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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. MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

Author

Scott M. Perry, Deseree J. Reid, Matthew A. Miller, Jessica M. Diesing, Jessica A. Wales, Michael T. Marty, and William R. Montfort

Subjects
Collision-induced dissociation, Chemistry, 010401 analytical chemistry, computer.file_format, Hierarchical Data Format, 010402 general chemistry, Mass spectrometry, Orbitrap, 01 natural sciences, Article, 0104 chemical sciences, law.invention, Structural Biology, law, Data analysis, Mass spectrum, Deconvolution, Biological system, computer, Spectroscopy, Oxygen binding
Abstract

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. Graphical abstract ᅟ.

Published
2018
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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. Structure and Activation of Soluble Guanylyl Cyclase, the Nitric Oxide Sensor

Author

William R. Montfort, Andrzej Weichsel, and Jessica A. Wales

Subjects
Models, Molecular, inorganic chemicals, 0301 basic medicine, Physiology, Clinical Biochemistry, Molecular Conformation, Gene Expression, Heme, Nitric Oxide, Biochemistry, Cyclase, Nitric oxide, Structure-Activity Relationship, 03 medical and health sciences, chemistry.chemical_compound, Soluble Guanylyl Cyclase, Drug Discovery, Animals, Humans, Protein Interaction Domains and Motifs, heterocyclic compounds, Receptor, Molecular Biology, General Environmental Science, Forum Review ArticlesNO Receptor – Part I of II (A. Beuve, Ed.), Cell Biology, Enzyme Activation, Protein Subunits, 030104 developmental biology, Förster resonance energy transfer, chemistry, Guanylate Cyclase, cardiovascular system, Biophysics, General Earth and Planetary Sciences, Guanosine Triphosphate, Signal transduction, Soluble guanylyl cyclase, Wound healing, Protein Binding, Signal Transduction
Abstract

Soluble guanylyl/guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) and is central to the physiology of blood pressure regulation, wound healing, memory formation, and other key physiological activities. sGC is increasingly implicated in disease and is targeted by novel therapeutic compounds. The protein displays a rich evolutionary history and a fascinating signal transduction mechanism, with NO binding to an N-terminal heme-containing domain, which activates the C-terminal cyclase domains. Recent Advances: Crystal structures of individual sGC domains or their bacterial homologues coupled with small-angle x-ray scattering, electron microscopy, chemical cross-linking, and Förster resonance energy transfer measurements are yielding insight into the overall structure for sGC, which is elongated and likely quite dynamic. Transient kinetic measurements reveal a role for individual domains in lowering NO affinity for heme. New sGC stimulatory drugs are now in the clinic and appear to function through binding near or directly to the sGC heme domain, relieving inhibitory contacts with other domains. New sGC-activating drugs show promise for recovering oxidized sGC in diseases with high inflammation by replacing lost heme.Despite the many recent advances, sGC regulation, NO activation, and mechanisms of drug binding remain unclear. Here, we describe the molecular evolution of sGC, new molecular models, and the linked equilibria between sGC NO binding, drug binding, and catalytic activity.Recent results and ongoing studies lay the foundation for a complete understanding of structure and mechanism, and they open the door for new drug discovery targeting sGC. Antioxid. Redox Signal. 26, 107-121.

Published
2017
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