National Doctoral Programme in
Informational and Structural Biology

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Publications 2009

• Aflakian N, Ravichandran S, Jamal MS, Jarvenpaa H, Lahesmaa R, Rao KVS (2009). Integration of signals from the B-cell antigen receptor and the IL-4 receptor leads to a cooperative shift in the cellular response axis. Mol Biosyst. 5: 1661-1671.
• Akhtar MK, Jones PR (2009). Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3). Metab Eng. 11: 139-147.
• Andberg M, Hakulinen N, Auer S, Saloheimo M, Koivula A, Rouvinen J, Kruus K (2009). Essential role of the C-terminus in Melanocarpus albomyces laccase for enzyme production, catalytic properties and structure. FEBS J. 276: 6285-6300.
• Aranko AS, Züger S, Buchinger E, Iwaï H (2009). In vivo and in vitro protein ligation by naturally occurring and engineered split DnaE inteins. PLoS One. 4: e5185.
• Ari H, Heli S, Lotta A, Kai K, Sami F, Santeri T, Ingmar S, Stella R, Tarja N, Kristiina T, Hans S (2009). Silicon-glass instrumented solid-phase extraction-zone electrophoresis microchip with thin amorphous silicon film electrodes: performance in immunoaffinity analysis Microsystem Technologies. 15: 611-619.
• Asakawa H, Tahara S, Nakamichi M, Takehara K, Ikeno S, Linder MB, Haruyama T (2009). The amphiphilic protein HFBII as a genetically taggable molecular carrier for the formation of a self-organized functional protein layer on a solid surface. Langmuir. 25: 8841-8844.
• Belevich NP, Verkhovskaya ML, Verkhovsky MI (2009). Chapter 4 Electron transfer in respiratory complexes resolved by an ultra-fast freeze-quench approach. Methods Enzymol. 456: 75-93.
• Björkqvist YJE, Brewer J, Bagatolli LA, Slotte JP, Westerlund B (2009). Thermotropic behavior and lateral distribution of very long chain sphingolipids. Biochim Biophys Acta. 1788: 1310-1320.
• Bloch DA, Borisov VB, Mogi T, Verkhovsky MI (2009). Heme/heme redox interaction and resolution of individual optical absorption spectra of the hemes in cytochrome bd from Escherichia coli. Biochim Biophys Acta. 1787: 1246-1253.
• Bloch DA, Jasaitis A, Verkhovsky MI (2009). Elevated proton leak of the intermediate OH in cytochrome c oxidase. Biophys J. 96: 4733-4742.
• Bogachev AV, Belevich NP, Bertsova YV, Verkhovsky MI (2009). Primary steps of the Na+-translocating NADH:ubiquinone oxidoreductase catalytic cycle resolved by the ultrafast freeze-quench approach. J Biol Chem. 284: 5533-5538.
• Bogachev AV, Bloch DA, Bertsova YV, Verkhovsky MI (2009). Redox properties of the prosthetic groups of Na(+)-translocating NADH:quinone oxidoreductase. 2. Study of the enzyme by optical spectroscopy. Biochemistry. 48: 6299-6304.
• Bogachev AV, Kulik LV, Bloch DA, Bertsova YV, Fadeeva MS, Verkhovsky MI (2009). Redox properties of the prosthetic groups of Na(+)-translocating nadh:quinone oxidoreductase. 1. Electron paramagnetic resonance study of the enzyme. Biochemistry. 48: 6291-6298.
• Borisov V, Verkhovsky M (2009). Oxygen as Acceptor in EcoSal-Escherichia coli and Salmonella: cellular and molecular biology., ed. A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch, C. L. Squires, and D. Ussery. ASM Press, Washington, DC.
• Busche AEL, Aranko AS, Talebzadeh-Farooji M, Bernhard F, Dötsch V, Iwaï H (2009). Segmental isotopic labeling of a central domain in a multidomain protein by protein trans-splicing using only one robust DnaE intein. Angew Chem Int Ed Engl. 48: 6128-6131.
• Byrne LJ, Sidhu A, Wallis AK, Ruddock LW, Freedman RB, Howard MJ, Williamson RA (2009). Mapping of the ligand-binding site on the b' domain of human PDI: interaction with peptide ligands and the x-linker region. Biochem J. 423: 209-217.
• Cho SH, Goenka S, Henttinen T, Gudapati P, Reinikainen A, Eischen CM, Lahesmaa R, Boothby M (2009). PARP-14, a member of the B aggressive lymphoma family, transduces survival signals in primary B cells. Blood. 113: 2416-2425.
• Collins R, Karlberg T, Lehtiö L, Schütz P, Berg Svd, Dahlgren L, Hammarström M, Weigelt J, Schüler H (2009). The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch. J Biol Chem. 284: 10296-10300.
• Cotton RGH, Aqeel AIA, Al-Mulla F, Carrera P, Claustres M, Ekong R, Hyland VJ, Macrae FA, Marafie MJ, Paalman MH, Patrinos GP, Qi M, Ramesar RS, Scott RJ, Sijmons RH, Sobrido M, Vihinen M, Laboratories motHVPDCfCDCf, Credit P, Groups IW (2009). Capturing all disease-causing mutations for clinical and research use: toward an effortless system for the Human Variome Project. Genet Med. 11: 843-849.
• Derda M, Winiecka-Krusnell J, Linder MB, Linder E (2009). Labeled Trichoderma reesei cellulase as a marker for Acanthamoeba cyst wall cellulose in infected tissues. Appl Environ Microbiol. 75: 6827-6830.
• Dunnen JTd, Sijmons RH, Andersen PS, Vihinen M, Beckmann JS, Rossetti S, Talbot CC, Hardison RC, Povey S, Cotton RGH (2009). Sharing data between LSDBs and central repositories. Hum Mutat. 30: 493-495.
• Euro L, Belevich G, Bloch DA, Verkhovsky MI, Wikström M, Verkhovskaya M (2009). The role of the invariant glutamate 95 in the catalytic site of Complex I from Escherichia coli. Biochim Biophys Acta. 1787: 68-73.
• Fallarero A, Ainasoja M, Sandberg M, Teeri TH, Vuorela PM (2009). GT1-7 cell-based cytoxicity screening assay on 96-well microplates as a platform for the safety assessment of genetically modified Gerbera hybrida extracts. Drug Chem Toxicol. 32: 120-127.
• Filén J, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R (2009). Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation. Mol Cell Proteomics. 8: 32-44.
• Frydenvang K, Lash LL, Naur P, Postila PA, Pickering DS, Smith CM, Gajhede M, Sasaki M, Sakai R, Pentikaïnen OT, Swanson GT, Kastrup JS (2009). Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine. J Biol Chem. 284: 14219-14229.
• Goldgur Y, Paavilainen S, Nikolov D, Himanen JP (2009). Structure of the ligand-binding domain of the EphB2 receptor at 2 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65: 71-74.
• Gopalacharyulu PV, Velagapudi VR, Lindfors E, Halperin E, Oresic M (2009). Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Mol Biosyst. 5: 276-287.
• Gorbikova E (2009). Oxygen reduction and proton translocation by cytochrome c oxidase. Institute of Biotechnology, Helsinki Bioenergetics Group, University of Helsinki (Dissertation)
• Hatahet F, Ruddock LW (2009). Modulating proteostasis: peptidomimetic inhibitors and activators of protein folding. Curr Pharm Des. 15: 2488-2507.
• Hatahet F, Ruddock LW (2009). Protein disulfide isomerase: a critical evaluation of its function in disulfide bond formation. Antioxid Redox Signal. 11: 2807-2850.
• Heikkinen OK, Ruskamo S, Konarev PV, Svergun DI, Iivanainen T, Heikkinen SM, Permi P, Koskela H, Kilpeläinen I, Ylänne J (2009). Atomic structures of two novel immunoglobulin-like domain pairs in the actin cross-linking protein filamin. J Biol Chem. 284: 25450-25458.
• Heino J, Huhtala M, Käpylä J, Johnson MS (2009). Evolution of collagen-based adhesion systems. Int J Biochem Cell Biol. 41: 341-348.
• Heino J, Käpylä J (2009). Cellular receptors of extracellular matrix molecules. Curr Pharm Des. 15: 1309-1317.
• Heinämäki K, Oeemig JS, Djupsjöbacka J, Iwaï H (2009). NMR resonance assignment of DnaE intein from Nostoc punctiforme Biomol NMR Assign. 3: 41-43.
• Ihalainen TO, Niskanen EA, Jylhävä J, Paloheimo O, Dross N, Smolander H, Langowski J, Timonen J, Vihinen-Ranta M (2009). Parvovirus induced alterations in nuclear architecture and dynamics. PLoS One. 4: e5948.
• Imanishi SY, Kouvonen P, Smått J, Heikkilä M, Peuhu E, Mikhailov A, Ritala M, Lindén M, Corthals GL, Eriksson JE (2009). Phosphopeptide enrichment with stable spatial coordination on a titanium dioxide coated glass slide. Rapid Commun Mass Spectrom. 23: 3661-3667.
• Jalasvuori M, Bamford JKH (2009). Did the ancient crenarchaeal viruses from the dawn of life survive exceptionally well the eons of meteorite bombardment? Astrobiology. 9: 131-137.
• Jalasvuori M, Jaatinen ST, Laurinavicius S, Ahola-Iivarinen E, Kalkkinen N, Bamford DH, Bamford JKH (2009). The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J Virol. 83: 9388-9397.
• Jalasvuori M, Örmälä A, Bamford JK (2009). On the astrobiological relevance of viruses in extraterrestrial ecosystems International Journal of Astrobiology. 8: 95-100.
• Johnson MS, Lu N, Denessiouk K, Heino J, Gullberg D (2009). Integrins during evolution: evolutionary trees and model organisms. Biochim Biophys Acta. 1788: 779-789.
• Juusola P, Partanen J, Vahteristo K, Sirén H (2009). Determination of the First and Second Dissociation Constants of Succinic Acid in Aqueous Sodium and Potassium Chloride Solutions in Report/Faculty of Technology Management, Chemical Technology. Lappeenranta University of Technology
• Juusola P, Partanen J, Vahteristo K, Sirén H (2009). Determination of the First, Second, and Third Dissociation Constants of Citric Acid in Aqueous Sodium and Potassium Chloride Solutions in Report/Faculty of Technology Management, Chemical Technology. Lappeenranta University of Technology
• Juusola P, Partanen J, Vahteristo K, Sirén H (2009). Determination of the First, Second, and Third Dissociation Constants of Glutamic Acid in Aqueous Sodium Chloride Solutions in Report/Faculty of Technology Management, Chemical Technology. Lappeenranta University of Technology
• Kaila VRI, Verkhovsky MI, Hummer G, Wikström M (2009). Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochim Biophys Acta. 1787: 1205-1214.
• Kajander T, Sachs JN, Goldman A, Regan L (2009). Electrostatic interactions of Hsp-organizing protein tetratricopeptide domains with Hsp70 and Hsp90: computational analysis and protein engineering. J Biol Chem. 284: 25364-25374.
• Kallio JM, Hakulinen N, Kallio JP, Niemi MH, Kärkkäinen S, Rouvinen J (2009). The contribution of polystyrene nanospheres towards the crystallization of proteins. PLoS One. 4: e4198.
• Kallio JP, Auer S, Jänis J, Andberg M, Kruus K, Rouvinen J, Koivula A, Hakulinen N (2009). Structure-function studies of a Melanocarpus albomyces laccase suggest a pathway for oxidation of phenolic compounds. J Mol Biol. 392: 895-909.
• Kallio JP, Jänis J, Nyyssölä A, Hakulinen N, Rouvinen J (2009). Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65: 805-808.
• Kalliokoski T, Salo HS, Lahtela-Kakkonen M, Poso A (2009). The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening. J Chem Inf Model. 49: 2742-2748.
• Kankaanpää HT, Sjövall O, Huttunen M, Olin M, Karlsson K, Hyvärinen K, Sneitz L, Härkönen J, Sipiä VO, Meriluoto JAO (2009). Production and sedimentation of peptide toxins nodularin-R and microcystin-LR in the northern Baltic Sea. Environ Pollut. 157: 1301-1309.
• Kaput J, Cotton RGH, Hardman L, Watson M, Aqeel AIA, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung Y, Claustres M, Cutting G, Dalgleish R, Dunnen JTd, Díaz C, Dobrowolski S, Santos MRNd, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee Y, Lee J, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SGE, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, Ramirez AMOd, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido M, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, Kranen HJv, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim S, Yoo H, Meeting CttHVPP (2009). Planning the human variome project: the Spain report. Hum Mutat. 30: 496-510.
• Karala A, Lappi A, Saaranen MJ, Ruddock LW (2009). Efficient peroxide-mediated oxidative refolding of a protein at physiological pH and implications for oxidative folding in the endoplasmic reticulum. Antioxid Redox Signal. 11: 963-970.
• Khan S, Vihinen M (2009). Evaluation of protein models: retrospective analysis of biological and biomedical predictions In Silico Biol.. 9: 0025.
• Kisko K, Szilvay GR, Vuorimaa E, Lemmetyinen H, Linder MB, Torkkeli M, Serimaa R (2009). Self-assembled films of hydrophobin proteins HFBI and HFBII studied in situ at the air/water interface. Langmuir. 25: 1612-1619.
• Kivioja J, Kurppa K, Kainlauri M, Linder M, Ahopelto J (2009). Electrical Transport Through Ordered Self-Assembled Protein Monolayer Measured by Constant Force Conductive Atomic Force Microscopy Appl. Phys. Lett.. 94: 183901.
• Kiviranta PH, Suuronen T, Wallén EAA, Leppänen J, Tervonen J, Kyrylenko S, Salminen A, Poso A, Jarho EM (2009). N(epsilon)-thioacetyl-lysine-containing tri-, tetra-, and pentapeptides as SIRT1 and SIRT2 inhibitors. J Med Chem. 52: 2153-2156.
• Kochin V (2009). Needles in a haystack: finding and characterizing protein phosphorylation sites that determine cellular decisions and functions. Department of Biochemistry, Åbo Akademi University (Dissertation)
• Kokocinski M, Dziga D, Spoof L, Stefaniak K, Jurczak T, Mankiewicz-Boczek J, Meriluoto J (2009). First report of the cyanobacterial toxin cylindrospermopsin in the shallow, eutrophic lakes of western Poland. Chemosphere. 74: 669-675.
• Koskela O (2009). NMR Spectroscopy of Multi-domain Proteins : Immunoglobulin-like Domains of Human Filamin A. University of Helsinki (Dissertation)
• Koskiniemi H, Grocholski T, Schneider G, Niemi J (2009). Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65: 256-259.
• Kouvonen P, McDonnell LA, Heeren RMA, Corthals GL (2009). Nitromatrix provides improved LC-MALDI signals and more protein identifications. Proteomics. 9: 1662-1671.
• Kyläniemi MK, Haveri A, Vuola JM, Puolakkainen M, Lahesmaa R (2009). Gene expression signatures characterizing the development of lymphocyte response during experimental Chlamydia pneumoniae infection. Microb Pathog. 46: 235-242.
• Käsnänen H, Myllymäki MJ, Minkkilä A, Kataja AO, Saario SM, Nevalainen T, Koskinen AMP, Poso A (2009). 3-Heterocycle-Phenyl N-Alkylcarbamates as FAAH Inhibitors: Design, Synthesis and 3D-QSAR Studies. ChemMedChem. 5: 213-231.
• Laajala E, Aittokallio T, Lahesmaa R, Elo LL (2009). Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies. Genome Biol. 10: R77.
• Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL (2009). A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics. 10: 618.
• Laakkonen JP, Mäkelä AR, Kakkonen E, Turkki P, Kukkonen S, Peränen J, Ylä-Herttuala S, Airenne KJ, Oker-Blom C, Vihinen-Ranta M, Marjomäki V (2009). Clathrin-independent entry of baculovirus triggers uptake of E. coli in non-phagocytic human cells. PLoS One. 4: e5093.
• Laaksonen P, Kivioja J, Paananen A, Kainlauri M, Kontturi K, Ahopelto J, Linder MB (2009). Selective nanopatterning using citrate-stabilized Au nanoparticles and cystein-modified amphiphilic protein. Langmuir. 25: 5185-5192.
• Laurila K, Vihinen M (2009). Prediction of disease-related mutations affecting protein localization. BMC Genomics. 10: 122.
• Lehtiö L, Jemth A, Collins R, Loseva O, Johansson A, Markova N, Hammarström M, Flores A, Holmberg-Schiavone L, Weigelt J, Helleday T, Schüler H, Karlberg T (2009). Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3. J Med Chem. 52: 3108-3111.
• Leo J (2009). Structural and Functional Studies on Trimeric Autotransporters. Institute of Biotechnology, University of Helsinki (Dissertation)
• Leo JC, Goldman A (2009). The immunoglobulin-binding Eib proteins from Escherichia coli are receptors for IgG Fc. Mol Immunol. 46: 1860-1866.
• Linder MB (2009). Hydrophobins: Proteins that self assemble at interfaces Current Opinion in Colloid \& Interface Science. 14: 356 - 363.
• Lindfors E, Gopalacharyulu PV, Halperin E, Oresic M (2009). Detection of molecular paths associated with insulitis and type 1 diabetes in non-obese diabetic mouse. PLoS One. 4: e7323.
• Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS (2009). Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med. 15: 559-565.
• Maksimainen M, Timoharju T, Kallio JM, Hakulinen N, Turunen O, Rouvinen J (2009). Crystallization and preliminary diffraction analysis of a beta-galactosidase from Trichoderma reesei. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65: 767-769.
• Malinen A (2009). Discovery and Characterization of Na+-Transporting Pyrophosphatases. Department of Biochemistry and Food Chemistry, University of Turku (Dissertation)
• Matero S, Poutiainen S, Leskinen J, Järvinen K, Ketolainen J, Reinikainen S, Hakulinen M, Lappalainen R, Poso A (2009). The feasibility of using acoustic emissions for monitoring of fluidized bed granulation Chemometrics and Intelligent Laboratory Systems. 97: 75 - 81.
• Matero S, Poutiainen S, Leskinen J, Reinikainen S, Ketolainen J, Järvinen K, Poso A (2009). Monitoring the wetting phase of fluidized bed granulation process using multi-way methods: The separation of successful from unsuccessful batches Chemometrics and Intelligent Laboratory Systems. 96: 88 - 93.
• Mattjus P (2009). Glycolipid transfer proteins and membrane interaction. Biochim Biophys Acta. 1788: 267-272.
• Maula T, Westerlund B, Slotte JP (2009). Differential ability of cholesterol-enriched and gel phase domains to resist benzyl alcohol-induced fluidization in multilamellar lipid vesicles Biochim Biophys Acta. 1788: 2454-61.
• Meir A, Helppolainen SH, Podoly E, Nordlund HR, Hytönen VP, Määttä JA, Wilchek M, Bayer EA, Kulomaa MS, Livnah O (2009). Crystal structure of rhizavidin: insights into the enigmatic high-affinity interaction of an innate biotin-binding protein dimer. J Mol Biol. 386: 379-390.
• Michino M, Abola E, participants GPCRD2, Brooks CL, Dixon JS, Moult J, Stevens RC (2009). Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov. 8: 455-463.
• Mikkonen KS, Heikkinen S, Soovre A, Peura M, Serimaa R, Talja RA, Helén H, Hyvönen L, Tenkanen M (2009). Films from oat spelt arabinoxylan plasticized with glycerol and sorbitol Journal of Applied Polymer Science. 114: 457-466.
• Minkkilä A, Savinainen JR, Käsnänen H, Xhaard H, Nevalainen T, Laitinen JT, Poso A, Leppänen J, Saario SM (2009). Screening of various hormone-sensitive lipase inhibitors as endocannabinoid-hydrolyzing enzyme inhibitors. ChemMedChem. 4: 1253-1259.
• Mohamed AJ, Yu L, Bäckesjö C, Vargas L, Faryal R, Aints A, Christensson B, Berglöf A, Vihinen M, Nore BF, Smith CIE (2009). Bruton's tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain. Immunol Rev. 228: 58-73.
• Myllymäki MJ, Käsnänen H, Kataja AO, Lahtela-Kakkonen M, Saario SM, Poso A, Koskinen AMP (2009). Chiral 3-(4,5-dihydrooxazol-2-yl)phenyl alkylcarbamates as novel FAAH inhibitors: Insight into FAAH enantioselectivity by molecular docking and interaction fields. Eur J Med Chem. 44: 4179-4191.
• Määttä JAE, Helppolainen SH, Hytönen VP, Johnson MS, Kulomaa MS, Airenne TT, Nordlund HR (2009). Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis. BMC Struct Biol. 9: 63.
• Nakamura F, Heikkinen O, Pentikäinen OT, Osborn TM, Kasza KE, Weitz DA, Kupiainen O, Permi P, Kilpeläinen I, Ylänne J, Hartwig JH, Stossel TP (2009). Molecular basis of filamin A-FilGAP interaction and its impairment in congenital disorders associated with filamin A mutations. PLoS One. 4: e4928.
• Nath AK, Krauthammer M, Li P, Davidov E, Butler LC, Copel J, Katajamaa M, Oresic M, Buhimschi I, Buhimschi C, Snyder M, Madri JA (2009). Proteomic-based detection of a protein cluster dysregulated during cardiovascular development identifies biomarkers of congenital heart defects. PLoS ONE. 4: e4221.
• Neffling M, Spoof L, Meriluoto J (2009). Rapid LC-MS detection of cyanobacterial hepatotoxins microcystins and nodularins--comparison of columns. Anal Chim Acta. 653: 234-241.
• Nylund M (2009). Parameters regulating the glycolipid transfer protein activity. Department of Biochemistry, Åbo Akademi University (Dissertation)
• Oeemig JS, Aranko AS, Djupsjöbacka J, Heinämäki K, Iwaï H (2009). Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS Lett. 583: 1451-1456.
• Oksanen E (2009). Enzyme Molecular Choreography - Studies of Soluble Inorganic Pyrophosphatases. University of Helsinki (Dissertation)
• Oksanen E, Blakeley MP, Bonneté F, Dauvergne MT, Dauvergne F, Budayova-Spano M (2009). Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase. J R Soc Interface. 6 Suppl 5: S599-S610.
• Olivier M, Petitjean A, Teague J, Forbes S, Dunnick JK, Dunnen JTd, Langerød A, Wilkinson JM, Vihinen M, Cotton RGH, Hainaut P, C. IAR, FP6 EC (2009). Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: proposed guidelines for improving data collection, distribution, and integration. Hum Mutat. 30: 275-282.
• Orchard S, Deutsch EW, Binz P, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H (2009). Annual spring meeting of the Proteomics Standards Initiative. Proteomics. 9: 4429-4432.
• Ortutay C, Vihinen M (2009). Immunome knowledge base (IKB): an integrated service for immunome research. BMC Immunol. 10: 3.
• Ortutay C, Vihinen M (2009). Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies. Nucleic Acids Res. 37: 622-628.
• Paakkunainen M, Matero S, Ketolainen J, Lahtela-Kakkonen M, Poso A, Reinikainen S (2009). Uncertainty in dissolution test of drug release Chemometrics and Intelligent Laboratory Systems. 97: 82 - 90.
• Parkash V, Goldman A (2009). Comparison of GFL-GFRalpha complexes: further evidence relating GFL bend angle to RET signalling. Acta Crystallogr Sect F Struct Biol Cryst Commun. 65: 551-558.
• Parkash V, Lindholm P, Peränen J, Kalkkinen N, Oksanen E, Saarma M, Leppänen V, Goldman A (2009). The structure of the conserved neurotrophic factors MANF and CDNF explains why they are bifunctional. Protein Eng Des Sel. 22: 233-241.
• Partanen R, Paananen A, Forssell P, Linder MB, Lille M, Buchert J, Lantto R (2009). Effect of transglutaminase-induced cross-linking of sodium caseinate on the properties of equilibrated interfaces and foams Colloids and Surfaces A: Physicochemical and Engineering Aspects. 344: 79 - 85.
• Patana A (2009). The Human UDP-Glucuronosyltransferases: Studies on Substrate Binding and Catalytic Mechanism. Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki (Dissertation)
• Pentikäinen U, Shaw KE, Senthilkumar K, Woods CJ, Mulholland AJ (2009). Lennard-Jones Parameters for B3LYP/CHARMM27 QM/MM Modeling of Nucleic Acid Bases Journal of Chemical Theory and Computation. 5: 396-410.
• Pentikäinen U, Ylänne J (2009). The regulation mechanism for the auto-inhibition of binding of human filamin A to integrin. J Mol Biol. 393: 644-657.
• Permyakov SE, Bakunts AG, Permyakova ME, Denesyuk AI, Uversky VN, Permyakov EA (2009). Metal-controlled interdomain cooperativity in parvalbumins. Cell Calcium. 46: 163-175.
• Peura M, Andersson S, Salmi A, Karppinen T, Torkkeli M, Hæggström E, Serimaa R (2009). Changes in nanostructure of wood cell wall during deformation in Advances in Materials Science of Wood, ed. P.O. Kettunen. Materials Science Forum
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