National Doctoral Programme in
Informational and Structural Biology

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Publications 2010

• Abrahams J, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dylag T, Förster F, Heck AJR, Henderson PJF, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GFX, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ (2010). "4D Biology for health and disease" workshop report. N Biotechnol. Published electronically ahead of print in Oct 2010.
• Ahlfors H (2010). Interleukin-4 Induced Leukocyte Differentiation. University of Turku (Dissertation)
• Ahlfors H, Limaye A, Elo LL, Tuomela S, Burute M, Gottimukkala KVP, Notani D, Rasool O, Galande S, Lahesmaa R (2010). SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood. 116: 1443-1453.
• Belogurov GA, Sevostyanova A, Svetlov V, Artsimovitch I (2010). Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol. 76: 286-301.
• Bhattacharjee A, Lehtinen MJ, Kajander T, Goldman A, Jokiranta TS (2010). Both domain 19 and domain 20 of factor H are involved in binding to complement C3b and C3d. Mol Immunol. 47: 1686-1691.
• Björkbom A (2010). Alterations in the Structure of Phosphosphingolipids - Effects on Membrane Properties and Interactions with Sterols. Åbo Akademi University (Dissertation)
• Björkbom A, Ohvo-Rekilä H, Kankaanpää P, Nyholm TKM, Westerlund B, Slotte JP (2010). Characterization of membrane properties of inositol phosphorylceramide. Biochim Biophys Acta. 1798: 453-460.
• Blom T, Bergelin N, Meinander A, Löf C, Slotte JP, Eriksson JE, Törnquist K (2010). An autocrine sphingosine-1-phosphate signaling loop enhances NF-kappaB-activation and survival. BMC Cell Biol. 11: 45.
• Bootorabi F, Jänis J, Smith E, Waheed A, Kukkurainen S, Hytönen V, Valjakka J, Supuran CT, Vullo D, Sly WS, Parkkila S (2010). Analysis of a shortened form of human carbonic anhydrase VII expressed in vitro compared to the full-length enzyme. Biochimie. 92: 1072-1080.
• Buchinger E, Aachmann FL, Aranko AS, Valla S, Skjåk-Braek G, Iwaï H, Wimmer R (2010). Use of protein trans-splicing to produce active and segmentally (2)H, (15)N labeled mannuronan C5-epimerase AlgE4. Protein Sci. 19: 1534-1543.
• Coleman SK, Möykkynen T, Hinkkuri S, Vaahtera L, Korpi ER, Pentikäinen OT, Keinänen K (2010). Ligand-binding domain determines endoplasmic reticulum exit of AMPA receptors. J Biol Chem. 285: 36032-36039.
• Costa MdC, Bajanca F, Rodrigues A, Tomé RJ, Corthals G, Macedo-Ribeiro S, Paulson HL, Logarinho E, Maciel P (2010). Ataxin-3 plays a role in mouse myogenic differentiation through regulation of integrin subunit levels. PLoS One. 5: e11728.
• Elo LL, Järvenpää H, Tuomela S, Raghav S, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R (2010). Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity. 32: 852-862.
• Elo LL, Mykkänen J, Nikula T, Järvenpää H, Simell S, Aittokallio T, Hyöty H, Ilonen J, Veijola R, Simell T, Knip M, Simell O, Lahesmaa R (2010). Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling. J Autoimmun. 35: 70-76.
• Esko O, Francois D, Adrian G, Monika B (2010). Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase Journal of Applied Crystallography. 43: 1113-1120.
• Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J, Ahlfors H, Coffey E, Rao KVS, Rasool O, Lahesmaa R (2010). Activating transcription factor 3 is a positive regulator of human IFNG gene expression. J Immunol. 184: 4990-4999.
• Grocholski T, Koskiniemi H, Lindqvist Y, Mäntsälä P, Niemi J, Schneider G (2010). Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism. Biochemistry. 49: 934-944.
• Haikarainen T, Papageorgiou AC (2010). Dps-like proteins: structural and functional insights into a versatile protein family. Cell Mol Life Sci. 67: 341-351.
• Haikarainen T, Tsou C, Wu J, Papageorgiou AC (2010). Crystal structures of Streptococcus pyogenes Dpr reveal a dodecameric iron-binding protein with a ferroxidase site. J Biol Inorg Chem. 15: 183-194.
• Haikarainen T, Tsou C, Wu J, Papageorgiou AC (2010). Structural characterization and biological implications of di-zinc binding in the ferroxidase center of Streptococcus pyogenes Dpr. Biochem Biophys Res Commun. 398: 361-365.
• Happonen LJ, Redder P, Peng X, Reigstad LJ, Prangishvili D, Butcher SJ (2010). Familial relationships in hyperthermo- and acidophilic archaeal viruses. J Virol. 84: 4747-4754.
• Hatahet F, Nguyen VD, Salo KEH, Ruddock LW (2010). Disruption of reducing pathways is not essential for efficient disulfide bond formation in the cytoplasm of E. coli. Microb Cell Fact. 9: 67.
• Howard HJ, Horaitis O, Cotton RGH, Vihinen M, Dalgleish R, Robinson P, Brookes AJ, Axton M, Hoffmann R, Tuffery-Giraud S (2010). The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards". Hum Mutat. 31: 366-367.
• Huhti L, Blazevic V, Nurminen K, Koho T, Hytönen VP, Vesikari T (2010). A comparison of methods for purification and concentration of norovirus GII-4 capsid virus-like particles. Arch Virol. 155: 1855-1858.
• Huhtiniemi T, Suuronen T, Lahtela-Kakkonen M, Bruijn T, Jääskeläinen S, Poso A, Salminen A, Leppänen J, Jarho E (2010). N(epsilon)-Modified lysine containing inhibitors for SIRT1 and SIRT2. Bioorg Med Chem. 18: 5616-5625.
• Huiskonen JT, Hepojoki J, Laurinmäki P, Vaheri A, Lankinen H, Butcher SJ, Grünewald K (2010). Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses. J Virol. 84: 4889-4897.
• Ihalainen TO, Laakkonen JP, Paloheimo O, Ylä-Herttuala S, Airenne KJ, Vihinen-Ranta M (2010). Morphological characterization of baculovirus Autographa californica multiple nucleopolyhedrovirus. Virus Res. 148: 71-74.
• Ivaska J, Heino J (2010). Interplay between cell adhesion and growth factor receptors: from the plasma membrane to the endosomes. Cell Tissue Res. 339: 111-120.
• Jaaskelainen S, Riikonen P, Salakoski T, Vihinen M (2010). Accuracy of protein hydropathy predictions International Journal of Data Mining and Bioinformatics. 4: 735 - 754.
• Jaikishan S, Björkbom A, Slotte JP (2010). Sphingomyelin analogs with branched N-acyl chains: the position of branching dramatically affects acyl chain order and sterol interactions in bilayer membranes. Biochim Biophys Acta. 1798: 1987-1994.
• Jaikishan S, Björkbom A, Slotte JP (2010). Phosphatidyl alcohols: effect of head group size on domain forming properties and interactions with sterols. Biochim Biophys Acta. 1798: 1615-1622.
• Jalasvuori M, Jalasvuori MP, Bamford JKH (2010). Dynamics of a laterally evolving community of ribozyme-like agents as studied with a rule-based computing system. Orig Life Evol Biosph. 40: 319-334.
• Jalasvuori M, Pawlowski A, Bamford JKH (2010). A unique group of virus-related, genome-integrating elements found solely in the bacterial family Thermaceae and the archaeal family Halobacteriaceae. J Bacteriol. 192: 3231-3234.
• Joensuu JJ, Conley AJ, Lienemann M, Brandle JE, Linder MB, Menassa R (2010). Hydrophobin fusions for high-level transient protein expression and purification in Nicotiana benthamiana. Plant Physiol. 152: 622-633.
• Jokinen J (2010). Conformational regulation of α2β1 integrin in ligand binding.. University of Turku (Dissertation)
• Jokinen J, White DJ, Salmela M, Huhtala M, Käpylä J, Sipilä K, Puranen JS, Nissinen L, Kankaanpää P, Marjomäki V, Hyypiä T, Johnson MS, Heino J (2010). Molecular mechanism of alpha2beta1 integrin interaction with human echovirus 1. EMBO J. 29: 196-208.
• Jääskeläinen P, Engelhardt P, Hynönen U, Torkkeli M, Palva A, Serimaa R (2010). Small angle X-ray scattering and transmission electron microscopy study of the Lactobacillus brevis S-layer protein Journal of Physics: Conference Series. 247: 012017.
• Kainov DE, Cura V, Vitorino M, Nierengarten H, Poussin P, Kieffer B, Cavarelli J, Poterszman A (2010). Structure determination of the minimal complex between Tfb5 and Tfb2, two subunits of the yeast transcription/DNA-repair factor TFIIH: a retrospective study. Acta Crystallogr D Biol Crystallogr. 66: 745-755.
• Kainov DE, Selth LA, Svejstrup JQ, Egly J, Poterzsman A (2010). Interacting partners of the Tfb2 subunit from yeast TFIIH DNA Repair. 9: 33 - 39.
• Karala A, Lappi A, Ruddock LW (2010). Modulation of an active-site cysteine pKa allows PDI to act as a catalyst of both disulfide bond formation and isomerization. J Mol Biol. 396: 883-892.
• Karala A, Ruddock LW (2010). Bacitracin is not a specific inhibitor of protein disulfide isomerase. FEBS J. 277: 2454-2462.
• Khan S, Vihinen M (2010). Performance of protein stability predictors. Hum Mutat. 31: 675-684.
• Koutsioulis D, Lyskowski A, Mäki S, Guthrie E, Feller G, Bouriotis V, Heikinheimo P (2010). Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci. 19: 75-84.
• Kouvonen P, Rainio EM, Suni V, Koskinen P, Corthals GL (2010). Data combination from multiple matrix-assisted laser desorption/ionization (MALDI) matrices: opportunities and limitations for MALDI analysis. Rapid Commun Mass Spectrom. 24: 3493-3495.
• Käsnänen H, Myllymäki MJ, Minkkilä A, Kataja AO, Saario SM, Nevalainen T, Koskinen AMP, Poso A (2010). 3-Heterocycle-phenyl N-alkylcarbamates as FAAH inhibitors: design, synthesis and 3D-QSAR studies. ChemMedChem. 5: 213-231.
• Laaksonen P, Kainlauri M, Laaksonen T, Shchepetov A, Jiang H, Ahopelto J, Linder MB (2010). Interfacial engineering by proteins: exfoliation and functionalization of graphene by hydrophobins. Angew Chem Int Ed Engl. 49: 4946-4949.
• Labrou NE, Papageorgiou AC, Avramis VI (2010). Structure-function relationships and clinical applications of L-asparaginases. Curr Med Chem. 17: 2183-2195.
• Lance E, Neffling M, Gérard C, Meriluoto J, Bormans M (2010). Accumulation of free and covalently bound microcystins in tissues of Lymnaea stagnalis (Gastropoda) following toxic cyanobacteria or dissolved microcystin-LR exposure. Environ Pollut. 158: 674-680.
• Lanzi G, Ferrari S, Vihinen M, Caraffi S, Kutukculer N, Schiaffonati L, Plebani A, Notarangelo LD, Fra AM, Giliani S (2010). Different molecular behavior of CD40 mutants causing hyper-IgM syndrome. Blood. 116: 5867-5874.
• Leo JC, Elovaara H, Bihan D, Pugh N, Kilpinen SK, Raynal N, Skurnik M, Farndale RW, Goldman A (2010). First analysis of a bacterial collagen-binding protein with collagen Toolkits: promiscuous binding of YadA to collagens may explain how YadA interferes with host processes. Infect Immun. 78: 3226-3236.
• Leo JC, Goldman A (2010). Jacks of all trades?--Probably not. The E. coli Eib proteins bind IgG Fc. Mol Immunol. 47: 1870-1872.
• Leppänen K, Pirkkalainen K, Penttilä P, Sievänen J, Kotelnikova N, Serimaa R (2010). Small-angle x-ray scattering study on the structure of microcrystalline and nanofibrillated cellulose Journal of Physics: Conference Series. 247: 012030.
• Leppänen V, Prota AE, Jeltsch M, Anisimov A, Kalkkinen N, Strandin T, Lankinen H, Goldman A, Ballmer-Hofer K, Alitalo K (2010). Structural determinants of growth factor binding and specificity by VEGF receptor 2. Proc Natl Acad Sci U S A. 107: 2425-2430.
• Li C, Yu S, Nakamura F, Pentikäinen, OT, Singh N, Yin S, Xin W, Sy M (2010). Pro-prion Binds Filamin A, Facilitating Its Interaction with Integrin β1, and Contributes to Melanomagenesis Journal of Biological Chemistry. 285: 30328-30339.
• Liljeblad A, Kallio P, Vainio M, Niemi J, Kanerva LT (2010). Formation and hydrolysis of amide bonds by lipase A from Candida antarctica; exceptional features. Org Biomol Chem. 8: 886-895.
• Locatelli GA, Pospiech H, Gac NTL, Loon Bv, Hubscher U, Parkkinen S, Syväoja JE, Villani G (2010). Effect of 8-oxoguanine and abasic site DNA lesions on in vitro elongation by human DNA polymerase in the presence of replication protein A and proliferating-cell nuclear antigen. Biochem J. 429: 573-582.
• Loseva O, Jemth A, Bryant HE, Schüler H, Lehtiö L, Karlberg T, Helleday T (2010). PARP-3 is a mono-ADP-ribosylase that activates PARP-1 in the absence of DNA. J Biol Chem. 285: 8054-8060.
• Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J (2010). Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site. J Struct Biol. Published electronically ahead of print in Dec 2010.
• McDonnell LA, Corthals GL, Willems SM, Remoortere Av, Zeijl RJMv, Deelder AM (2010). Peptide and protein imaging mass spectrometry in cancer research. J Proteomics. 73: 1921-1944.
• Medina-Aunon JA, Paradela A, Macht M, Thiele H, Corthals G, Albar JP (2010). Protein Information and Knowledge Extractor: Discovering biological information from proteomics data. Proteomics. 10: 3262-3271.
• Melissis SC, Papageorgiou AC, Labrou NE, Clonis YD (2010). Purification of M-MLVH- RT on a 9-aminoethyladenine-(1,6-diamine-hexane)-triazine selected from a combinatorial library of dNTP-mimetic ligands. J Chromatogr Sci. 48: 496-502.
• Mikkonen K, Mathew A, Pirkkalainen K, Serimaa R, Xu C, Willför S, Oksman K, Tenkanen M (2010). Glucomannan composite films with cellulose nanowhiskers Cellulose. 17: 69-81.
• Moulder R, Lönnberg T, Elo LL, Filén J, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R (2010). Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation. Mol Cell Proteomics. 9: 1937-1953.
• Muona M, Aranko AS, Raulinaitis V, Iwaï H (2010). Segmental isotopic labeling of multi-domain and fusion proteins by protein trans-splicing in vivo and in vitro. Nat Protoc. 5: 574-587.
• Mutka A, Haapanen A, Käkelä R, Lindfors M, Wright AK, Inkinen T, Hermansson M, Rokka A, Corthals G, Jauhiainen M, Gillingwater TH, Ikonen E, Tyynelä J (2010). Murine cathepsin D deficiency is associated with dysmyelination/myelin disruption and accumulation of cholesteryl esters in the brain. J Neurochem. 112: 193-203.
• Mähönen AJ, Makkonen K, Laakkonen JP, Ihalainen TO, Kukkonen SP, Kaikkonen MU, Vihinen-Ranta M, Ylä-Herttuala S, Airenne KJ (2010). Culture medium induced vimentin reorganization associates with enhanced baculovirus-mediated gene delivery. J Biotechnol. 145: 111-119.
• Määttä J (2010). Structural and Functional Characterization of Engineered Avidin Proteins. University of Tampere (Dissertation)
• Neffling M (2010). Fast LC-MS Detection of Cyanobacterial Peptide Hepatotoxins - Method Development for Determination of Total Contamination Levels in Biological Materials. Åbo Akademi University (Dissertation)
• Neffling M, Lance E, Meriluoto J (2010). Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry. Environ Pollut. 158: 948-952.
• Neffling M, Spoof L, Quilliam M, Meriluoto J (2010). LC-ESI-Q-TOF-MS for faster and accurate determination of microcystins and nodularins in serum. J Chromatogr B Analyt Technol Biomed Life Sci. 878: 2433-2441.
• Nevo J, Mai A, Tuomi S, Pellinen T, Pentikäinen OT, Heikkilä P, Lundin J, Joensuu H, Bono P, Ivaska J (2010). Mammary-derived growth inhibitor (MDGI) interacts with integrin α-subunits and suppresses integrin activity and invasion. Oncogene. 29: 6452-6463.
• Niemi M (2010). A Molecular Basis for Antibody Specificity - Crystal Structures of IgE-Allergen and IgG-Hapten Complexes. University of Eastern Finland (Dissertation)
• Niemi MH, Turunen L, Pulli T, Nevanen TK, Höyhtyä M, Söderlund H, Rouvinen J, Takkinen K (2010). A structural insight into the molecular recognition of a (-)-Delta9-tetrahydrocannabinol and the development of a sensitive, one-step, homogeneous immunocomplex-based assay for its detection. J Mol Biol. 400: 803-814.
• Niskanen E (2010). On dynamics of parvoviral replication protein NS1. University of Jyväskylä (Dissertation)
• Niskanen EA, Ihalainen TO, Kalliolinna O, Häkkinen MM, Vihinen-Ranta M (2010). Effect of ATP binding and hydrolysis on dynamics of canine parvovirus NS1. J Virol. 84: 5391-5403.
• Nissinen L, Pentikäinen OT, Jouppila A, Käpylä J, Ojala M, Nieminen J, Lipsanen A, Lappalainen H, Eckes B, Johnson MS, Lassila R, Marjamäki A, Heino J (2010). A small-molecule inhibitor of integrin alpha2 beta1 introduces a new strategy for antithrombotic therapy. Thromb Haemost. 103: 387-397.
• Nurminen EM, Pihlavisto M, Lázár L, Szakonyi Z, Pentikäinen U, Fülöp F, Pentikäinen OT (2010). Synthesis, in vitro activity, and three-dimensional quantitative structure-activity relationship of novel hydrazine inhibitors of human vascular adhesion protein-1. J Med Chem. 53: 6301-6315.
• Nyholm TKM, Grandell P, Westerlund B, Slotte JP (2010). Sterol affinity for bilayer membranes is affected by their ceramide content and the ceramide chain length. Biochim Biophys Acta. 1798: 1008-1013.
• Nyrönen T, Söderholm A (2010). Structural basis for computational screening of non-steroidal androgen receptor ligands Expert Opinion on Drug Discovery. 5: 5-20.
• Nyström JH, Lönnfors M, Nyholm TKM (2010). Transmembrane peptides influence the affinity of sterols for phospholipid bilayers. Biophys J. 99: 526-533.
• Närvä E, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R (2010). High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol. 28: 371-377.
• Oksanen E, Goldman A (2010). Introduction to Macromolecular X-ray Crystallography in Comprehensive Natural Products Chemistry, ed. L.N. Mander and H. Liu. Elsevier
• Ora A, Oksanen E, Kajander T, Goldman A, Butcher SJ (2010). Crystallization and preliminary crystallographic analysis of mouse peroxiredoxin II with significant pseudosymmetry. Acta Crystallogr Sect F Struct Biol Cryst Commun. 66: 357-360.
• Ortutay C, Olatubosun A, Parkkila S, Vihinen M, Tolvanen M (2010). An evolutionary analysis of insect carbonic anhydrases Adv. Med. Biol.
• Paasonen L, Sipilä T, Subrizi A, Laurinmäki P, Butcher SJ, Rappolt M, Yaghmur A, Urtti A, Yliperttula M (2010). Gold-embedded photosensitive liposomes for drug delivery: triggering mechanism and intracellular release. J Control Release. 147: 136-143.
• Penttilä PA, Várnai A, Leppänen K, Peura M, Kallonen A, Jääskeläinen P, Lucenius J, Ruokolainen J, Siika-Aho M, Viikari L, Serimaa R (2010). Changes in submicrometer structure of enzymatically hydrolyzed microcrystalline cellulose. Biomacromolecules. 11: 1111-1117.
• Playford MP, Nurminen E, Pentikäinen OT, Milgram SL, Hartwig JH, Stossel TP, Nakamura F (2010). Cystic fibrosis transmembrane conductance regulator interacts with multiple immunoglobulin domains of filamin A. J Biol Chem. 285: 17156-17165.
• Postila P (2010). Dynamics of the Ligand-Binding Domains of Ionotropic Glutamate Receptors. University of Jyväskylä (Dissertation)
• Postila PA, Swanson GT, Pentikäinen OT (2010). Exploring kainate receptor pharmacology using molecular dynamics simulations. Neuropharmacology. 58: 515-527.
• Puranen S (2010). Electrostatics in Molecular Modeling. Åbo Akademi University (Dissertation)
• Psencik J, Torkkeli M, Zupcanova A, Vácha F, Serimaa R, Tuma R (2010). The lamellar spacing in self-assembling bacteriochlorophyll aggregates is proportional to the length of the esterifying alcohol Photosynthesis Research. 104: 211-219.
• Rappu P, Nylund C, Ristiniemi N, Kulpakko J, Vihinen P, Hernberg M, Mirtti T, Alanen K, Kallajoki M, Vuoristo M, Pyrhönen S, Heino J (2010). Detection of melanoma-derived cancer-testis antigen CT16 in patient sera by a novel immunoassay. Int J Cancer. Published electronically ahead of print in Jul 2010.
• Rouvinen J, Jänis J, Laukkanen M, Jylhä S, Niemi M, Päivinen T, Mäkinen-Kiljunen S, Haahtela T, Söderlund H, Takkinen K (2010). Transient dimers of allergens. PLoS One. 5: e9037.
• Rovio S, Kalliola A, Sirén H, Tamminen T (2010). Determination of the carboxylic acids in acidic and basic process samples by capillary zone electrophoresis. J Chromatogr A. 1217: 1407-1413.
• Saaranen MJ, Karala A, Lappi A, Ruddock LW (2010). The role of dehydroascorbate in disulfide bond formation. Antioxid Redox Signal. 12: 15-25.
• Salminen S, Nybom S, Meriluoto J, Collado MC, Vesterlund S, El-Nezami H (2010). Interaction of probiotics and pathogens--benefits to human health? Curr Opin Biotechnol. 21: 157-167.
• Seitsonen J, Susi P, Heikkilä O, Sinkovits RS, Laurinmäki P, Hyypiä T, Butcher SJ (2010). Interaction of alphaVbeta3 and alphaVbeta6 integrins with human parechovirus 1. J Virol. 84: 8509-8519.
• Singla N, Goldgur Y, Xu K, Paavilainen S, Nikolov DB, Himanen JP (2010). Crystal structure of the ligand-binding domain of the promiscuous EphA4 receptor reveals two distinct conformations. Biochem Biophys Res Commun. 399: 555-559.
• Siponen MI, Wisniewska M, Lehtiö L, Johansson I, Svensson L, Raszewski G, Nilsson L, Sigvardsson M, Berglund H (2010). Structural determination of functional domains in early B-cell factor (EBF) family of transcription factors reveals similarities to Rel DNA-binding proteins and a novel dimerization motif. J Biol Chem. 285: 25875-25879.
• Sokka M, Parkkinen S, Pospiech H, Syväoja JE (2010). Function of TopBP1 in genome stability. Subcell Biochem. 50: 119-141.
• Spoof L, Neffling M, Meriluoto J (2010). Fast separation of microcystins and nodularins on narrow-bore reversed-phase columns coupled to a conventional HPLC system. Toxicon. 55: 954-964.
• Syrjänen L, Tolvanen M, Hilvo M, Olatubosun A, Innocenti A, Scozzafava A, Leppiniemi J, Niederhauser B, Hytönen VP, Gorr TA, Parkkila S, Supuran CT (2010). Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates. BMC Biochem. 11: 28.
• Söderholm A (2010). Computational Designs of Non-Steroidal Modulators of Androgen Receptor. Åbo Akademi University (Dissertation)
• Tiikkainen P (2010). Study of ligand-based virtual screening tools in computer-aided drug design. University of Turku (Dissertation)
• Tuominen H, Salminen A, Oksanen E, Jämsen J, Heikkilä O, Lehtiö L, Magretova NN, Goldman A, Baykov AA, Lahti R (2010). Crystal structures of the CBS and DRTGG domains of the regulatory region of Clostridiumperfringens pyrophosphatase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate. J Mol Biol. 398: 400-413.
• Tuomo K, P. RT, Antti P (2010). Increasing the Throughput of Shape-Based Virtual Screening with GPU Processing and Single Conformation Databases Molecular Informatics. 29: 293-296.
• Turkia H, Sirén H, Pitkänen J, Wiebe M, Penttilä M (2010). Capillary electrophoresis for the monitoring of carboxylic acid production by Gluconobacter oxydans. J Chromatogr A. 1217: 1537-1542.
• Valo HK, Laaksonen PH, Peltonen LJ, Linder MB, Hirvonen JT, Laaksonen TJ (2010). Multifunctional hydrophobin: toward functional coatings for drug nanoparticles. ACS Nano. 4: 1750-1758.
• Verkhovsky MI, Bogachev AV (2010). Sodium-translocating NADH:quinone oxidoreductase as a redox-driven ion pump. Biochim Biophys Acta. 1797: 738-746.
• Viitanen L (2010). Structural Features of Ligand Binding: Sterol Carrier Protein-2 and Glycolipid Transfer Protein. Åbo Akademi University (Dissertation)
• Virtanen SI, Pentikäinen OT (2010). Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site. J Chem Inf Model. 50: 1005-1011.
• Volkmann G, Iwaï H (2010). Protein trans-splicing and its use in structural biology: opportunities and limitations. Mol Biosyst. 6: 2110-2121.
• Wakadkar S, Hermawan S, Jendrossek D, Papageorgiou AC (2010). The structure of PhaZ7 at atomic (1.2 A) resolution reveals details of the active site and suggests a substrate-binding mode. Acta Crystallogr Sect F Struct Biol Cryst Commun. 66: 648-654.
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