Publications


2011

  • Illergård K, Kauko A, Elofsson A (2011). Why are polar residues within the membrane core evolutionary conserved? Proteins. 79: 79-91.

2010

  • Brandt A, Raksajit W, Yodsang P, Mulo P, Incharoensakdi A, Salminen TA, Mäenpää P (2010). Characterization of the substrate-binding PotD subunit in Synechocystis sp. strain PCC 6803. Arch Microbiol. 192: 791-801.
  • Garg D, Henrich S, Salo-Ahen OMH, Myllykallio H, Costi MP, Wade RC (2010). Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs. J Med Chem. 53: 6539-6549.
  • Hedin LE, Ojemalm K, Bernsel A, Hennerdal A, Illergård K, Enquist K, Kauko A, Cristobal S, Heijne Gv, Lerch-Bader M, Nilsson I, Elofsson A (2010). Membrane insertion of marginally hydrophobic transmembrane helices depends on sequence context. J Mol Biol. 396: 221-229.
  • 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.
  • Kauko A, Hedin LE, Thebaud E, Cristobal S, Elofsson A, Heijne Gv (2010). Repositioning of transmembrane alpha-helices during membrane protein folding. J Mol Biol. 397: 190-201.
  • 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.
  • Pinta E, Duda KA, Hanuszkiewicz A, Salminen TA, Bengoechea JA, Hyytiäinen H, Lindner B, Radziejewska-Lebrecht J, Holst O, Skurnik M (2010). Characterization of the six glycosyltransferases involved in the biosynthesis of Yersinia enterocolitica serotype O:3 lipopolysaccharide outer core. J Biol Chem. 285: 28333-28342.
  • Puranen JS, Vainio MJ, Johnson MS (2010). Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery. J Comput Chem. 31: 1722-1732.
  • Puranen S (2010). Electrostatics in molecular modeling. Åbo Akademi University (Dissertation)
  • Söderholm A (2010). Computational design of non-steroidal modulators of androgen receptor. Åbo Akademi University (Dissertation)
  • Viitanen L (2010). Structural Features of Ligand Binding: Sterol Carrier Protein-2 and Glycolipid Transfer Protein. Åbo Akademi University (Dissertation)

2009

  • Brandt A, Raksajit W, Mulo P, Incharoensakdi A, Salminen TA, Mäenpää P (2009). Transcriptional regulation and structural modeling of the FutC subunit of an ABC-type iron transporter in Synechocystis sp. strain PCC 6803. Arch Microbiol. 191: 561-570.
  • Heino J, Huhtala M, Käpylä J, Johnson MS (2009). Evolution of collagen-based adhesion systems. Int J Biochem Cell Biol. 41: 341-348.
  • 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.
  • Kaitaniemi S, Elovaara H, Grön K, Kidron H, Liukkonen J, Salminen T, Salmi M, Jalkanen S, Elima K (2009). The unique substrate specificity of human AOC2, a semicarbazide-sensitive amine oxidase. Cell Mol Life Sci. 66: 2743-2757.
  • Kivi E, Elima K, Aalto K, Nymalm Y, Auvinen K, Koivunen E, Otto DM, Crocker PR, Salminen TA, Salmi M, Jalkanen S (2009). Human Siglec-10 can bind to vascular adhesion protein-1 and serves as its substrate. Blood. 114: 5385-5392.
  • 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.
  • Permyakov SE, Bakunts AG, Permyakova ME, Denesyuk AI, Uversky VN, Permyakov EA (2009). Metal-controlled interdomain cooperativity in parvalbumins. Cell Calcium. 46: 163-175.
  • Salminen TA (2009). Amine Oxidase Crystal Structures: Vascular adhesion protein-1 in "Copper amine oxidases: structures, catalytic mechanisms and role in pathophysiology". The CRC Press/Taylor and Francis Books, Boca Raton, USA: 137-142.
  • Sandqvist A, Björk JK, Akerfelt M, Chitikova Z, Grichine A, Vourc'h C, Jolly C, Salminen TA, Nymalm Y, Sistonen L (2009). Heterotrimerization of heat-shock factors 1 and 2 provides a transcriptional switch in response to distinct stimuli. Mol Biol Cell. 20: 1340-1347.
  • Sicora CI, Ho FM, Salminen T, Styring S, Aro E (2009). Transcription of a "silent" cyanobacterial psbA gene is induced by microaerobic conditions. Biochim Biophys Acta. 1787: 105-112.
  • Toivanen PI, Nieminen T, Viitanen L, Alitalo A, Roschier M, Jauhiainen S, Markkanen JE, Laitinen OH, Airenne TT, Salminen TA, Johnson MS, Airenne KJ, Ylä-Herttuala S (2009). Novel vascular endothelial growth factor D variants with increased biological activity. J Biol Chem. 284: 16037-16048.
  • Tvorogov D, Sundvall M, Kurppa K, Hollmén M, Repo S, Johnson MS, Elenius K (2009). Somatic mutations of ErbB4: selective loss-of-function phenotype affecting signal transduction pathways in cancer. J Biol Chem. 284: 5582-5591.
  • Vainio MJ, Puranen JS, Johnson MS (2009). ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model. 49: 492-502.

2008

  • Denessiouk K A, Denesyuk A I, Johnson M S. (2008) Negative modulation of signal transduction via interleukin splice variation. Proteins. 71:751-70. PubMed
  • Holmström TH, Mialon A, Kallio M, Nymalm Y, Mannermaa L, Holm T, Johansson H, Black E, Gillespie D, Salminen TA, Langel U, Valdez BC, Westermarck J (2008). c-Jun supports ribosomal RNA processing and nucleolar localization of RNA helicase DDX21. J Biol Chem. 283: 7046-7053.
  • Määttä JAE, Airenne TT, Nordlund HR, Jänis J, Paldanius TA, Vainiotalo P, Johnson MS, Kulomaa MS, Hytönen VP (2008). Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis. Chembiochem. 9: 1124-1135.
  • Permyakov SE, Bakunts AG, Denesyuk AI, Knyazeva EL, Uversky VN, Permyakov EA (2008). Apo-parvalbumin as an intrinsically disordered protein. Proteins. 72: 822-836.
  • Pollari M, Gunnelius L, Tuominen I, Ruotsalainen V, Tyystjärvi E, Salminen T, Tyystjärvi T (2008). Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol. 147: 1994-2005.
  • Repo S, Jyrkkärinne J, Pulkkinen J T, Laatikainen R, Honkakoski P, Johnson M S. (2008) Ligand Specificity of Constitutive Androstane Receptor as Probed by Induced-Fit Docking and Mutagenesis. J Med Chem. 51:7119-7131. PubMed
  • Tulla M, Lahti M, Puranen J S, Brandt A M, Käpylä J, Domogatskaya A, Salminen T A, Tryggvason K, Johnson M S, Heino J. (2008) Effects of conformational activation of integrin alpha 1I and alpha 2I domains on selective recognition of laminin and collagen subtypes. Exp Cell Res. 314:1734-43. PubMed
  • Vainio M (2008). Chemoinformatics in Targeted Drug Design. Department of Biochemistry and Pharmacy, Åbo Akademi University (Dissertation)
  • West G, Viitanen L, Alm C, Mattjus P, Salminen T A, Edqvist J. Identification of a glycosphingolipid transfer protein GLTP1 in Arabidopsis thaliana. FEBS J. 275:3421-37. Pubmed
  • Xhaard H, Backström V, Denessiouk K, Johnson M S. (2008) Coordination of na(+) by monoamine ligands in dopamine, norepinephrine, and serotonin transporters. J Chem Inf Model. 48:1423-37. PubMed
  • Zheng B S, Rönnberg E, Viitanen L, Salminen T A, Lundgren K, Moritz T, Edqvist J. (2008) Arabidopsis sterol carrier protein-2 is required for normal development of seeds and seedlings. J Exp Bot. 59:3485-99. PubMed

2007

  • Connors W L, Jokinen J, White D J, Puranen J S, Kankaanpää P, Upla P, Tulla M, Johnson M S, Heino J. (2007) Two synergistic activation mechanisms of alpha2beta1 integrin-mediated collagen binding. J Biol Chem. 282:14675-83. PubMed
  • Denessiouk K A, Denesyuk A I, Johnson M S. (2007) Negative modulation of signal transduction via interleukin splice variation. Proteins (published ahead of print electronically on Nov 2) PubMed
  • Hytönen V P, Määttä J A, Niskanen E A, Huuskonen J, Helttunen K J, Halling K K, Nordlund H R, Rissanen K, Johnson M S, Salminen T A, Kulomaa M S, Laitinen O H, Airenne T T. (2007) Structure and characterization of a novel chicken biotin-binding protein A (BBP-A). BMC Struct Biol. 7:8. PubMed
  • Jakobsson E, Jokilammi A, Aalto J, Ollikka P, Lehtonen JV, Hirvonen H, Finne J. (2007) Identification of amino acid residues at the active site of endosialidase that dissociate the polysialic acid binding and cleaving activities in Escherichia coli K1 bacteriophages.Biochem J. 405:465-72. PubMed
  • Kidron H, Repo S, Johnson M, Salminen T. (2007) Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies. Mol Biol Evol. 24:79-89. PubMed
  • Käpylä, J, Pentikäinen O T, Nyrönen T, Nissinen L, Lassander S, Jokinen J, Lahti M, Marjamäki A, Johnson M S, Heino J. (2007) Small Molecule Designed to Target Metal Binding Site in the alpha2I Domain Inhibits Integrin Function. J. Med. Chem. 50:2742-2746. Pubmed
  • Laurila J M, Xhaard H, Ruuskanen J O, Rantanen M J, Karlsson H K, Johnson M S, Scheinin M. (2007) The second extracellular loop of alpha(2A)-adrenoceptors contributes to the binding of yohimbine analogues. Br J Pharmacol. 151:1293-304. Pubmed
  • Lintala M, Allahverdiyeva Y, Kidron H, Piippo M, Battchikova N, Suorsa M, Rintamäki E, Salminen T A, Aro E M, Mulo P. (2007) Structural and functional characterization of ferredoxin-NADP+-oxidoreductase using knock-out mutants of Arabidopsis. Plant J. 6:1041-52. PubMed
  • Permyakov, S E, Nazipova A A, Denesyuk A I, Bakunts A G, Zinchenko D V, Lipkin V M, Uversky V N, Permyakov E A. (2007) Recoverin as a Redox-Sensitive Protein. Journal of Proteome Research 6:1855-1863. Pubmed
  • Vainio M J, Johnson M S. (2007) Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. J Chem Inf Model. 47:2462-74. PubMed

2006

  • Airenne T T, Kidron H, Nymalm Y, Nylund M, West G, Mattjus P, Salminen T A. (2006) Structural evidence for adaptive ligand binding of glycolipid transfer protein. J Mol Biol. 355:224-36. PubMed
  • Alvesalo, J K O, Siiskonen, A, Vainio, M J, Tammela, P S M, Vuorela, P M. (2006) Similarity Based Virtual Screening: A Tool for Targeted Library Design. J Med Chem. 49: 2353-2356. PubMed
  • Anckar, J, Hietakangas, V, Denessiouk, K, Thiele, D J, Johnson, M S, Sistonen, L. (2006) Inhibition of DNA Binding by Differential Sumoylation of Heat Shock Factors. Molecular and Cellular Biology 26: 955-964. PubMed
  • Denessiouk K, Johnson M S. (2006) Novel Structural Motifs within Contiguous Tripeptide Segments of Protein Structure Recognize Different Ligand Moieties. Proceedings of Japanese Peptide Symposium: Peptide Science 2005, 509-512.
  • Dudich E, Semenkova L, Dudich I, Denesyuk A, Tatulov E, Korpela T. (2006) Alpha-fetoprotein antagonizes X-linked inhibitor of apoptosis protein anticaspase activity and disrupts XIAP-caspase interaction. FEBS Journal 273: 3837-3849. PubMed
  • Hytönen V P, Hörhä J, Airenne T T, Niskanen E A, Helttunen K J, Johnson M S, Salminen T A, Kulomaa M S, Nordlund H R (2006) Controlling quaternary structure assembly: subunit interface engineering and crystal structure of dual chain avidin. J. Mol. Biol. 359:1352-1363.
  • Marttila-Ichihara F, Smith D J, Stolen C, Yegutkin G, Elima K, Mercier N, Merinen M, Kiviranta R, Pihlavisto M, Alaranta S, Pentikäinen U, Pentikäinen O T, Fülöp F, Jalkanen S, Salmi M. (2006) Vascular amine oxidases are needed for leukocyte extravasation into inflamed joints in vivo. Arthritis & Rheumatism 54: 2852-2862. PubMed
  • Pentikäinen U, Settimo L, Johnson M S, Pentikäinen O. (2006) Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding. Organic & Biomolecular Chemistry 4: 1058-1070. PubMed
  • Repo S, Paldanius T A, Hytönen V P, Nyholm T K, Halling K K, Huuskonen J, Pentikäinen O T, Rissanen K, Slotte J P, Airenne, T T, Salminen T A, Kulomaa M S, Johnson M S. (2006) Properties of HABA-Type Azo Derivatives to Avidin and Avidin-Related Protein 4. Chem Biol. 10: 1029-39. PubMed
  • Viitanen L, Nylund M, Eklund D M, Alm C, Eriksson A-K, Tuuf J, Salminen T A, Mattjus P, Edqvist J. (2006) Characterization of SCP-2 from Euphorbia lagascae reveals that a single Leu/Met exchange enhances sterol transfer activity. FEBS 273: 5641-5655.
  • Sanders J M, Pentikäinen O T, Settimo L, Pentikäinen U, Shoji M, Sasaki M, Sakai R, Johnson M S, Swanson G T. (2006) Determination of Binding Site Residues Responsible for the Subunit Selectivity of Novel Marine-Derived Compounds on Kainate Receptors. Molecular Pharmacology 69: 1849-1860. PubMed
  • Xhaard H, Rantanen V-V, Nyrönen T and Johnson M S. (2006) Molecular evolution of adrenoceptors and dopamine receptors: implications for the binding of catecholamines. J Med Chem. 49: 1706-1719. PubMed

2005

  • Airenne T T, Nymalm Y, Kidron H, Smith D J, Pihlavisto M, Salmi M, Jalkanen S, Johnson M S, Salminen T A. (2005) Crystal structure of the human vascular adhesion protein-1: unique structural features with functional implications. Protein Science. 14:1964-74. PubMed
  • Denessiouk K A, Johnson M S, Denesyuk A I (2005) Novel CalphaNN structural motif for protein recognition of phosphate ions. J Mol Biol. 345: 611-629. PubMed
  • Huhtala M, Heino J, Casciari D, de Luise A, Johnson M S. (2005) Integrin evolution: insights from ascidian and teleost fish genomes. Matrix Biol. 24:83-95. PubMed
  • Hytönen V P, Määttä J A, Kidron H, Halling K K, Hörhä J, Kulomaa T, Nyholm T K, Johnson M S, Salminen T A, Kulomaa M S, Airenne T T (2005) Avidin related protein 2 shows unique structural and functional features among the avidin protein family. BMC Biotechnol. 5:28.
  • 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. PubMed
  • Maula S M, Salminen T, Kaitaniemi S, Nymalm Y, Smith D J, Jalkanen S. (2005) Carbohydrates located on the top of the "cap" contribute to the adhesive and enzymatic functions of vascular adhesion protein-1. Eur J Immunol. 35:2718-2727. PubMed
  • Rantanen V-V, Gyllenberg M, Koski T, Johnson M S. (2005) A priori contact preferences in molecular recognition. J Bioinform Comput Biol. 3:861-90. PubMed
  • Riikonen R, Matilainen H, Rajala N, Pentikäinen O, Johnson M, Heino J, Oker-Blom C. (2005) Functional Display of an alpha(2) Integrin-Specific Motif (RKK) on the Surface of Baculovirus Particles. Technol Cancer Res Treat. 4:437-446. PubMed
  • Ruuskanen J O, Laurila J, Xhaard H, Rantanen V-V, Vuoriluoto K, Wurster S, Marjamäki A, Vainio M, Johnson M S, and Scheinin M. (2005) Conserved structural, pharmacological and functional properties among the three human and five zebrafish alpha-2 -adrenoceptors. Br J Pharmacol. 144:165-177. PubMed
  • Sanders J M, Ito K, Settimo L, Pentikäinen O T, Shoji M, Sasaki M, Johnson M S, Sakai R, Swanson G T. (2005) Divergent pharmacological activity of novel marine-derived excitatory amino acids on glutamate receptors. J Pharmacol Exp Thera. 314:1068-1078. PubMed
  • Vainio M J, Johnson M S. (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J Chem Inf Model. 45:1953-1961. PubMed
  • Xhaard H, Nyrönen T, Rantanen V-V, Ruuskanen J O, Laurila J, Salminen T, Scheinin M, and 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. PubMed
  • Jantaro S, Kidron H, Chesnel D, Incharoensakdi A, Mulo P, Salminen T, Mäenpää P. (2005) Structural modeling and environmental regulation of arginine decarboxylase in Synechocystis sp. PCC 6803. Arch Microbiol. [Epub ahead of print on Dec 14] PubMed

2004

  • Edqvist J, Rönnberg E, Rosenquist S, Blomqvist K, Viitanen L, Salminen T A, Nylund M, Tuuf J, and Mattjus P. (2004). Plants express a lipid transfer protein with high similarity to mammalian sterol carrier protein-2. J Biol Chem. 279:53544-53. PubMed
  • Hytönen V P, Laitinen O H, Airenne T T, Kidron H, Meltola N J, Porkka E, Hörhä J, Paldanius T, Määttä; J A, Nordlund H R, Johnson M S, Salminen T A, Airenne K J, Ylä;-Herttuala S, Kulomaa M S (2004) Efficient production of active chicken avidin using a bacterial signal peptide in Escherichia coli. Biochem J. 384:385-90. PubMed
  • Hytönen V P, Nyholm T K M, Pentikäinen O T, Vaarno J, Porkka E J, Nordlund H R, Johnson M S, Slotte J P, Laitinen O H, Kulomaa M S (2004). Chicken avidin related protein 4/5 shows superior heat stability when compared to avidin and retains high affinity to biotin. J Biol Chem. 279: 9337-9343. PubMed
  • Karisola P, Mikkola J, Kalkkinen N, Airenne K J, Laitinen O H, Repo S, Pentikäinen O T, Reunala T, Turjanmaa K, Johnson M S, Palosuo T, Kulomaa M S, Alenius H (2004) Construction of hevein (Hev b 6.02) with reduced allerginity for immunotherapy of latex allergy by co-mutation of six amino acid residues on the conformational IgE epitopes. J Immunol. 172: 2621-2628. PubMed
  • Khorram O, Garthwaite M, Johnson M S, Denessiouk K A, Han G, Guo T, McPhaul L W, Magee T R, Westerman B, Golos T G (2004) Identification and characterization of a novel luciferase-like protein in the human female reproductive tract. J Clin Endocrin Metab. 89:5837-46. PubMed
  • Lehtonen J V, Still D-J, Rantanen V-V, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M, Johnson M S (2004) BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des. 18:401--419. PubMed
  • Moretti L, Pentikäinen O T, Settimo L, Johnson M S (2004) Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands. J Struc Biol. 145:205-15. PubMed
  • Nymalm Y, Puranen J S, Nyholm T K, Kapyla J, Kidron H, Pentikäinen O T, Airenne T T, Heino J, Slotte J P, Johnson M S, Salminen T A (2004) Jararhagin-derived RKKH-peptides induce structural changes in alpha 1 I domain of human integrin alpha 1beta 1. J Biol Chem. 279: 7962 - 7970. PubMed
  • Ruuskanen J, Xhaard H, Marjamaki A, Salaneck E, Salminen T, Yan Y L, Postlethwait J H, Johnson, M S, Larhammar D, Scheinin M. (2004) Identification of Duplicated Fourth {alpha}2-Adrenergic Receptor Subtype by Cloning and Mapping of Five Receptor Genes in Zebrafish. Mol Biol Evol. 21:14-28. PubMed
  • West G, Nymalm Y, Airenne T T, Kidron H, Mattjus P, Salminen T A (2004) Crystallization and preliminary X-ray analysis of bovine glycolipid transfer protein. Acta Crystallogr D. 60:703-705. PubMed
  • White D J, Puranen J S, Johnson M S, Heino J (2004) The collagen receptor subfamily of integrins. Int J Biochem Cell Biol. 36:1405-10. PubMed
  • Xing L, Huhtala M, Pietiäinen, Käpylä; J, Vuorinen K, Marjomäki V, Heino J, Johnson M S, Hyypiä; T, Cheng R H (2004) Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1. J Biol Chem. 279:11632-8. PubMed
  • Yegutkin G G, Salminen T, Koskinen K, Jalkanen S, Salmi M. (2004) A peptide inhibitor of vascular adhesion protein-1/semicarbazide-sensitive amine oxidase blocks leukocyte-endothelial interactions under shear stress. Eur J Immunol. 34:2276-2285. PubMed

2003

  • Denessiouk K A, Johnson M S (2003) "Acceptor-donor-acceptor" motifs recognize the Watson-Crick, Hoogsteen and Sugar "donor-acceptor-donor" edges of adenine and adenosine-containing ligands. J Mol Biol. 333:1025-43. PubMed
  • Denessiouk K A, Johnson M S (2003) Rules for ligand recognition by proteins: Nucleotide recognition in ATP-, NAD-, NADP- and FAD-dependent proteins with different folds, in Protein Structures: Kaleidoscope of Structural Properties and Functions, ed. Uversky, V. N. Research Signpost, USA. ISBN: 81-7736-177-5.
  • Denesyuk A I, Denessiouk K A, Korpela T, Johnson M S (2003) Phosphate group binding "cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations. Biochim Biophys Acta. 1647:234-8. PubMed
  • Jansen T, Kidron H, Soitamo A, Salminen T, Mäenpää P (2003) Transcriptional regulation and structural modelling of the Synechocystis sp. PCC 6803 carboxyl-terminal endoprotease family. FEMS Microbiol Lett. 228: 121-128. PubMed
  • Johnson M S, Tuckwell D (2003) Evolution of integrin I-domains, in I-domains in integrins, ed.Gullberg, D. Landes Bioscience, USA, pp. 1-27.
  • Nymalm Y, Kidron H, Söderholm A, Viitanen L, Kaukonen K, Pihlavisto M, Smith D, Veromaa T, Airenne T T, Johnson M S, Salminen T A (2003) Crystallization and preliminary x-ray analysis of the human vascular adhesion protein-1. Acta Crystallogr D. 59:1288-1290.
  • Peltonen J M, Nyrönen T, Wurster S, Pihlavisto, M, Hoffrén A-M, Marjamäki A, Xhaard H, Kanerva L, Savola J-M, Johnson M S, Scheinin M (2003) Molecular mechanisms of ligand-receptor interactions in transmembrane domain V of the {alpha}2A-adrenoceptor. Br J Pharmacol. 140:347-58. PubMed
  • Pentikäinen O T, Settimo L, Keinänen K, Johnson M S (2003) Selective agonist binding of (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) and 2S-(2alpha,3beta,4beta)-2-carboxy-4-(1-methylethenyl)-3-pyrrolidineacetic acid (kainate) receptors: a molecular modeling study. Biochem Pharmacol. 66:2413-2425. PubMed
  • Rantanen V-V, Gyllenberg M, Johnson M S (2003) A Bayesian molecular interaction library. J Comp Aided Mol Design. 17:435-461. PubMed
  • Wahlroos T, Soukka J, Denesyuk A, Wahlroos R, Korpela T, Kilby N J (2003) Oleosin expression and trafficking during oil body biogenesis in tobacco leaf cells. Genesis. 35:125-32. PubMed
  • Zhang W M, Käpylä J, Puranen J S, Knight C G, Tiger C F, Pentikäinen O T, Johnson M S, Farndale R W, Heino J, Gullberg D (2003) alpha 11 beta 1 Integrin recognizes the GFOGER sequence in interstitial collagens. J Biol Chem. 278:7270-7. PubMed

2002

  • Denesyuk A I, Denessiouk K A, Korpela T, Johnson M S (2002) Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes. J. Mol. Biol. 316:155-72. PubMed
  • Bengoechea J A, Pinta E, Salminen T, Oertelt C, Holst O, Radziejewska-Lebrecht J, Piotrowska-Seget Z, Venho R, Skurnik M (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. J Bacteriol. 184: 4277-87. PubMed
  • Jouppila A, Pentikäinen O T, Settimo L, Nyrönen T, Haapalahti J P, Lampinen M, Mottershead D G, Johnson, M S, Keinänen K. (2002) Determinants of antagonist binding at the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit, GluR-D. Eur. J. Biochem. 269: 6261-6270. PubMed
  • Lampinen M, Settimo L, Pentikäinen O T, Jouppila A, Mottershead D G, Johnson M S, Keinänen K. (2002) Discrimination between agonists and antagonists by the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid -selective glutamate receptor. J. Biol. Chem. 277: 41940-41947. PubMed
  • Nymalm Y, Kravchuk Z, Salminen T, Chumanevich A, Dubnovitsky A, Kankare J, Pentikäinen O, Lehtonen J, Arosio P, Martsev S, Johnson M S (2002) Antiferritin VL homodimer binds human spleen ferritin with high specificity. J. Struct. Biol. 138:171-186. PubMed
  • Rantanen V-V, Gyllenberg M, Koski T, Johnson M (2002) A dissimilarity matrix between protein atom classes based on Gaussian mixtures. Bioinformatics 18:1257-1263. PubMed
  • Karisola P, Alenius H, Mikkola J, Kalkkinen N, Helin J, Pentikäinen O T, Repo S, Reunala T, Turjanmaa K, Johnson M S, Palosuo T, Kulomaa M S (2002) The Major Conformational IgE-binding Epitopes of Hevein (Hev b6.02) Are Identified by a Novel Chimera-based Allergen Epitope Mapping Strategy. J. Biol. Chem. 277:22656-22661. PubMed
  • Laitinen O H, Hytonen V P, Ahlroth M K, Pentikainen O T, Gallagher C, Nordlund H R, Ovod V, Marttila A T, Porkka E, Heino S, Johnson M S, Airenne K J, Kulomaa M S (2002) Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin. Biochem. J. 363: 609-617. PubMed

2001

  • Tulla M., Pentikäinen O. T., Viitasalo T., Käpylä J., Impola U., Nykvist P., Nissinen L., Johnson M. S., Heino J. (2001) Selective binding of collagen subtypes by integrin alpha 1I, alpha 2I, and alpha 10I domains. J. Biol. Chem. 276: 48206-12. PubMed
  • Rantanen V.-V., Denessiouk K. A., Gyllenberg M., Koski T., Johnson M. S. (2001) A fragment library based on Gaussian mixtures predicting favorable molecular interactions. J. Mol. Biol. 313: 197-214. PubMed
  • Ollila F., Pentikäinen O. T., Forss S., Johnson M. S., Slotte J. P. (2001). Characterization of Bile Salt/Cyclodextrin Interactions Using Isothermal Titration Calorimetry. Langmuir 17: 7107-7111
  • Denessiouk K. A., Rantanen V.-V., Johnson M. S. (2001). Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins 44 (3): 282-291. PubMed
  • Nyrönen T., Pihlavisto M., Peltonen J. M., Hoffren A.-M., Varis M., Salminen T., Wurster S., Marjamäki A., Kanerva L., Katainen E., Laaksonen L., Savola J.-M., Scheinin M., Johnson M. S. (2001). Molecular mechanism for agonist-promoted alpha2A-adrenoceptor activation by norepinephrine and epinephrine. Mol. Pharmacol. 59 (5): 1-12. PubMed
  • Salmi M., Yegutkin G. G., Lehvonen R., Koskinen K., Salminen T., Jalkanen S. (2001). A cell surface amine oxidase directly controls lymphocyte migration. Immunity 14 (3): 265-76. PubMed

2000

  • Denesyuk A. I., Denessiouk K. A., Lehtonen J. V., Korpela T., Johnson M. S. (2000). Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes. In Iriarte A., Kagan H. M., Martinez-Carrion M. (eds.) Biochemistry and Molecular Biology of Vitamin B6 and PQQ-dependent Proteins, pp. 123-128. Birkhäuser Verlag Basel, Switzerland.
  • Johnson M. S., Lehtonen, J. V. (2000). Comparison of protein three-dimensional structures. In Higgins, D., Taylor, W. (eds.) Bioinformatics: Sequence, structure and databanks, pp 15-50. Oxford University Press, England.
  • Denessiouk K., Johnson M. S. (2000). When fold is not important: A common structural framework for adenine and AMP binding in 13 unrelated protein families. Proteins 38:310-326. PubMed
  • Käpylä, J., Ivaska, J., Riikonen, R., Nykvist, P., Pentikäinen, O., Johnson, M.S. and Heino, J. (2000). Integrin alpha2 I domain recognizes type I and type IV collagens by different mechanisms. J. Biol. Chem. 275 (05): 3348-3354. PubMed

1999

  • Pentikäinen, O., Hoffrén, A.-M., Ivaska, J., Käpylä, J., Nyrönen, T., Heino, J. and Johnson, M.S. (1999). RKKH peptides from the snake venom metalloproteinase of Bothrops jararaca bind near the metal ion-dependent adhesion site of the human integrin alpha2 I-domain. J. Biol. Chem. 274 (44): 31493-31505. PubMed
  • Nyrönen, T., Johnson, M.S. (1999). Customized molecules - engineering new drugs with biocomputing. In High Technology Today. The Finnish Academies of Technology, Finland. pp. 78-79
  • Lehtonen, J.V., Denessiouk, K.A., and Johnson, M.S. (1999). Speeding up comparison of three-dimensional protein structures CSC News 11 (4): 16-18
  • Salminen, T., Varis, M., Nyrönen, T., Pihlavisto, M., Hoffrén, A.-M., Lönnberg, T., Marjamäki, A., Frang, H., Savola, J.-M., Scheinin, M. and Johnson, M.S. (1999). Three-dimensional models of alpha-2A-adrenergic receptor complexes provide a structural explanation for ligand binding. J. Biol. Chem. 274 (33): 23405-23413 PubMed
  • Marjamaki, A., Frang, H., Pihlavisto, M., Hoffren, A.-M., Salminen, T., Johnson, M. S., Kallio, J., Javitch, J. A., Scheinin, M. (1999). Chloroethylclonidine and 2-aminoethyl methanethiosulfonate recognize two different conformations of the human alpha(2A)-adrenergic receptor. J. Biol. Chem. 274(31):21867-72 PubMed
  • Salminen, T.A., Nymalm, Y., Kankare, J., Käpylä, J., Heino, J. and Johnson, M.S. (1999). Production, crystallization and preliminary X-ray analysis of the human integrin alpha1 I domain. Acta Cryst. D 55: 1365-1367 PubMed
  • Huhtala, M.T, Pentikäinen, O. and Johnson, M.S. (1999). A dimeric ternary complex of FGFR, heparin and FGF-1 leads to an "'"electrostatic sandwich"'" model for heparin binding. Structure 7: 699-709 PubMed
  • Ivaska, J., Käpylä, J., Pentikäinen, O., Hoffrén, A.-M., Hermonen, J., Huttunen, P. Johnson, M.S. and Heino, J. (1999). A peptide inhibiting the collagen binding function of integrin alpha2I domain. J. Biol. Chem. 274: 3513-3521 PubMed
  • Denessiouk, K.A., Denesyuk, A.I., Lehtonen, J.V., Korpela, T. and Johnson, M.S. (1999). Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes. Proteins 35 (2): 250-261 PubMed
  • Lehtonen, J.V., Denessiouk, K.A, May, A.C.W. and Johnson, M.S. (1999). Finding local structural similarities among families of unrelated protein structures: A generic non-linear algorithm. Proteins 34 (3): 341-355 PubMed

1998

  • Salminen, T.A., Smith, D.J., Jalkanen, S. and Johnson, M.S. (1998). Structural model of the catalytic domain of an enzyme with cell adhesion activity: human vascular adhesion protein-1 (HVAP-1) D4 domain is an amine oxidase. Protein Engineering 11: 1195-1204 PubMed
  • Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson, M.S. and Overington, J.P. (1998). JOY: protein sequence-structure representation and analysis. Bioinformatics 14 (7): 617-623 PubMed
  • Lampinen, M., Pentikäinen, O., Johnson, M.S. and Keinänen, K. (1998). AMPA receptors and bacterial amino acid-binding proteins share the ionic mechanism of ligand recognition. EMBO J. 17: 4704-4711 PubMed
  • Suoniemi, A., Tanskanen, J., Pentikäinen, O., Johnson, M.S. and Schulman, A. (1998). The core domain of retrotransposon integrase in Hordeum: Predicted structure and evolution. Mol. Biol. Evol. 15 (9): 1135-1144 PubMed
  • Denessiouk, K.A, Lehtonen, J.V. and Johnson, M.S. (1998). Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition. Protein Science 7: 1768-1771 PubMed
  • Denessiouk, K.A., Lehtonen, J.V., Korpela, T. and Johnson, M.S. (1998). Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites. Protein Science 7: 1136-1146 PubMed