Mark S. Johnson Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering Åbo Akademi University Biography Publications Institution JoVE Articles Mark S. Johnson has not added a biography. If you are Mark S. Johnson and would like to personalize this page please email our Author Liaison for assistance. Publications System Approach for Building of Calcium-Binding Sites in Proteins Biomolecules. Apr, 2020 | Pubmed ID: 32290360 NBCZone: Universal Three-dimensional Construction of Eleven Amino Acids Near the Catalytic Nucleophile and Base in the Superfamily of (chymo)trypsin-like Serine Fold Proteases International Journal of Biological Macromolecules. Jun, 2020 | Pubmed ID: 32151723 The Acid-base-nucleophile Catalytic Triad in ABH-fold Enzymes is Coordinated by a Set of Structural Elements PloS One. 2020 | Pubmed ID: 32084230 Discovery of Compounds Inhibiting the ADP-Ribosyltransferase Activity of Pertussis Toxin ACS Infectious Diseases. 04, 2020 | Pubmed ID: 31899865 Structural Characterization of EGFR Exon 19 Deletion Mutation Using Molecular Dynamics Simulation PloS One. 2019 | Pubmed ID: 31536605 Evolution and Functional Classification of Mammalian Copper Amine Oxidases Molecular Phylogenetics and Evolution. 10, 2019 | Pubmed ID: 31351182 An Unbiased Screen for Activating Epidermal Growth Factor Receptor Mutations The Journal of Biological Chemistry. 06, 2019 | Pubmed ID: 30952700 Molecular Features of Steroid-binding Antidins and Their Use for Assaying Serum Progesterone PloS One. 2019 | Pubmed ID: 30785944 Distinctive Structural Motifs Co-ordinate the Catalytic Nucleophile and the Residues of the Oxyanion Hole in the Alpha/beta-hydrolase Fold Enzymes Protein Science : a Publication of the Protein Society. 02, 2019 | Pubmed ID: 30311984 Phylogenetic and Mutational Analyses of Human LEUTX, a Homeobox Gene Implicated in Embryogenesis Scientific Reports. 11, 2018 | Pubmed ID: 30479355 Top Surface Blade Residues and the Central Channel Water Molecules Are Conserved in Every Repeat of the Integrin-like β-propeller Structures Journal of Structural Biology. 02, 2018 | Pubmed ID: 29054403 In Silico Identification of Milk Antihypertensive Di- and Tripeptides Involved in Angiotensin I-converting Enzyme Inhibitory Activity Nutrition Research (New York, N.Y.). Oct, 2017 | Pubmed ID: 29173648 Building Kit for Metal Cation Binding Sites in Proteins Biochemical and Biophysical Research Communications. 12, 2017 | Pubmed ID: 29017922 SUMOylation Regulates Nuclear Accumulation and Signaling Activity of the Soluble Intracellular Domain of the ErbB4 Receptor Tyrosine Kinase The Journal of Biological Chemistry. 12, 2017 | Pubmed ID: 28974580 Joint Inflammation Related Citrullination of Functional Arginines in Extracellular Proteins Scientific Reports. 08, 2017 | Pubmed ID: 28811641 Alpha/beta-hydrolases: A Unique Structural Motif Coordinates Catalytic Acid Residue in 40 Protein Fold Families Proteins. Oct, 2017 | Pubmed ID: 28643343 Structural Characterization of Core-bradavidin in Complex with Biotin PloS One. 2017 | Pubmed ID: 28426764 Novel Calcium Recognition Constructions in Proteins: Calcium Blade and EF-hand Zone Biochemical and Biophysical Research Communications. 02, 2017 | Pubmed ID: 28089868 Plasma Protein Binding of Anisomelic Acid: Spectroscopy and Molecular Dynamic Simulations Journal of Chemical Information and Modeling. 12, 2016 | Pubmed ID: 28024399 Extracellular Citrullination Inhibits the Function of Matrix Associated TGF-β Matrix Biology : Journal of the International Society for Matrix Biology. 09, 2016 | Pubmed ID: 26923761 Artificial Avidin-Based Receptors for a Panel of Small Molecules ACS Chemical Biology. Jan, 2016 | Pubmed ID: 26550684 Early Chordate Origin of the Vertebrate Integrin αI Domains PloS One. 2014 | Pubmed ID: 25409021 Two Structural Motifs Within Canonical EF-hand Calcium-binding Domains Identify Five Different Classes of Calcium Buffers and Sensors PloS One. 2014 | Pubmed ID: 25313560 Evolution of Integrin I Domains Advances in Experimental Medicine and Biology. 2014 | Pubmed ID: 25023164 Citrullination of Collagen II Affects Integrin-mediated Cell Adhesion in a Receptor-specific Manner FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology. Aug, 2014 | Pubmed ID: 24823363 A Novel Chimeric Avidin with Increased Thermal Stability Using DNA Shuffling PloS One. 2014 | Pubmed ID: 24632863 Zebavidin--an Avidin-like Protein from Zebrafish PloS One. 2013 | Pubmed ID: 24204770 Probabilistic Prediction of Contacts in Protein-ligand Complexes PloS One. 2012 | Pubmed ID: 23155467 Structure of Bradavidin-C-terminal Residues Act As Intrinsic Ligands PloS One. 2012 | Pubmed ID: 22574129 Active Site Opening and Closure Control Translocation of Multisubunit RNA Polymerase Nucleic Acids Research. Aug, 2012 | Pubmed ID: 22570421 Molecular Docking Guided Comparative GFA, G/PLS, SVM and ANN Models of Structurally Diverse Dual Binding Site Acetylcholinesterase Inhibitors Molecular Informatics. Aug, 2011 | Pubmed ID: 27467261 Conservation of the Human Integrin-type Beta-propeller Domain in Bacteria PloS One. 2011 | Pubmed ID: 22022374 Accurate Conformation-dependent Molecular Electrostatic Potentials for High-throughput in Silico Drug Discovery Journal of Computational Chemistry. Jun, 2010 | Pubmed ID: 20020481 Molecular Mechanism of Alpha2beta1 Integrin Interaction with Human Echovirus 1 The EMBO Journal. Jan, 2010 | Pubmed ID: 19927126 Structural and Functional Characteristics of Xenavidin, the First Frog Avidin from Xenopus Tropicalis BMC Structural Biology. Sep, 2009 | Pubmed ID: 19788720 ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential Journal of Chemical Information and Modeling. Feb, 2009 | Pubmed ID: 19434847 Novel Vascular Endothelial Growth Factor D Variants with Increased Biological Activity The Journal of Biological Chemistry. Jun, 2009 | Pubmed ID: 19366703 Ligand Specificity of Constitutive Androstane Receptor As Probed by Induced-fit Docking and Mutagenesis Journal of Medicinal Chemistry. Nov, 2008 | Pubmed ID: 18973326 Coordination of Na(+) by Monoamine Ligands in Dopamine, Norepinephrine, and Serotonin Transporters Journal of Chemical Information and Modeling. Jul, 2008 | Pubmed ID: 18543980 Negative Modulation of Signal Transduction Via Interleukin Splice Variation Proteins. May, 2008 | Pubmed ID: 17979192 Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm Journal of Chemical Information and Modeling. Nov-Dec, 2007 | Pubmed ID: 17892278 Structure and Characterization of a Novel Chicken Biotin-binding Protein A (BBP-A) BMC Structural Biology. Mar, 2007 | Pubmed ID: 17343730 Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies Molecular Biology and Evolution. Jan, 2007 | Pubmed ID: 16997906 Binding Properties of HABA-type Azo Derivatives to Avidin and Avidin-related Protein 4 Chemistry & Biology. Oct, 2006 | Pubmed ID: 17052607 Subtype Selectivity and Flexibility of Ionotropic Glutamate Receptors Upon Antagonist Ligand Binding Organic & Biomolecular Chemistry. Mar, 2006 | Pubmed ID: 16525550 Molecular Evolution of Adrenoceptors and Dopamine Receptors: Implications for the Binding of Catecholamines Journal of Medicinal Chemistry. Mar, 2006 | Pubmed ID: 16509586 Inhibition of DNA Binding by Differential Sumoylation of Heat Shock Factors Molecular and Cellular Biology. Feb, 2006 | Pubmed ID: 16428449 McQSAR: a Multiconformational Quantitative Structure-activity Relationship Engine Driven by Genetic Algorithms Journal of Chemical Information and Modeling. Nov-Dec, 2005 | Pubmed ID: 16309302 Avidin Related Protein 2 Shows Unique Structural and Functional Features Among the Avidin Protein Family BMC Biotechnology. Oct, 2005 | Pubmed ID: 16212654 Crystal Structure of the Human Vascular Adhesion Protein-1: Unique Structural Features with Functional Implications Protein Science : a Publication of the Protein Society. Aug, 2005 | Pubmed ID: 16046623 Integrin Evolution: Insights from Ascidian and Teleost Fish Genomes Matrix Biology : Journal of the International Society for Matrix Biology. Apr, 2005 | Pubmed ID: 15890260 Rapid Turnover of C-FLIPshort is Determined by Its Unique C-terminal Tail The Journal of Biological Chemistry. Jul, 2005 | Pubmed ID: 15886205 Model Structures of Alpha-2 Adrenoceptors in Complex with Automatically Docked Antagonist Ligands Raise the Possibility of Interactions Dissimilar from Agonist Ligands Journal of Structural Biology. May, 2005 | Pubmed ID: 15866736 Conserved Structural, Pharmacological and Functional Properties Among the Three Human and Five Zebrafish Alpha 2-adrenoceptors British Journal of Pharmacology. Jan, 2005 | Pubmed ID: 15655522 Novel CalphaNN Structural Motif for Protein Recognition of Phosphate Ions Journal of Molecular Biology. Jan, 2005 | Pubmed ID: 15581902 BODIL: a Molecular Modeling Environment for Structure-function Analysis and Drug Design Journal of Computer-aided Molecular Design. Jun, 2004 | Pubmed ID: 15663001 Efficient Production of Active Chicken Avidin Using a Bacterial Signal Peptide in Escherichia Coli The Biochemical Journal. Dec, 2004 | Pubmed ID: 15324300 Model Structures of the N-methyl-D-aspartate Receptor Subunit NR1 Explain the Molecular Recognition of Agonist and Antagonist Ligands Journal of Structural Biology. Mar, 2004 | Pubmed ID: 14960371 Jararhagin-derived RKKH Peptides Induce Structural Changes in Alpha1I Domain of Human Integrin Alpha1beta1 The Journal of Biological Chemistry. Feb, 2004 | Pubmed ID: 14660600 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 Biochemical Pharmacology. Dec, 2003 | Pubmed ID: 14637199 "Acceptor-donor-acceptor" Motifs Recognize the Watson-Crick, Hoogsteen and Sugar "donor-acceptor-donor" Edges of Adenine and Adenosine-containing Ligands Journal of Molecular Biology. Nov, 2003 | Pubmed ID: 14583197 Molecular Mechanisms of Ligand-receptor Interactions in Transmembrane Domain V of the Alpha2A-adrenoceptor British Journal of Pharmacology. Sep, 2003 | Pubmed ID: 12970108 Crystallization and Preliminary X-ray Analysis of the Human Vascular Adhesion Protein-1 Acta Crystallographica. Section D, Biological Crystallography. Jul, 2003 | Pubmed ID: 12832789 Phosphate Group Binding "cup" of PLP-dependent and Non-PLP-dependent Enzymes: Leitmotif and Variations Biochimica Et Biophysica Acta. Apr, 2003 | Pubmed ID: 12686139 Antiferritin VL Homodimer Binds Human Spleen Ferritin with High Specificity Journal of Structural Biology. Jun, 2002 | Pubmed ID: 12217656 Discrimination Between Agonists and Antagonists by the Alpha-amino-3-hydroxy-5-methyl-4-isoxazole Propionic Acid-selective Glutamate Receptor. A Mutation Analysis of the Ligand-binding Domain of GluR-D Subunit The Journal of Biological Chemistry. Nov, 2002 | Pubmed ID: 12167621 Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation Mahlet Z. Tamirat1, Kari J. Kurppa2, Klaus Elenius2,3,4, Mark S. Johnson1 1Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 2Medicity Research Laboratories and Institute of Biomedicine, University of Turku, 3Turku Bioscience Centre, University of Turku and Åbo Akademi University, 4Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital JoVE 61125 Biochemistry
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation Mahlet Z. Tamirat1, Kari J. Kurppa2, Klaus Elenius2,3,4, Mark S. Johnson1 1Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 2Medicity Research Laboratories and Institute of Biomedicine, University of Turku, 3Turku Bioscience Centre, University of Turku and Åbo Akademi University, 4Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital JoVE 61125 Biochemistry
