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Ngo K, Lopez Mateos D, Han Y, Rouen KC, Ahn SH, Wulff H, Clancy CE, Yarov-Yarovoy V, Vorobyov I. Elucidating molecular mechanisms of protoxin-II state-specific binding to the human NaV1.7 channel. J Gen Physiol 2024; 156:e202313368. [PMID: 38127314 PMCID: PMC10737443 DOI: 10.1085/jgp.202313368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells, and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-II (PTx2) has high selectivity for hNaV1.7 and is a valuable scaffold for designing novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2's residues R22, K26, K27, K28, and W30 with VSD and the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.
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Affiliation(s)
- Khoa Ngo
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
| | - Diego Lopez Mateos
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
| | - Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
| | - Kyle C. Rouen
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis, Davis, CA, USA
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
- Center for Precision Medicine and Data Science, University of California, Davis, Davis, CA, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
- Department of Pharmacology, University of California, Davis, Davis, CA, USA
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Ngo K, Mateos DL, Han Y, Rouen KC, Ahn SH, Wulff H, Clancy CE, Yarov-Yarovoy V, Vorobyov I. Elucidating Molecular Mechanisms of Protoxin-2 State-specific Binding to the Human Na V1.7 Channel. bioRxiv 2023:2023.02.27.530360. [PMID: 36909474 PMCID: PMC10002706 DOI: 10.1101/2023.02.27.530360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and serves as a valuable scaffold to design novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2's residues R22, K26, K27, K28, and W30 with VSD as well as the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.
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Affiliation(s)
- Khoa Ngo
- Biophysics Graduate Group, University of California, Davis
- Department of Physiology and Membrane Biology, University of California, Davis
| | - Diego Lopez Mateos
- Biophysics Graduate Group, University of California, Davis
- Department of Physiology and Membrane Biology, University of California, Davis
| | - Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis
| | - Kyle C. Rouen
- Biophysics Graduate Group, University of California, Davis
- Department of Physiology and Membrane Biology, University of California, Davis
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis
- Department of Pharmacology, University of California, Davis
- Center for Precision Medicine and Data Science, University of California, Davis
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis
- Department of Anesthesiology and Pain Medicine, University of California, Davis
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis
- Department of Pharmacology, University of California, Davis
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Han Y, Dawson JRD, DeMarco KR, Rouen KC, Bekker S, Yarov-Yarovoy V, Clancy CE, Xiang YK, Vorobyov I. Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein. Proc Natl Acad Sci U S A 2023; 120:e2215916120. [PMID: 36853938 PMCID: PMC10013855 DOI: 10.1073/pnas.2215916120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest group of membrane receptors for transmembrane signal transduction. Ligand-induced activation of GPCRs triggers G protein activation followed by various signaling cascades. Understanding the structural and energetic determinants of ligand binding to GPCRs and GPCRs to G proteins is crucial to the design of pharmacological treatments targeting specific conformations of these proteins to precisely control their signaling properties. In this study, we focused on interactions of a prototypical GPCR, beta-2 adrenergic receptor (β2AR), with its endogenous agonist, norepinephrine (NE), and the stimulatory G protein (Gs). Using molecular dynamics (MD) simulations, we demonstrated the stabilization of cationic NE, NE(+), binding to β2AR by Gs protein recruitment, in line with experimental observations. We also captured the partial dissociation of the ligand from β2AR and the conformational interconversions of Gs between closed and open conformations in the NE(+)-β2AR-Gs ternary complex while it is still bound to the receptor. The variation of NE(+) binding poses was found to alter Gs α subunit (Gsα) conformational transitions. Our simulations showed that the interdomain movement and the stacking of Gsα α1 and α5 helices are significant for increasing the distance between the Gsα and β2AR, which may indicate a partial dissociation of Gsα The distance increase commences when Gsα is predominantly in an open state and can be triggered by the intracellular loop 3 (ICL3) of β2AR interacting with Gsα, causing conformational changes of the α5 helix. Our results help explain molecular mechanisms of ligand and GPCR-mediated modulation of G protein activation.
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Affiliation(s)
- Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - John R. D. Dawson
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - Kyle C. Rouen
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Science and Engineering, American River College, Sacramento, CA95841
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA95616
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
| | - Yang K. Xiang
- Department of Pharmacology, University of California, Davis, CA95616
- VA Northern California Health Care System, Mather, CA95655
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
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Rouen KC, Ngo K, Kognole AA, Goel H, Orr A, Kumar A, Emigh Cortez A, Maly J, Yarov-Yarovoy V, MacKerell AD, Vorobyov I. Molecular simulations of state-specific drug interactions with multiple cardiac ion channels to reveal mechanisms of arrhythmogenesis. Biophys J 2023; 122:252a-253a. [PMID: 36783239 DOI: 10.1016/j.bpj.2022.11.1462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Kyle C Rouen
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Khoa Ngo
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Abhishek A Kognole
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Himanshu Goel
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Asuka Orr
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Anmol Kumar
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA
| | - Aiyana Emigh Cortez
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Jan Maly
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | | | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA; Department of Pharmacology, University of California Davis, Davis, CA, USA
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Dawson JR, Rouen KC, Han Y, Hernandez Hernandez G, Yang PC, Bekker B, Clancy CE, Vorobyov I. Modeling state-dependent and stereospecific interactions of beta-blockers with the beta-adrenergic receptor for multiscale modeling. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Han Y, Hernandez-Hernandez G, Yang PC, Dawson JR, DeMarco KR, Rouen KC, Ngo K, Bekker S, Yarov-Yarovoy V, Clancy CE, Vorobyov IV. Multiscale modeling of sympathetic cardiovascular stimulation. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Ngo K, Rouen KC, Dawson JR, Emigh Cortez AM, Lopez Mateos D, Maly J, DeMarco K, Yarov-Yarovoy V, Vorobyov I, Clancy CE. Multi-Scale modeling of state-dependent drug binding to the hERG channel. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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