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Yen YC, Li Y, Chen CL, Klose T, Watts VJ, Dessauer CW, Tesmer JJG. Structure of adenylyl cyclase 5 in complex with Gβγ offers insights into ADCY5-related dyskinesia. Nat Struct Mol Biol 2024; 31:1189-1197. [PMID: 38589608 PMCID: PMC11329361 DOI: 10.1038/s41594-024-01263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
The nine different membrane-anchored adenylyl cyclase isoforms (AC1-9) in mammals are stimulated by the heterotrimeric G protein, Gαs, but their response to Gβγ regulation is isoform specific. In the present study, we report cryo-electron microscope structures of ligand-free AC5 in complex with Gβγ and a dimeric form of AC5 that could be involved in its regulation. Gβγ binds to a coiled-coil domain that links the AC transmembrane region to its catalytic core as well as to a region (C1b) that is known to be a hub for isoform-specific regulation. We confirmed the Gβγ interaction with both purified proteins and cell-based assays. Gain-of-function mutations in AC5 associated with human familial dyskinesia are located at the interface of AC5 with Gβγ and show reduced conditional activation by Gβγ, emphasizing the importance of the observed interaction for motor function in humans. We propose a molecular mechanism wherein Gβγ either prevents dimerization of AC5 or allosterically modulates the coiled-coil domain, and hence the catalytic core. As our mechanistic understanding of how individual AC isoforms are uniquely regulated is limited, studies such as this may provide new avenues for isoform-specific drug development.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yong Li
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Thomas Klose
- Purdue Cryo-EM Facility, Hockmeyer Hall for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - John J G Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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2
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Wittrien T, Ziegler A, Rühle A, Stomberg S, Meyer R, Bonneau D, Rodien P, Prunier-Mirebeau D, Coutant R, Behrends S. Heterozygous gain of function variant in GUCY1A2 may cause autonomous ovarian hyperfunction. Eur J Endocrinol 2024; 190:266-274. [PMID: 38578777 DOI: 10.1093/ejendo/lvae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
PURPOSE The purpose of this study was to characterize the phenotype associated with a de novo gain-of-function variant in the GUCY1A2 gene. METHODS An individual carrying the de novo heterozygous variant c.1458G>T p.(E486D) in GUCY1A2 was identified by exome sequencing. The effect of the corresponding enzyme variant α2E486D/β1 was evaluated using concentration-response measurements with wild-type enzyme and the variant in cytosolic fractions of HEK293 cells, UV-vis absorbance spectra of the corresponding purified enzymes, and examination of overexpressed fluorescent protein-tagged constructs by confocal laser scanning microscopy. RESULTS The patient presented with precocious peripheral puberty resembling the autonomous ovarian puberty seen in McCune-Albright syndrome. Additionally, the patient displayed severe intellectual disability. In vitro activity assays revealed an increased nitric oxide affinity for the mutant enzyme. The response to carbon monoxide was unchanged, while thermostability was decreased compared to wild type. Heme content, susceptibility to oxidation, and subcellular localization upon overexpression were unchanged. CONCLUSION Our data define a syndromic autonomous ovarian puberty likely due to the activating allele p.(E486D) in GUCY1A2 leading to an increase in cGMP. The overlap with the ovarian symptoms of McCune-Albright syndrome suggests an impact of this cGMP increase on the cAMP pathway in the ovary. Additional cases will be needed to ensure a causal link.
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Affiliation(s)
- Theresa Wittrien
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Alban Ziegler
- Department of Genetics, University Hospital of Angers, 49933 Angers, France
- Department of Genetics, CRMR AnDDI-Rares, University Hospital of Reims, 51092 Reims, France
| | - Anne Rühle
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Svenja Stomberg
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Ruben Meyer
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
| | - Dominique Bonneau
- Department of Genetics, University Hospital of Angers, 49933 Angers, France
| | - Patrice Rodien
- Department of Endocrinology, Reference Center for Rare Thyroid and Hormone Receptor Diseases, University Hospital of Angers, 49933 Angers, France
| | - Delphine Prunier-Mirebeau
- Department of Biochemistry and Molecular Biology, University Hospital of Angers, 49933 Angers, France
| | - Régis Coutant
- Department of Pediatric Endocrinology, University Hospital, 49933 Angers, France
| | - Sönke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig-Institute of Technology, 38106 Braunschweig, Germany
- Semmelweiss University Budapest, Asklepios Campus, 20099 Hamburg, Germany
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3
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Montfort WR. Per-ARNT-Sim Domains in Nitric Oxide Signaling by Soluble Guanylyl Cyclase. J Mol Biol 2024; 436:168235. [PMID: 37572934 PMCID: PMC10858291 DOI: 10.1016/j.jmb.2023.168235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
Nitric oxide (NO) regulates large swaths of animal physiology including wound healing, vasodilation, memory formation, odor detection, sexual function, and response to infectious disease. The primary NO receptor is soluble guanyly/guanylate cyclase (sGC), a dimeric protein of ∼150 kDa that detects NO through a ferrous heme, leading to a large change in conformation and enhanced production of cGMP from GTP. In humans, loss of sGC function contributes to multiple disease states, including cardiovascular disease and cancer, and is the target of a new class of drugs, sGC stimulators, now in clinical use. sGC evolved through the fusion of four ancient domains, a heme nitric oxide / oxygen (H-NOX) domain, a Per-ARNT-Sim (PAS) domain, a coiled coil, and a cyclase domain, with catalysis occurring at the interface of the two cyclase domains. In animals, the predominant dimer is the α1β1 heterodimer, with the α1 subunit formed through gene duplication of the β1 subunit. The PAS domain provides an extensive dimer interface that remains unchanged during sGC activation, acting as a core anchor. A large cleft formed at the PAS-PAS dimer interface tightly binds the N-terminal end of the coiled coil, keeping this region intact and unchanged while the rest of the coiled coil repacks, and the other domains reposition. This interface buries ∼3000 Å2 of monomer surface and includes highly conserved apolar and hydrogen bonding residues. Herein, we discuss the evolutionary history of sGC, describe the role of PAS domains in sGC function, and explore the regulatory factors affecting sGC function.
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Affiliation(s)
- William R Montfort
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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4
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Vide U, Kasapović D, Fuchs M, Heimböck MP, Totaro MG, Zenzmaier E, Winkler A. Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases. SCIENCE ADVANCES 2023; 9:eadh4721. [PMID: 37531459 PMCID: PMC10396304 DOI: 10.1126/sciadv.adh4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for lifestyle transitions, such as cell proliferation or apoptosis, switch-like characteristics are desirable. While nature frequently uses regulatory circuits to amplify or dampen signals, stand-alone protein switches are interesting for applications like biosensors, diagnostic tools, or optogenetics. However, such stand-alone systems frequently feature limited dynamic and operational ranges and suffer from slow response times. Here, we characterize a LOV-activated diguanylate cyclase (LadC) that offers precise temporal and spatial control of enzymatic activity with an exceptionally high dynamic range over four orders of magnitude. To establish this pronounced activation, the enzyme exhibits a two-stage activation process in which its activity is inhibited in the dark by caging its effector domains and stimulated upon illumination by the formation of an extended coiled-coil. These switch-like characteristics of the LadC system can be used to develop new optogenetic tools with tight regulation.
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Affiliation(s)
- Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Dženita Kasapović
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Maximilian Fuchs
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Martin P. Heimböck
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Massimo G. Totaro
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Elfriede Zenzmaier
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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5
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Wittenborn EC, Thomas WC, Houghton KA, Wirachman ES, Wu Y, Marletta MA. Role of the Coiled-Coil Domain in Allosteric Activity Regulation in Soluble Guanylate Cyclase. Biochemistry 2023; 62:1568-1576. [PMID: 37129924 PMCID: PMC10686098 DOI: 10.1021/acs.biochem.3c00052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Soluble guanylate cyclase (sGC) is the primary nitric oxide (NO) receptor in higher eukaryotes, including humans. NO-dependent signaling via sGC is associated with important physiological effects in the vascular, pulmonary, and neurological systems, and sGC itself is an established drug target for the treatment of pulmonary hypertension due to its central role in vasodilation. Despite isolation in the late 1970s, high-resolution structural information on full-length sGC remained elusive until recent cryo-electron microscopy structures were determined of the protein in both the basal unactivated state and the NO-activated state. These structures revealed large-scale conformational changes upon activation that appear to be centered on rearrangements within the coiled-coil (CC) domains in the enzyme. Here, a structure-guided approach was used to engineer constitutively unactivated and constitutively activated sGC variants through mutagenesis of the CC domains. These results demonstrate that the activation-induced conformational change in the CC domains is necessary and sufficient for determining the level of sGC activity.
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Affiliation(s)
- Elizabeth C. Wittenborn
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - William C. Thomas
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kimberly A. Houghton
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erika S. Wirachman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yang Wu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael A. Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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6
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Yen YC, Li Y, Chen CL, Klose T, Watts VJ, Dessauer CW, Tesmer JJG. Isoform Specific Regulation of Adenylyl Cyclase 5 by Gβγ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539090. [PMID: 37205557 PMCID: PMC10187219 DOI: 10.1101/2023.05.02.539090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The nine different membrane-anchored adenylyl cyclase isoforms (AC1-9) in mammals are stimulated by the heterotrimeric G protein Gαs, but their response to Gβγ regulation is isoform-specific. For example, AC5 is conditionally activated by Gβγ. Here, we report cryo-EM structures of ligand-free AC5 in complex with Gβγ and of a dimeric form of AC5 that could be involved in its regulation. Gβγ binds to a coiled-coil domain that links the AC transmembrane region to its catalytic core as well as to a region (C1b) that is known to be a hub for isoform-specific regulation. We confirmed the Gβγ interaction with both purified proteins and cell-based assays. The interface with Gβγ involves AC5 residues that are subject to gain-of-function mutations in humans with familial dyskinesia, indicating that the observed interaction is important for motor function. A molecular mechanism wherein Gβγ either prevents dimerization of AC5 or allosterically modulates the coiled-coil domain, and hence the catalytic core, is proposed. Because our mechanistic understanding of how individual AC isoforms are uniquely regulated is limited, studies such as this may provide new avenues for isoform-specific drug development.
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Affiliation(s)
- Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Yong Li
- Department Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Thomas Klose
- Purdue CryoEM Facility, Suite 171, Hockmeyer Hall for Structural Biology, Purdue University, West Lafayette, IN, USA
| | - Val J Watts
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | - Carmen W Dessauer
- Department Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Molecular Pharmacology and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
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7
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Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold. Biomolecules 2022; 12:biom12121798. [PMID: 36551226 PMCID: PMC9775385 DOI: 10.3390/biom12121798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
RNase Y is a crucial component of genetic translation, acting as the key enzyme initiating mRNA decay in many Gram-positive bacteria. The N-terminal domain of Bacillus subtilis RNase Y (Nter-BsRNaseY) is thought to interact with various protein partners within a degradosome complex. Bioinformatics and biophysical analysis have previously shown that Nter-BsRNaseY, which is in equilibrium between a monomeric and a dimeric form, displays an elongated fold with a high content of α-helices. Using multidimensional heteronuclear NMR and AlphaFold models, here, we show that the Nter-BsRNaseY dimer is constituted of a long N-terminal parallel coiled-coil structure, linked by a turn to a C-terminal region composed of helices that display either a straight or bent conformation. The structural organization of the N-terminal domain is maintained within the AlphaFold model of the full-length RNase Y, with the turn allowing flexibility between the N- and C-terminal domains. The catalytic domain is globular, with two helices linking the KH and HD modules, followed by the C-terminal region. This latter region, with no function assigned up to now, is most likely involved in the dimerization of B. subtilis RNase Y together with the N-terminal coiled-coil structure.
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8
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Li J, Zhou Y, Lin YW, Tan X. A novel insight into the molecular mechanism of human soluble guanylyl cyclase focused on catalytic domain in living cells. Biochem Biophys Res Commun 2022; 604:51-56. [DOI: 10.1016/j.bbrc.2022.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
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9
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Böhm C, Todorović N, Balasso M, Gourinchas G, Winkler A. The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains. J Mol Biol 2021; 433:167092. [PMID: 34116122 PMCID: PMC7615318 DOI: 10.1016/j.jmb.2021.167092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Protein dynamics play a major role for the catalytic function of enzymes, the interaction of protein complexes or signal integration in regulatory proteins. In the context of multi-domain proteins involved in light-regulation of enzymatic effectors, the central role of conformational dynamics is well established. Light activation of sensory modules is followed by long-range signal transduction to different effectors; rather than domino-style structural rearrangements, a complex interplay of functional elements is required to maintain functionality. One family of such sensor-effector systems are red-light-regulated phytochromes that control diguanylate cyclases involved in cyclic-dimeric-GMP formation. Based on structural and functional studies of one prototypic family member, the central role of the coiled-coil sensor-effector linker was established. Interestingly, subfamilies with different linker lengths feature strongly varying biochemical characteristics. The dynamic interplay of the domains involved, however, is presently not understood. Here we show that the PHY domain dimer interface plays an essential role in signal integration, and that a functional coupling with the coiled-coil linker element is crucial. Chimaeras of two biochemically different family members highlight the phytochrome-spanning helical spine as an essential structural element involved in light-dependent upregulation of enzymatic turnover. However, isolated structural elements can frequently not be assigned to individual characteristics, which further emphasises the importance of global conformational dynamics. Our results provide insights into the intricate processes at play during light signal integration and transduction in these photosensory systems and thus provide additional guidelines for a more directed design of novel sensor-effector combinations with potential applications as optogenetic tools.
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Affiliation(s)
- Cornelia Böhm
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Nikolina Todorović
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Marco Balasso
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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12
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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Chen CY, Lee W, Renhowe PA, Jung J, Montfort WR. Solution structures of the Shewanella woodyi H-NOX protein in the presence and absence of soluble guanylyl cyclase stimulator IWP-051. Protein Sci 2020; 30:448-463. [PMID: 33236796 DOI: 10.1002/pro.4005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
Heme-nitric oxide/oxygen binding (H-NOX) domains bind gaseous ligands for signal transduction in organisms spanning prokaryotic and eukaryotic kingdoms. In the bioluminescent marine bacterium Shewanella woodyi (Sw), H-NOX proteins regulate quorum sensing and biofilm formation. In higher animals, soluble guanylyl cyclase (sGC) binds nitric oxide with an H-NOX domain to induce cyclase activity and regulate vascular tone, wound healing and memory formation. sGC also binds stimulator compounds targeting cardiovascular disease. The molecular details of stimulator binding to sGC remain obscure but involve a binding pocket near an interface between H-NOX and coiled-coil domains. Here, we report the full NMR structure for CO-ligated Sw H-NOX in the presence and absence of stimulator compound IWP-051, and its backbone dynamics. Nonplanar heme geometry was retained using a semi-empirical quantum potential energy approach. Although IWP-051 binding is weak, a single binding conformation was found at the interface of the two H-NOX subdomains, near but not overlapping with sites identified in sGC. Binding leads to rotation of the subdomains and closure of the binding pocket. Backbone dynamics are similar across both domains except for two helix-connecting loops, which display increased dynamics that are further enhanced by compound binding. Structure-based sequence analyses indicate high sequence diversity in the binding pocket, but the pocket itself appears conserved among H-NOX proteins. The largest dynamical loop lies at the interface between Sw H-NOX and its binding partner as well as in the interface with the coiled coil in sGC, suggesting a critical role for the loop in signal transduction.
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Affiliation(s)
- Cheng-Yu Chen
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Chemistry, University of Colorado Denver, Denver, Colorado, USA
| | | | - Joon Jung
- Cyclerion Therapeutics, Cambridge, Massachusetts, USA
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
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14
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The chilling of adenylyl cyclase 9 and its translational potential. Cell Signal 2020; 70:109589. [PMID: 32105777 DOI: 10.1016/j.cellsig.2020.109589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 12/26/2022]
Abstract
A recent break-through paper has revealed for the first time the high-resolution, three-dimensional structure of a mammalian trans-membrane adenylyl cyclase (tmAC) obtained by cryo-electronmicroscopy (cryo-EM). Reporting the structure of adenylyl cyclase 9 (AC9) in complex with activated Gsα, the cryo-EM study revealed that AC9 has three functionally interlinked, yet structurally distinct domains. The array of the twelve transmembrane helices is connected to the cytosolic catalytic core by two helical segments that are stabilized through the formation of a parallel coiled-coil. Surprisingly, in the presence of Gsα, the isoform-specific carboxyl-terminal tail of AC9 occludes the forskolin- as well as the active substrate-sites, resulting in marked autoinhibition of the enzyme. As AC9 has the lowest primary sequence homology with the eight further mammalian tmAC paralogues, it appears to be the best candidate for selective pharmacologic targeting. This is now closer to reality as the structural insight provided by the cryo-EM study indicates that all of the three structural domains are potential targets for bioactive agents. The present paper summarizes for molecular physiologists and pharmacologists what is known about the biological role of AC9, considers the potential modes of physiologic regulation, as well as pharmacologic targeting on the basis of the high-resolution cryo-EM structure. The translational potential of AC9 is considered upon highlighting the current state of genome-wide association screens, and the corresponding experimental evidence. Overall, whilst the high- resolution structure presents unique opportunities for the full understanding of the control of AC9, the data on the biological role of the enzyme and its translational potential are far from complete, and require extensive further study.
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15
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Friebe A, Sandner P, Schmidtko A. cGMP: a unique 2nd messenger molecule - recent developments in cGMP research and development. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2020; 393:287-302. [PMID: 31853617 PMCID: PMC7260148 DOI: 10.1007/s00210-019-01779-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022]
Abstract
Cyclic guanosine monophosphate (cGMP) is a unique second messenger molecule formed in different cell types and tissues. cGMP targets a variety of downstream effector molecules and, thus, elicits a very broad variety of cellular effects. Its production is triggered by stimulation of either soluble guanylyl cyclase (sGC) or particulate guanylyl cyclase (pGC); both enzymes exist in different isoforms. cGMP-induced effects are regulated by endogenous receptor ligands such as nitric oxide (NO) and natriuretic peptides (NPs). Depending on the distribution of sGC and pGC and the formation of ligands, this pathway regulates not only the cardiovascular system but also the kidney, lung, liver, and brain function; in addition, the cGMP pathway is involved in the pathogenesis of fibrosis, inflammation, or neurodegeneration and may also play a role in infectious diseases such as malaria. Moreover, new pharmacological approaches are being developed which target sGC- and pGC-dependent pathways for the treatment of various diseases. Therefore, it is of key interest to understand this pathway from scratch, beginning with the molecular basis of cGMP generation, the structure and function of both guanylyl cyclases and cGMP downstream targets; research efforts also focus on the subsequent signaling cascades, their potential crosstalk, and also the translational and, ultimately, the clinical implications of cGMP modulation. This review tries to summarize the contributions to the "9th International cGMP Conference on cGMP Generators, Effectors and Therapeutic Implications" held in Mainz in 2019. Presented data will be discussed and extended also in light of recent landmark findings and ongoing activities in the field of preclinical and clinical cGMP research.
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Affiliation(s)
- Andreas Friebe
- Institute of Physiology, University of Würzburg, Röntgenring 9, D-97070 Würzburg, Germany
| | - Peter Sandner
- Drug Discovery, Bayer AG, Aprather Weg 18a, D-42096 Wuppertal, Germany and Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | - Achim Schmidtko
- Institute of Pharmacology and Clinical Pharmacy, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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16
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Elgert C, Rühle A, Sandner P, Behrends S. Thermal shift assay: Strengths and weaknesses of the method to investigate the ligand-induced thermostabilization of soluble guanylyl cyclase. J Pharm Biomed Anal 2019; 181:113065. [PMID: 32032919 DOI: 10.1016/j.jpba.2019.113065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 02/01/2023]
Abstract
Thermal shift assay is a fluorescence dye based biochemical method to determine the melting point of a protein. It can be used to investigate the ligand-induced stabilization of proteins and helps to increase the likelihood of crystallization in biological samples. Dimeric proteins like soluble guanylyl cyclase (sGC) have specific structural and functional properties which may pose a challenge in thermal shift measurements. In this paper, thermal shift assay was used to examine ligand-induced thermostabilization of the dimeric heme-containing protein soluble guanylyl cyclase. Adjustment of the parameters buffer solution, pH, protein / dye ratio and protein amount per well yielded a one-phase melting curve of sGC with a sharp transition and high reproducibility. We found that thermal shift measurement is not affected by heme state or heme content of the enzyme preparation. We used the method to investigate the thermostabilization of sGC induced by the heme-mimetic activator drugs cinaciguat, BAY 60-2770 and BR 11257 in combination with non-hydrolyzable nucleotides. Measurements with the dicarboxylic drugs cinaciguat and BAY 60-2770 yielded steep melting curves with high amplitudes. In contrast, in the presence of the monocarboxylic sGC activator BR 11257, melting curves appear flattened in the dye-based measurements. In the present paper, we show that activity-based thermostability measurements are superior to dye-based measurements in detecting the thermostabilizing influence of sGC activator drugs.
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Affiliation(s)
- Christin Elgert
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
| | - Anne Rühle
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
| | | | - Sönke Behrends
- Department of Pharmacology, Toxicology and Clinical Pharmacy, University of Braunschweig - Institute of Technology, Germany.
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17
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Childers KC, Yao XQ, Giannakoulias S, Amason J, Hamelberg D, Garcin ED. Synergistic mutations in soluble guanylyl cyclase (sGC) reveal a key role for interfacial regions in the sGC activation mechanism. J Biol Chem 2019; 294:18451-18464. [PMID: 31645439 PMCID: PMC6885636 DOI: 10.1074/jbc.ra119.011010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/17/2019] [Indexed: 01/20/2023] Open
Abstract
Soluble guanylyl cyclase (sGC) is the main receptor for nitric oxide (NO) and a central component of the NO-cGMP pathway, critical to cardiovascular function. NO binding to the N-terminal sensor domain in sGC enhances the cyclase activity of the C-terminal catalytic domain. Our understanding of the structural elements regulating this signaling cascade is limited, hindering structure-based drug design efforts that target sGC to improve the management of cardiovascular diseases. Conformational changes are thought to propagate the NO-binding signal throughout the entire sGC heterodimer, via its coiled-coil domain, to reorient the catalytic domain into an active conformation. To identify the structural elements involved in this signal transduction cascade, here we optimized a cGMP-based luciferase assay that reports on heterologous sGC activity in Escherichia coli and identified several mutations that activate sGC. These mutations resided in the dorsal flaps, dimer interface, and GTP-binding regions of the catalytic domain. Combinations of mutations from these different elements synergized, resulting in even greater activity and indicating a complex cross-talk among these regions. Molecular dynamics simulations further revealed conformational changes underlying the functional impact of these mutations. We propose that the interfacial residues play a central role in the sGC activation mechanism by coupling the coiled-coil domain to the active site via a series of hot spots. Our results provide new mechanistic insights not only into the molecular pathway for sGC activation but also for other members of the larger nucleotidyl cyclase family.
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Affiliation(s)
- Kenneth C Childers
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965
| | - Sam Giannakoulias
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250
| | - Joshua Amason
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250.
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250.
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Weichsel A, Kievenaar JA, Curry R, Croft JT, Montfort WR. Instability in a coiled-coil signaling helix is conserved for signal transduction in soluble guanylyl cyclase. Protein Sci 2019; 28:1830-1839. [PMID: 31411784 DOI: 10.1002/pro.3707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 01/01/2023]
Abstract
How nitric oxide (NO) activates its primary receptor, α1/β1 soluble guanylyl cyclase (sGC or GC-1), remains unknown. Likewise, how stimulatory compounds enhance sGC activity is poorly understood, hampering development of new treatments for cardiovascular disease. NO binding to ferrous heme near the N-terminus in sGC activates cyclase activity near the C-terminus, yielding cGMP production and physiological response. CO binding can also stimulate sGC, but only weakly in the absence of stimulatory small-molecule compounds, which together lead to full activation. How ligand binding enhances catalysis, however, has yet to be discovered. Here, using a truncated version of sGC from Manduca sexta, we demonstrate that the central coiled-coil domain, the most highly conserved region of the ~150,000 Da protein, not only provides stability to the heterodimer but is also conformationally active in signal transduction. Sequence conservation in the coiled coil includes the expected heptad-repeating pattern for coiled-coil motifs, but also invariant positions that disfavor coiled-coil stability. Full-length coiled coil dampens CO affinity for heme, while shortening of the coiled coil leads to enhanced CO binding. Introducing double mutation αE447L/βE377L, predicted to replace two destabilizing glutamates with leucines, lowers CO binding affinity while increasing overall protein stability. Likewise, introduction of a disulfide bond into the coiled coil results in reduced CO affinity. Taken together, we demonstrate that the heme domain is greatly influenced by coiled-coil conformation, suggesting communication between heme and catalytic domains is through the coiled coil. Highly conserved structural imperfections in the coiled coil provide needed flexibility for signal transduction.
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Affiliation(s)
- Andrzej Weichsel
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Jessica A Kievenaar
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Roslyn Curry
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Jacob T Croft
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - William R Montfort
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
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