1
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Wong A, Bi C, Chi W, Hu N, Gehring C. Amino acid motifs for the identification of novel protein interactants. Comput Struct Biotechnol J 2022; 21:326-334. [PMID: 36582434 PMCID: PMC9791077 DOI: 10.1016/j.csbj.2022.12.012] [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: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy
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2
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Jehle A, Garaschuk O. The Interplay between cGMP and Calcium Signaling in Alzheimer's Disease. Int J Mol Sci 2022; 23:7048. [PMID: 35806059 PMCID: PMC9266933 DOI: 10.3390/ijms23137048] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/31/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Cyclic guanosine monophosphate (cGMP) is a ubiquitous second messenger and a key molecule in many important signaling cascades in the body and brain, including phototransduction, olfaction, vasodilation, and functional hyperemia. Additionally, cGMP is involved in long-term potentiation (LTP), a cellular correlate of learning and memory, and recent studies have identified the cGMP-increasing drug Sildenafil as a potential risk modifier in Alzheimer's disease (AD). AD development is accompanied by a net increase in the expression of nitric oxide (NO) synthases but a decreased activity of soluble guanylate cyclases, so the exact sign and extent of AD-mediated imbalance remain unclear. Moreover, human patients and mouse models of the disease present with entangled deregulation of both cGMP and Ca2+ signaling, e.g., causing changes in cGMP-mediated Ca2+ release from the intracellular stores as well as Ca2+-mediated cGMP production. Still, the mechanisms governing such interplay are poorly understood. Here, we review the recent data on mechanisms underlying the brain cGMP signaling and its interconnection with Ca2+ signaling. We also discuss the recent evidence stressing the importance of such interplay for normal brain function as well as in Alzheimer's disease.
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Affiliation(s)
| | - Olga Garaschuk
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, 72074 Tübingen, Germany;
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3
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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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4
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Biswas C, Chu N, Burn TN, Kreiger PA, Behrens EM. Amelioration of Murine Macrophage Activation Syndrome by Monomethyl Fumarate in Both a Heme Oxygenase 1-Dependent and Heme Oxygenase 1-Independent Manner. Arthritis Rheumatol 2021; 73:885-895. [PMID: 33191652 DOI: 10.1002/art.41591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/10/2020] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Macrophage activation syndrome (MAS) is characterized by increased serum levels of ferritin and heme oxygenase 1 (HO-1), and yet no known function is ascribed to these molecules in MAS. Because HO-1 is antiinflammatory, we hypothesized that pharmacologic activation of HO-1 could ameliorate MAS disease activity. Dimethyl fumarate (DMF), a treatment approved by the US Food and Drug Administration for multiple sclerosis, activates HO-1. Monomethyl fumarate (MMF) is the active metabolite of DMF. We therefore evaluated whether MMF could elicit HO-1-dependent therapeutic improvements in a murine model of MAS. METHODS We induced MAS by repeated activation of Toll-like receptor 9 (TLR-9) in wild-type and myeloid-specific HO-1-deficient mice. MMF was administered twice daily to test its efficacy. We assessed organ weights, serum cytokine levels, histologic features of the spleen and liver tissue, and complete blood cell counts to evaluate disease activity. Statistical testing was performed using Student's t-test or by 2-way analysis of variance as appropriate. RESULTS The presence of HO-1 was required for the majority of TLR-9-induced interleukin-10 (IL-10). IL-10 production in TLR-9-induced MAS was found to correlate with the myeloid-HO-1 gene dose in myeloid cells (P < 0.001). MMF treatment increased the levels of HO-1 in splenic macrophages by ~2-fold (P < 0.01), increased serum levels of IL-10 in an HO-1-dependent manner in mice with TLR-9-induced MAS (P < 0.005), and improved multiple disease parameters in both an HO-1-dependent and HO-1-independent manner. CONCLUSION TLR-9-induced production of IL-10 is regulated by HO-1 activity both in vitro and in vivo. Therapeutic enhancement of the HO-1/IL-10 axis in a murine model was able to significantly ameliorate MAS disease activity. These results suggest that HO-1 may be viable as a MAS therapeutic target, and treatment with DMF and MMF should be considered in future investigations of MAS therapy.
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Affiliation(s)
- Chhanda Biswas
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Niansheng Chu
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Thomas N Burn
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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5
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Akanji MA, Adeyanju AA, Rotimi D, Adeyemi OS. Nitric Oxide Balance in Health and Diseases: Implications for New Treatment Strategies. Open Biochem J 2020. [DOI: 10.2174/1874091x02014010025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nitric Oxide (NO) is an essential signaling molecule with diverse physiological functions in humans. The steady-state concentration and site of production of nitric oxide determine its effects in biological systems. The human cells are exposed to both beneficial and harmful effects of NO. These dual effects of NO could depend on its local concentration in the cells. Additionally, the rate of synthesis, translocation, direct interaction with other molecules, and signals contribute to the biochemical and physiological effects of NO. In this review, the biochemical and physiological role of NO, particularly in health and disease as touching on cell signaling, oxidative stress, immunity, as well as cardiovascular protection amongst others, is focused on. Therefore, this review objectively discusses the dual functionality of NO in living cells.
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6
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Rozza AM, Menyhárd DK, Oláh J. Gas Sensing by Bacterial H-NOX Proteins: An MD Study. Molecules 2020; 25:molecules25122882. [PMID: 32585836 PMCID: PMC7356049 DOI: 10.3390/molecules25122882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
Gas sensing is crucial for both prokaryotes and eukaryotes and is primarily performed by heme-based sensors, including H-NOX domains. These systems may provide a new, alternative mode for transporting gaseous molecules in higher organisms, but for the development of such systems, a detailed understanding of the ligand-binding properties is required. Here, we focused on ligand migration within the protein matrix: we performed molecular dynamics simulations on three bacterial (Ka, Ns and Cs) H-NOX proteins and studied the kinetics of CO, NO and O2 diffusion. We compared the response of the protein structure to the presence of ligands, diffusion rate constants, tunnel systems and storage pockets. We found that the rate constant for diffusion decreases in the O2 > NO > CO order in all proteins, and in the Ns > Ks > Cs order if single-gas is considered. Competition between gases seems to seriously influence the residential time of ligands spent in the distal pocket. The channel system is profoundly determined by the overall fold, but the sidechain pattern has a significant role in blocking certain channels by hydrophobic interactions between bulky groups, cation-π interactions or hydrogen bonding triads. The majority of storage pockets are determined by local sidechain composition, although certain functional cavities, such as the distal and proximal pockets are found in all systems. A major guideline for the design of gas transport systems is the need to chemically bind the gas molecule to the protein, possibly joining several proteins with several heme groups together.
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Affiliation(s)
- Ahmed M. Rozza
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology & MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Correspondence: (D.K.M.); (J.O.)
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology, Budapest Szent Gellért tér 4, H-1111 Budapest, Hungary;
- Correspondence: (D.K.M.); (J.O.)
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7
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Khalid RR, Maryam A, Sezerman OU, Mylonas E, Siddiqi AR, Kokkinidis M. Probing the Structural Dynamics of the Catalytic Domain of Human Soluble Guanylate Cyclase. Sci Rep 2020; 10:9488. [PMID: 32528025 PMCID: PMC7289801 DOI: 10.1038/s41598-020-66310-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 05/04/2020] [Indexed: 01/25/2023] Open
Abstract
In the nitric oxide (NO) signaling pathway, human soluble guanylate cyclase (hsGC) synthesizes cyclic guanosine monophosphate (cGMP); responsible for the regulation of cGMP-specific protein kinases (PKGs) and phosphodiesterases (PDEs). The crystal structure of the inactive hsGC cyclase dimer is known, but there is still a lack of information regarding the substrate-specific internal motions that are essential for the catalytic mechanism of the hsGC. In the current study, the hsGC cyclase heterodimer complexed with guanosine triphosphate (GTP) and cGMP was subjected to molecular dynamics simulations, to investigate the conformational dynamics that have functional implications on the catalytic activity of hsGC. Results revealed that in the GTP-bound complex of the hsGC heterodimer, helix 1 of subunit α (α:h1) moves slightly inwards and comes close to helix 4 of subunit β (β:h4). This conformational change brings loop 2 of subunit β (β:L2) closer to helix 2 of subunit α (α:h2). Likewise, loop 2 of subunit α (α:L2) comes closer to helix 2 of subunit β (β:h2). These structural events stabilize and lock GTP within the closed pocket for cyclization. In the cGMP-bound complex, α:L2 detaches from β:h2 and establishes interactions with β:L2, which results in the loss of global structure compactness. Furthermore, with the release of pyrophosphate, the interaction between α:h1 and β:L2 weakens, abolishing the tight packing of the binding pocket. This study discusses the conformational changes induced by the binding of GTP and cGMP to the hsGC catalytic domain, valuable in designing new therapeutic strategies for the treatment of cardiovascular diseases.
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Affiliation(s)
- Rana Rehan Khalid
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.,Department of Biology, University of Crete, 70013, Heraklion, Greece.,Department of Biostatistics and Medical Informatics, Acibadem M. A. A. University, Istanbul, 34752, Turkey
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.,Department of Pharmaceutical Chemistry, Biruni Universitesi, Istanbul, 34010, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem M. A. A. University, Istanbul, 34752, Turkey
| | - Efstratios Mylonas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013, Heraklion, Greece
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.
| | - Michael Kokkinidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece. .,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas (IMBB-FORTH), 70013, Heraklion, Greece.
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8
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Dai Y, Sweeny EA, Schlanger S, Ghosh A, Stuehr DJ. GAPDH delivers heme to soluble guanylyl cyclase. J Biol Chem 2020; 295:8145-8154. [PMID: 32358060 DOI: 10.1074/jbc.ra120.013802] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/28/2020] [Indexed: 12/17/2022] Open
Abstract
Soluble guanylyl cyclase (sGC) is a key component of NO-cGMP signaling in mammals. Although heme must bind in the sGC β1 subunit (sGCβ) for sGC to function, how heme is delivered to sGCβ remains unknown. Given that GAPDH displays properties of a heme chaperone for inducible NO synthase, here we investigated whether heme delivery to apo-sGCβ involves GAPDH. We utilized an sGCβ reporter construct, tetra-Cys sGCβ, whose heme insertion can be followed by fluorescence quenching in live cells, assessed how lowering cell GAPDH expression impacts heme delivery, and examined whether expressing WT GAPDH or a GAPDH variant defective in heme binding recovers heme delivery. We also studied interaction between GAPDH and sGCβ in cells and their complex formation and potential heme transfer using purified proteins. We found that heme delivery to apo-sGCβ correlates with cellular GAPDH expression levels and depends on the ability of GAPDH to bind intracellular heme, that apo-sGCβ associates with GAPDH in cells and dissociates when heme binds sGCβ, and that the purified GAPDH-heme complex binds to apo-sGCβ and transfers its heme to sGCβ. On the basis of these results, we propose a model where GAPDH obtains mitochondrial heme and then forms a complex with apo-sGCβ to accomplish heme delivery to sGCβ. Our findings illuminate a critical step in sGC maturation and uncover an additional mechanism that regulates its activity in health and disease.
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Affiliation(s)
- Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Elizabeth A Sweeny
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Simon Schlanger
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Arnab Ghosh
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, Cleveland, Ohio, USA
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9
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Kadlec M, Ros-Santaella JL, Pintus E. The Roles of NO and H 2S in Sperm Biology: Recent Advances and New Perspectives. Int J Mol Sci 2020; 21:E2174. [PMID: 32245265 PMCID: PMC7139502 DOI: 10.3390/ijms21062174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 01/24/2023] Open
Abstract
After being historically considered as noxious agents, nitric oxide (NO) and hydrogen sulfide (H2S) are now listed as gasotransmitters, gaseous molecules that play a key role in a variety of cellular functions. Both NO and H2S are endogenously produced, enzymatically or non-enzymatically, and interact with each other in a range of cells and tissues. In spite of the great advances achieved in recent decades in other biological systems, knowledge about H2S function and interactions with NO in sperm biology is in its infancy. Here, we aim to provide an update on the importance of these molecules in the physiology of the male gamete. Special emphasis is given to the most recent advances in the metabolism, mechanisms of action, and effects (both physiological and pathophysiological) of these gasotransmitters. This manuscript also illustrates the physiological implications of NO and H2S observed in other cell types, which might be important for sperm function. The relevance of these gasotransmitters to several signaling pathways within sperm cells highlights their potential use for the improvement and successful application of assisted reproductive technologies.
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Affiliation(s)
| | | | - Eliana Pintus
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha 6-Suchdol, Czech Republic; (M.K.); (J.L.R.-S.)
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10
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Dai Y, Schlanger S, Haque MM, Misra S, Stuehr DJ. Heat shock protein 90 regulates soluble guanylyl cyclase maturation by a dual mechanism. J Biol Chem 2019; 294:12880-12891. [PMID: 31311859 DOI: 10.1074/jbc.ra119.009016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/28/2019] [Indexed: 01/07/2023] Open
Abstract
The enzyme soluble guanylyl cyclase (sGC) is a heterodimer composed of an α subunit and a heme-containing β subunit. It participates in signaling by generating cGMP in response to nitric oxide (NO). Heme insertion into the β1 subunit of sGC (sGCβ) is critical for function, and heat shock protein 90 (HSP90) associates with heme-free sGCβ (apo-sGCβ) to drive its heme insertion. Here, we tested the accuracy and relevance of a modeled apo-sGCβ-HSP90 complex by constructing sGCβ variants predicted to have an impaired interaction with HSP90. Using site-directed mutagenesis, purified recombinant proteins, mammalian cell expression, and fluorescence approaches, we found that (i) three regions in apo-sGCβ predicted by the model mediate direct complex formation with HSP90 both in vitro and in mammalian cells; (ii) such HSP90 complex formation directly correlates with the extent of heme insertion into apo-sGCβ and with cyclase activity; and (iii) apo-sGCβ mutants possessing an HSP90-binding defect instead bind to sGCα in cells and form inactive, heme-free sGC heterodimers. Our findings uncover the molecular features of the cellular apo-sGCβ-HSP90 complex and reveal its dual importance in enabling heme insertion while preventing inactive heterodimer formation during sGC maturation.
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Affiliation(s)
- Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Simon Schlanger
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Mohammad Mahfuzul Haque
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| | - Saurav Misra
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506
| | - Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195.
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11
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Khalid RR, Maryam A, Fadouloglou VE, Siddiqi AR, Zhang Y. Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding. J Mol Graph Model 2019; 90:109-119. [PMID: 31055154 PMCID: PMC7956049 DOI: 10.1016/j.jmgm.2019.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/05/2019] [Accepted: 04/17/2019] [Indexed: 01/19/2023]
Abstract
The human soluble Guanylate Cyclase (hsGC) is a heterodimeric heme-containing enzyme which regulates many important physiological processes. In eukaryotes, hsGC is the only known receptor for nitric oxide (NO) signaling. Improper NO signaling results in various disease conditions such as neurodegeneration, hypertension, stroke and erectile dysfunction. To understand the mechanisms of these diseases, structure determination of the hsGC dimer complex is crucial. However, so far all the attempts for the experimental structure determination of the protein were unsuccessful. The current study explores the possibility to model the quaternary structure of hsGC using a hybrid approach that combines state-of-the-art protein structure prediction tools with cryo-EM experimental data. The resultant 3D model shows close consistency with structural and functional insights extracted from biochemistry experiment data. Overall, the atomic-level complex structure determination of hsGC helps to unveil the inter-domain communication upon NO binding, which should be of important usefulness for elucidating the biological function of this important enzyme and for developing new treatments against the hsGC associated human diseases.
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Affiliation(s)
- Rana Rehan Khalid
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan; Department of Biostatistics and Medical Informatics, Acibadem Universitesi, Istanbul, 34752, Turkey; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA.
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan; Department of Pharmaceutical Chemistry, Biruni Universitesi, Istanbul, 34010, Turkey.
| | - Vasiliki E Fadouloglou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA.
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12
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Sömmer A, Behrends S. Methods to investigate structure and activation dynamics of GC-1/GC-2. Nitric Oxide 2018; 78:S1089-8603(17)30348-8. [PMID: 29705716 DOI: 10.1016/j.niox.2018.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/19/2018] [Accepted: 04/23/2018] [Indexed: 12/18/2022]
Abstract
Soluble guanylyl cyclase (sGC) is a heterodimeric enzyme consisting of one α and one β subunit. The α1β1 (GC-1) and α2β1 (GC-2) heterodimers are important for NO signaling in humans and catalyse the conversion from GTP to cGMP. Each sGC subunit consists of four domains. Several crystal structures of the isolated domains are available. However, crystals of full-length sGC have failed to materialise. In consequence, the detailed three dimensional structure of sGC remains unknown to date. Different techniques including stopped-flow spectroscopy, Förster-resonance energy transfer, direct fluorescence, analytical ultracentrifugation, chemical cross-linking, small-angle X-ray scattering, electron microscopy, hydrogen-deuterium exchange and protein thermal shift assays, were used to collect indirect information. Taken together, this circumstantial evidence from different groups brings forth a plausible model of sGC domain arrangement, spatial orientation and dynamic rearrangement upon activation. For analysis of the active conformation the stable binding mode of sGC activators has a significant methodological advantage over the transient, elusive, complex and highly concentration dependent effects of NO in many applications. The methods used and the results obtained are reviewed and discussed in this article.
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Affiliation(s)
- Anne Sömmer
- 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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13
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Childers KC, Garcin ED. Structure/function of the soluble guanylyl cyclase catalytic domain. Nitric Oxide 2018; 77:53-64. [PMID: 29702251 PMCID: PMC6005667 DOI: 10.1016/j.niox.2018.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
Abstract
Soluble guanylyl cyclase (GC-1) is the primary receptor of nitric oxide (NO) in smooth muscle cells and maintains vascular function by inducing vasorelaxation in nearby blood vessels. GC-1 converts guanosine 5′-triphosphate (GTP) into cyclic guanosine 3′,5′-monophosphate (cGMP), which acts as a second messenger to improve blood flow. While much work has been done to characterize this pathway, we lack a mechanistic understanding of how NO binding to the heme domain leads to a large increase in activity at the C-terminal catalytic domain. Recent structural evidence and activity measurements from multiple groups have revealed a low-activity cyclase domain that requires additional GC-1 domains to promote a catalytically-competent conformation. How the catalytic domain structurally transitions into the active conformation requires further characterization. This review focuses on structure/function studies of the GC-1 catalytic domain and recent advances various groups have made in understanding how catalytic activity is regulated including small molecules interactions, Cys-S-NO modifications and potential interactions with the NO-sensor domain and other proteins.
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Affiliation(s)
- Kenneth C Childers
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA
| | - Elsa D Garcin
- University of Maryland Baltimore County, Department of Chemistry and Biochemistry, Baltimore, USA.
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14
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Patent highlights August-September 2017. Pharm Pat Anal 2017; 7:7-14. [PMID: 29219751 DOI: 10.4155/ppa-2017-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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