waris M. (2005) High sensitivity measurement of CRP and disease progression in multiple sclerosis. Neurology. 65:153-155.
• Suhonen H, Fernández M, Serimaa R & Suortti P. (2005) Simulation of small-angle x-ray scattering from collagen fibrils and comparison with experimental patterns. Phys Med Biol. 50:4501-5416.
• Söderholm A, Lehtovuori P & Nyrönen TH. (2005), Three-Dimensional Structure-Activity Relationships of Non-Steroidal Ligands in Complex with Androgen Receptor Ligand-Binding Domain. J Med Chem. 48:917-925.
• Tammenkoski M, Benini S, Magretova NN, Baykov AA & Lahti R. (2005) An unusual, His-dependent family I pyrophosphatase from Mycobacterium tuberculosis. J. Biol. Chem. 280:41819-26
• Tammiruusu A, Haveri A, Pascolo S, Lahesmaa R, Stevanovic S, Rammensee HG, Sarvas M, Puolakkainen M & Vuola JM. (2005) Clearance of Chlamydia pneumoniae infection in H-2 class I human leucocyte antigen-A2.1 monochain transgenic mice. Scand J Immunol. 62:131-9.
• Tanner R, Kangur K, Spoof L & Meriluoto J. (2005) Hepatotoxic cyanobacterial peptides in Estonian fresh water bodies and inshore marine water. Proc Estonian Acad Sci Biol Ecol. 54:40-52.
• Technau U, Rudd S, Maxwell P, Gordon PM, Saina M, Grasso LC, Hayward DC, Sensen CW, Saint R, Holstein TW, Ball EE & Miller DJ. (2005) Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends Genet. 21:633-9
• Terova B, Heczko R & Slotte JP. (2005) On the importance of the phosphocholine methyl groups for sphingomyelin/cholesterol interactions in membranes - a study with ceramide phosphoethanolamine. Biophys J. 88:2661-9.
• Terova B, Petersen G, Hansen HS & Slotte JP. (2005) N-acyl phosphatidylethanolamines affect the lateral distribution of cholesterol in membranes. Biochim Biophys Acta. 1715:49-56.
• Tervo AJ, Rönkkö T, Nyrönen TH & Poso A. (2005) BRUTUS: Optimization of a Grid-Based Similarity Function for Rigid-Body Molecular Superposition 1. Alignment and Virtual Screening Applications, J Med Chem. 48:4076-4086.
• Tirri M, Huttunen R, Toivonen J, Härkönen PL, Soini JT & Hänninen PE. (2005) Two-photon excitation in fluorescence polarisation ligand-receptor binding assay. J Biomol Screen. 10:314-319.
• Tsamaloukas AD, Szadkowska H, Slotte JP & Heerklotz HH. (2005) Interactions of cholesterol with lipid membranes and cyclodextrin characterized by calorimetry. Biophys J. 89:1109-1119.
• Tuma R. (2005). Raman spectroscopy of proteins: From peptides to large assemblies. J Raman Spectrosc. 36:307-319.
• Vainio MJ & Johnson MS. (2005) McQSAR: A multiconformational quantitative structure-activity relationship engine driven by genetic algorithms. J Chem Inf Model. 45:1953-1961.
• Venäläinen JI, Wallen EAA, Poso A, Garcia-Horsman JA & Männistö PT. (2005) Synthesis and Characterization of the Novel Fluorescent Prolyl Oligopeptidase Inhibitor 4-Fluoresceinthiocarbamoyl-6-aminocaproyl-L-prolyl-2(S)-(Hydroxy-acetyl)-pyrrolidine. J Med Chem. 48:7093-7095.
• Virta P, Koch A, Roslund MU, Mattjus P, Kleinpeter P, Kronberg L, Sjöholm R & Klika KD. (2005) Synthesis, characterisation and theoretical calculations of new 2,6-diaminopurine etheno derivatives. Organic & Biomolecular Chemistry. 3:2924-2929.
• Virtanen H, Yang J, Bespalov MM, Hiltunen JO, Leppänen V-M, Goldman A, Saarma M & Runeberg-Roos P. (2005) The first cysteine-rich domain of the GFRα1 receptor stabilises the binding of GDNF. Biochem J. 387:817-824.
• Väänänen T, Ikonen T, Rokka V-M, Kuronen P, Serimaa R, & Ollilainen V. (2005) Influence of incorporated wild Solanum genomes on potato properties in terms of starch nanostructure and glycoalkaloid content. Journal Of Agricultural And Food Chemistry. 53:5313-5325.
• Wikman LEK, Krasotkina J, Kuchumova A, Sokolov NN & Papageorgiou AC. (2005) Crystallization and preliminary crystallographic analysis of L-asparaginase from Erwinia carotovora. Acta Crystallogr F. 61:407-409.
• Wikstrom M, Ribacka C, Molin M, Laakkonen L, Verkhovsky MI & Puustinen A. (2005) Gating of proton and water transfer in the respiratory enzyme. Proc Natl Acad Sci USA. 102:10478-10481.
• Willame R, Jurczak T, Iffly J-F, Kull T, Meriluoto J & Hoffmann L. (2005) Distribution of hepatotoxic cyanobacterial blooms in Belgium and Luxembourg. Hydrobiologia 551:99-117.
• Windshügel B, Jyrkkärinne J, Poso A, Honkakoski P & Sippl W. (2005) Molecular dynamics simulations of the human CAR ligand binding domain: Deciphering the molecular basis for constitutive activity. J Mol Mod. 11:69-79.
• Xhaard H, Nyrönen T, Rantanen V-V, Ruuskanen J O, Laurila J, Salminen T, Scheinin M & Johnson M S. (2005) Model structures of alpha-2 adrenoceptors in complex with automatically docked antagonist ligands raise the possibility of interactions dissimilar from agonist ligands. J Struct Biol. 150:126-143.
• Ylikoski E, Lund R, Kylaniemi M, Filen S, Kilpelainen M, Savolainen J & Lahesmaa R. (2006) IL-12 up-regulates T-bet independently of IFN-gamma in human CD4+ T cells. Eur J Immunol. 35:3297-306. Erratum in: Eur J Immunol. 2006:36:1058.
• Ylikoski E, Lund R, Zhu F, Kosonen M, Kilpeläinen M, Savolainen J & Lahesmaa R. (2005) TCR- and cytokine-mediated regulation of T-bet and Gata-3 expression in CD4+ T cells. Eur J Immunol. 5:3297-306.
• Ylipaasto P, Kutlu B, Rasilainen S, Rasschaert J, Salmela K, Teerijoki H, Korsgren O, Lahesmaa R, Hovi T, Eizirik DL, Otonkoski T & Roivainen M. (2005) Global profiling of coxsackievirus- and cytokine-induced gene expression in human pancreatic islets. Diabetologia. 48:1510-22.
• Zyryanov AB, Lahti R & Baykov AA. (2005) Inhibition of family II pyrophosphatases by analogs of pyrophosphate and phosphate. Biochemistry (Moscow). 70:908-912.
  
• * = equal contribution