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1. Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications

Author

G. Todd Milne, on behalf of the Ironwood team, Peter Sandner, Kathleen A. Lincoln, Paul C. Harrison, Hongxing Chen, Hong Wang, Holly Clifford, Hu Sheng Qian, Diane Wong, Chris Sarko, Ryan Fryer, Jeremy Richman, Glenn A. Reinhart, Carine M. Boustany, Steven S. Pullen, Henriette Andresen, Lise Román Moltzau, Alessandro Cataliotti, Finn Olav Levy, Robert Lukowski, Sandra Frankenreiter, Andreas Friebe, Timothy Calamaras, Robert Baumgartner, Angela McLaughlin, Mark Aronovitz, Wendy Baur, Guang-Rong Wang, Navin Kapur, Richard Karas, Robert Blanton, Stefan Hell, Scott A. Waldman, Jieru E. Lin, Francheska Colon-Gonzalez, Gilbert W. Kim, Erik S. Blomain, Dante Merlino, Adam Snook, Jeanette Erdmann, Jana Wobst, Thorsten Kessler, Heribert Schunkert, Ulrich Walter, Oliver Pagel, Elena Walter, Stepan Gambaryan, Albert Smolenski, Kerstin Jurk, Rene Zahedi, James R. Klinger, Raymond L. Benza, Paul A. Corris, David Langleben, Robert Naeije, Gérald Simonneau, Christian Meier, Pablo Colorado, Mi Kyung Chang, Dennis Busse, Marius M. Hoeper, Jaime L. Masferrer, Sarah Jacobson, Guang Liu, Renee Sarno, Sylvie Bernier, Ping Zhang, Roger Flores-Costa, Mark Currie, Katherine Hall, Dorit Möhrle, Katrin Reimann, Steffen Wolter, Markus Wolters, Evanthia Mergia, Nicole Eichert, Hyun-Soon Geisler, Peter Ruth, Robert Feil, Ulrike Zimmermann, Doris Koesling, Marlies Knipper, Lukas Rüttiger, Yasutake Tanaka, Atsuko Okamoto, Takashi Nojiri, Motofumi Kumazoe, Takeshi Tokudome, Koichi Miura, Jun Hino, Hiroshi Hosoda, Mikiya Miyazato, Kenji Kangawa, Vikas Kapil, Amrita Ahluwalia, Nazareno Paolocci, Philip Eaton, James C. Campbell, Philipp Henning, Eugen Franz, Banumathi Sankaran, Friedrich W. Herberg, Choel Kim, M. Wittwer, Q. Luo, V. Kaila, S. A. Dames, Andrew Tobin, Mahmood Alam, Olena Rudyk, Susanne Krasemann, Kristin Hartmann, Oleksandra Prysyazhna, Min Zhang, Lan Zhao, Astrid Weiss, Ralph Schermuly, Amie J. Moyes, Sandy M. Chu, Reshma S. Baliga, Adrian J. Hobbs, Stylianos Michalakis, Regine Mühlfriedel, Christian Schön, Dominik M. Fischer, Barbara Wilhelm, Ditta Zobor, Susanne Kohl, Tobias Peters, Eberhart Zrenner, Karl Ulrich Bartz-Schmidt, Marius Ueffing, Bernd Wissinger, Mathias Seeliger, Martin Biel, RD-CURE consortium, Mark J. Ranek, Kristen M. Kokkonen, Dong I. Lee, Ronald J. Holewinski, Vineet Agrawal, Cornelia Virus, Donté A. Stevens, Masayuki Sasaki, Huaqun Zhang, Mathew M. Mannion, Peter P. Rainer, Richard C. Page, Jonathan C. Schisler, Jennifer E. Van Eyk, Monte S. Willis, David A. Kass, Manuela Zaccolo, Michael Russwurm, Jan Giesen, Corina Russwurm, Ernst-Martin Füchtbauer, Nadja I. Bork, Viacheslav O. Nikolaev, Luis Agulló, Martin Floor, Jordi Villà-Freixa, Ornella Manfra, Gaia Calamera, Nicoletta C. Surdo, Silja Meier, Alexander Froese, Kjetil Wessel Andressen, Annemarie Aue, Fabian Schwiering, Dieter Groneberg, Gzona Bajraktari, Jürgen Burhenne, Walter E. Haefeli, Johanna Weiss, Katharina Beck, Barbara Voussen, Alexander Vincent, Sean P. Parsons, Jan D. Huizinga, Fabiola Zakia Mónica, Edward Seto, Ferid Murad, Ka Bian, Joseph R. Burgoyne, Daniel Richards, Marianne Bjørnerem, Andrea Hembre Ulsund, Jeong Joo Kim, Sonia Donzelli, Mara Goetz, Kjestine Schmidt, Konstantina Stathopoulou, Jenna Scotcher, Christian Dees, Hariharan Subramanian, Elke Butt, Alisa Kamynina, S. Bruce King, Cor de Witt, Lars I. Leichert, Friederike Cuello, Hyazinth Dobrowinski, Moritz Lehners, Michael Paolillo Hannes Schmidt, Susanne Feil, Lai Wen, Martin Thunemann, Marcus Olbrich, Harald Langer, Meinrad Gawaz, Cor de Wit, Daniela Bertinetti, Hossein-Ardeschir Ghofrani, Friedrich Grimminger, Ekkehard Grünig, Yigao Huang, Pavel Jansa, Zhi Cheng Jing, David Kilpatrick, Stephan Rosenkranz, Flavia Menezes, Arno Fritsch, Sylvia Nikkho, Reiner Frey, Marc Humbert, Manuela Harloff, Joerg Reinders, Jens Schlossmann, Joon Jung, Jessica A. Wales, Cheng-Yu Chen, Linda Breci, Andrzej Weichsel, Sylvie G. Bernier, Robert Solinga, James E. Sheppeck, Paul A. Renhowe, William R. Montfort, Liying Qin, Ying-Ju Sung, Darren Casteel, Alexander Kollau, Andrea Neubauer, Astrid Schrammel, Bernd Mayer, Mika Takai, Chieri Takeuchi, Mai Kadomatsu, Shun Hiroi, Kanako Takamatsu, Hirofumi Tachibana, Marissa Opelt, Emrah Eroglu, Markus Waldeck-Weiermair, Roland Malli, Wolfgang F. Graier, John T. Fassett, Selene J. Sollie, Maria Hernandez-Valladares, Frode Berven, Kjetil W. Andressen, Miki Arai, Yutaka Suzuki, Meinoshin Okumura, Shinpei Kawaoka, Stefanie Peters, Hannes Schmidt, B. Selin Kenet, Sarah Helena Nies, Katharina Frank, Fritz G. Rathjen, Olga N. Petrova, Isabelle Lamarre, Michel Négrerie, Jerid W. Robinson, Jeremy R. Egbert, Julia Davydova, Laurinda A. Jaffe, Lincoln R. Potter, Nicholas Blixt, Leia C. Shuhaibar, Gordon L. Warren, Kim C. Mansky, Simone Romoli, Tobias Bauch, Karoline Dröbner, Frank Eitner, Mihály Ruppert, Tamás Radovits, Sevil Korkmaz-Icöz, Shiliang Li, Péter Hegedűs, Sivakanan Loganathan, Balázs Tamás Németh, Attila Oláh, Csaba Mátyás, Kálmán Benke, Béla Merkely, Matthias Karck, Gábor Szabó, Ulrike Scheib, Matthias Broser, Shatanik Mukherjee, Katja Stehfest, Christine E. Gee, Heinz G. Körschen, Thomas G. Oertner, Peter Hegemann, Deborah M. Dickey, Alexandre Dumoulin, Ralf Kühn, Laurinda Jaffe, Sophie Schobesberger, Peter Wright, Claire Poulet, Catherine Mansfield, Sian E. Harding, Julia Gorelik, Gerald Wölkart, Antonius C. F. Gorren, Gerburg K. Schwaerzer, Darren E. Casteel, Nancy D. Dalton, Yusu Gu, Shunhui Zhuang, Dianna M. Milewicz, Kirk L. Peterson, Renate Pilz, Aikaterini I. Argyriou, Garyfalia Makrynitsa, Ioannis I. Alexandropoulos, Andriana Stamopoulou, Marina Bantzi, Athanassios Giannis, Stavros Topouzis, Andreas Papapetropoulos, Georgios A. Spyroulias, Dennis J. Stuehr, Arnab Ghosh, Yue Dai, Saurav Misra, Boris Tchernychev, Inmaculada Silos-Santiago, Gerhard Hannig, Vu Thao-Vi Dao, Martin Deile, Pavel I. Nedvetsky, Andreas Güldner, César Ibarra-Alvarado, Axel Gödecke, Harald H. H. W. Schmidt, Angelos Vachaviolos, Andrea Gerling, Stefan Z. Lutz, Hans-Ulrich Häring, Marcel A. Krüger, Bernd J. Pichler, Michael J. Shipston, Sara Vandenwijngaert, Clara D. Ledsky, Obiajulu Agha, Dongjian Hu, Ibrahim J. Domian, Emmanuel S. Buys, Christopher Newton-Cheh, Donald B. Bloch, Nadine Mauro, Jonas Keppler, Wilson A. Ferreira, Hanan Chweih, Pamela L. Brito, Camila B. Almeida, Carla F. F. Penteado, Sara S. O. Saad, Fernando F. Costa, Paul S. Frenette, Damian Brockschnieder, Johannes-Peter Stasch, Nicola Conran, Daniel P. Zimmer, Jenny Tobin, Courtney Shea, Kimberly Long, Kim Tang, Peter Germano, James Wakefield, Ali Banijamali, G-Yoon Jamie Im, Albert T. Profy, and Mark G. Currie

Subjects
Therapeutics. Pharmacology, RM1-950, Toxicology. Poisons, RA1190-1270
Published
2017
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2. Identification of an immunogenic protein of Giardia lamblia using monoclonal antibodies generated from infected mice

Author

Jael Quintero, Diana Carolina Figueroa, Rafael Barcelo, Linda Breci, Humberto Astiazaran-Garcia, Lucila Rascon, Ramon Robles-Zepeda, Adriana Garibay-Escobar, Enrique Velazquez-Contreras, Gloria Leon Avila, Jose Manuel Hernandez-Hernandez, and Carlos Velazquez

Subjects
Giardia lamblia, immunogenic antigen, monoclonal antibody, Microbiology, QR1-502, Infectious and parasitic diseases, RC109-216
Abstract

The humoral immune response plays an important role in the clearance of Giardia lamblia. However, our knowledge about the specific antigens of G. lamblia that induce a protective immune response is limited. The purpose of this study was to identify and characterise the immunogenic proteins of G. lamblia in a mouse model. We generated monoclonal antibodies (moAbs) specific to G. lamblia (1B10, 2C9.D11, 3C10.E5, 3D10, 5G8.B5, 5F4, 4C7, 3C5 and 3C6) by fusing splenocytes derived from infected mice. Most of these moAbs recognised a band of ± 71 kDa (5G8 protein) and this protein was also recognised by serum from the infected mice. We found that the moAbs recognised conformational epitopes of the 5G8 protein and that this antigen is expressed on the cell surface and inside trophozoites. Additionally, antibodies specific to the 5G8 protein induced strong agglutination (> 70-90%) of trophozoites. We have thus identified a highly immunogenic antigen of G. lamblia that is recognised by the immune system of infected mice. In summary, this study describes the identification and partial characterisation of an immunogenic protein of G. lamblia. Additionally, we generated a panel of moAbs specific for this protein that will be useful for the biochemical and immunological characterisation of this immunologically interesting Giardia molecule.

Published
2013
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3. Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase

Author

Robert Solinga, Paul Allan Renhowe, Linda Breci, Joon Jung, Cheng-Yu Chen, James E. Sheppeck, Andrzej Weichsel, Jessica A. Wales, Sylvie G. Bernier, William R. Montfort, and Takashi Nakai

Subjects
inorganic chemicals, 0301 basic medicine, Mutation, Missense, Heme, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Soluble Guanylyl Cyclase, Bacterial Proteins, Protein Domains, Binding site, Shewanella oneidensis, Receptor, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, Binding Sites, Bacteria, 030102 biochemistry & molecular biology, biology, Photoaffinity labeling, Drug discovery, Cell Biology, biology.organism_classification, 030104 developmental biology, Amino Acid Substitution, chemistry, Protein Structure and Folding, Diazirine, cardiovascular system, Soluble guanylyl cyclase
Abstract

Soluble guanylyl cyclase (sGC) is the receptor for nitric oxide and a highly sought-after therapeutic target for the management of cardiovascular diseases. New compounds that stimulate sGC show clinical promise, but where these stimulator compounds bind and how they function remains unknown. Here, using a photolyzable diazirine derivative of a novel stimulator compound, IWP-051, and MS analysis, we localized drug binding to the β1 heme domain of sGC proteins from the hawkmoth Manduca sexta and from human. Covalent attachments to the stimulator were also identified in bacterial homologs of the sGC heme domain, referred to as H-NOX domains, including those from Nostoc sp. PCC 7120, Shewanella oneidensis, Shewanella woodyi, and Clostridium botulinum, indicating that the binding site is highly conserved. The identification of photoaffinity-labeled peptides was aided by a signature MS fragmentation pattern of general applicability for unequivocal identification of covalently attached compounds. Using NMR, we also examined stimulator binding to sGC from M. sexta and bacterial H-NOX homologs. These data indicated that stimulators bind to a conserved cleft between two subdomains in the sGC heme domain. L12W/T48W substitutions within the binding pocket resulted in a 9-fold decrease in drug response, suggesting that the bulkier tryptophan residues directly block stimulator binding. The localization of stimulator binding to the sGC heme domain reported here resolves the longstanding question of where stimulators bind and provides a path forward for drug discovery.

Published
2018
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4. Molecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-Linking

Author

Wenzhou Li, Bradley G. Fritz, Andrzej Weichsel, Vicki H. Wysocki, William R. Montfort, Aqeel Ahmed, Florence Tama, Linda Breci, Jacqueline L. Brailey, and Sue A. Roberts

Subjects
Models, Molecular, inorganic chemicals, Indazoles, GTP', Molecular model, Protein Conformation, Stereochemistry, Receptors, Cytoplasmic and Nuclear, Plasma protein binding, Nitric Oxide, Biochemistry, Cyclase, Mass Spectrometry, Article, chemistry.chemical_compound, Soluble Guanylyl Cyclase, Protein structure, X-Ray Diffraction, Manduca, Scattering, Small Angle, Animals, Heme, Histidine, Carbon Monoxide, Recombinant Proteins, Cross-Linking Reagents, chemistry, Guanylate Cyclase, Structural Homology, Protein, cardiovascular system, Soluble guanylyl cyclase, Ultracentrifugation, Protein Binding
Abstract

Soluble guanylyl/guanylate cyclase (sGC) converts GTP to cGMP after binding nitric oxide, leading to smooth muscle relaxation and vasodilation. Impaired sGC activity is common in cardiovascular disease, and sGC stimulatory compounds are vigorously sought. sGC is a 150 kDa heterodimeric protein with two H-NOX domains (one with heme, one without), two PAS domains, a coiled-coil domain, and two cyclase domains. Binding of NO to the sGC heme leads to proximal histidine release and stimulation of catalytic activity. To begin to understand how binding leads to activation, we examined truncated sGC proteins from Manduca sexta (tobacco hornworm) that bind NO, CO, and stimulatory compound YC-1 but lack the cyclase domains. We determined the overall shape of truncated M. sexta sGC using analytical ultracentrifugation and small-angle X-ray scattering (SAXS), revealing an elongated molecule with dimensions of 115 Å × 90 Å × 75 Å. Binding of NO, CO, or YC-1 had little effect on shape. Using chemical cross-linking and tandem mass spectrometry, we identified 20 intermolecular contacts, allowing us to fit homology models of the individual domains into the SAXS-derived molecular envelope. The resulting model displays a central parallel coiled-coil platform upon which the H-NOX and PAS domains are assembled. The β1 H-NOX and α1 PAS domains are in contact and form the core signaling complex, while the α1 H-NOX domain can be removed without a significant effect on ligand binding or overall shape. Removal of 21 residues from the C-terminus yields a protein with dramatically increased proximal histidine release rates upon NO binding.

Published
2013
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5. Analysis of secreted proteins fromAspergillus flavus

Author

Martha L. Medina, Linda Breci, Wilson A. Francisco, and Paul A. Haynes

Subjects
Proteomics, Time Factors, Rutin, Genes, Fungal, Aspergillus flavus, Biology, Tandem mass spectrometry, Biochemistry, Mass Spectrometry, Microbiology, Fungal Proteins, Protein sequencing, Electrophoresis, Gel, Two-Dimensional, Secretion, Databases, Protein, Molecular Biology, Gene, Polyacrylamide gel electrophoresis, Proteins, food and beverages, biology.organism_classification, Carbon, Glucose, Secretory protein, Electrophoresis, Polyacrylamide Gel, Isoelectric Focusing
Abstract

MS/MS techniques in proteomics make possible the identification of proteins from organisms with little or no genome sequence information available. Peptide sequences are obtained from tandem mass spectra by matching peptide mass and fragmentation information to protein sequence information from related organisms, including unannotated genome sequence data. This peptide identification data can then be grouped and reconstructed into protein data. In this study, we have used this approach to study protein secretion by Aspergillus flavus, a filamentous fungus for which very little genome sequence information is available. A. flavus is capable of degrading the flavonoid rutin (quercetin 3-O-glycoside), as the only source of carbon via an extracellular enzyme system. In this continuing study, a proteomic analysis was used to identify secreted proteins from A. flavus when grown on rutin. The growth media glucose and potato dextrose were used to identify differentially expressed secreted proteins. The secreted proteins were analyzed by 1- and 2-DE and MS/MS. A total of 51 unique A. flavus secreted proteins were identified from the three growth conditions. Ten proteins were unique to rutin-, five to glucose- and one to potato dextrose-grown A. flavus. Sixteen secreted proteins were common to all three media. Fourteen identifications were of hypothetical proteins or proteins of unknown functions. To our knowledge, this is the first extensive proteomic study conducted to identify the secreted proteins from a filamentous fungus.

Published
2005
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6. The Identity of Proteins Associated with a Small Heat Shock Protein during Heat Stress in Vivo Indicates That These Chaperones Protect a Wide Range of Cellular Functions

Author

Elizabeth Vierling, Garrett J. Lee, Eman Basha, Andrew C. Hausrath, Nicole R. Buan, Kim C. Giese, and Linda Breci

Subjects
Cell signaling, Hot Temperature, Transcription, Genetic, Immunoprecipitation, Protein aggregation, Cyanobacteria, Biochemistry, Chromatography, Affinity, Mass Spectrometry, Cell Physiological Phenomena, Adenosine Triphosphate, Bacterial Proteins, Affinity chromatography, Heat shock protein, HSP70 Heat-Shock Proteins, Molecular Biology, Heat-Shock Proteins, Immunosorbent Techniques, HSPA12A, biology, Escherichia coli Proteins, fungi, Esterases, Cell Biology, Mutagenesis, Protein Biosynthesis, Chaperone (protein), biology.protein, Electrophoresis, Polyacrylamide Gel, Gene Deletion, Molecular Chaperones, Signal Transduction, Protein Renaturation
Abstract

The small heat shock proteins (sHSPs) are a ubiquitous class of ATP-independent chaperones believed to prevent irreversible protein aggregation and to facilitate subsequent protein renaturation in cooperation with ATP-dependent chaperones. Although sHSP chaperone activity has been studied extensively in vitro, understanding the mechanism of sHSP function requires identification of proteins that are sHSP substrates in vivo. We have used both immunoprecipitation and affinity chromatography to recover 42 proteins that specifically interact with Synechocystis Hsp16.6 in vivo during heat treatment. These proteins can all be released from Hsp16.6 by the ATP-dependent activity of DnaK and co-chaperones and are heat-labile. Thirteen of the putative substrate proteins were identified by mass spectrometry and reveal the potential for sHSPs to protect cellular functions as diverse as transcription, translation, cell signaling, and secondary metabolism. One of the putative substrates, serine esterase, was purified and tested directly for interaction with purified Hsp16.6. Hsp16.6 effectively formed soluble complexes with serine esterase in a heat-dependent fashion, thereby preventing formation of insoluble serine esterase aggregates. These data offer critical insights into the characteristics of native sHSP substrates and extend and provide in vivo support for the chaperone model of sHSP function.

Published
2004
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