1
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Nguyen PT, Harris BJ, Mateos DL, González AH, Murray AM, Yarov-Yarovoy V. Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold. Channels (Austin) 2024; 18:2325032. [PMID: 38445990 PMCID: PMC10936637 DOI: 10.1080/19336950.2024.2325032] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/14/2024] [Indexed: 03/07/2024] Open
Abstract
Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.
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Affiliation(s)
- Phuong Tran Nguyen
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
| | - Brandon John Harris
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | - Adriana Hernández González
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Biophysics Graduate Group, University of California School of Medicine, Davis, CA, USA
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA, USA
- Department of Anesthesiology and Pain Medicine, University of California School of Medicine, Davis, CA, USA
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2
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Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe JG. H3K4me1 recruits DNA repair proteins in plants. Plant Cell 2024:koae089. [PMID: 38531669 DOI: 10.1093/plcell/koae089] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
Abstract
DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined two proteins which, in plants, contain Tudor histone reader domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved in homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch repair protein. The MSH6 Tudor domain of Arabidopsis (Arabidopsis thaliana) binds to H3K4me1 as previously demonstrated for PDS5C, which localizes to H3K4me1-rich gene bodies and essential genes. Mutations revealed by ultradeep sequencing of wild-type and msh6 knockout lines in Arabidopsis show that functional MSH6 is critical for the reduced rate of single base substitution mutations in gene bodies and H3K4me1-rich regions. We explored the breadth of these mechanisms among plants by examining a large rice (Oryza sativa) mutation dataset. H3K4me1-associated hypomutation is conserved in rice as are the H3K4me1 binding residues of MSH6 and PDS5C Tudor domains. Recruitment of DNA repair proteins by H3K4me1 in plants reveals convergent, but distinct, epigenome-recruited DNA repair mechanisms from those well described in humans. The emergent model of H3K4me1-recruited repair in plants is consistent with evolutionary theory regarding mutation modifier systems and offers mechanistic insight into intragenomic mutation rate variation in plants.
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Affiliation(s)
- Daniela Quiroz
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA 95616
| | - Satoyo Oya
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Diego Lopez-Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA 95616
- Biophysics Graduate Group, University of California Davis, Davis, California
| | - Kehan Zhao
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
- Plant Biology Graduate Group, University of California Davis, Davis, CA, USA 95616
| | - Alice Pierce
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
- Plant Biology Graduate Group, University of California Davis, Davis, CA, USA 95616
| | - Lissandro Ortega
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
| | - Alissza Ali
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
| | | | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA 95616
- Biophysics Graduate Group, University of California Davis, Davis, California
| | - Sae Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA 95616
- Plant Biology Graduate Group, University of California Davis, Davis, CA, USA 95616
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3
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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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4
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Yang PC, Jeng MT, Yarov-Yarovoy V, Santana LF, Vorobyov I, Clancy CE. Toward Digital Twin Technology for Precision Pharmacology. JACC Clin Electrophysiol 2024; 10:359-364. [PMID: 38069976 DOI: 10.1016/j.jacep.2023.10.024] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 03/01/2024]
Abstract
The authors demonstrate the feasibility of technological innovation for personalized medicine in the context of drug-induced arrhythmia. The authors use atomistic-scale structural models to predict rates of drug interaction with ion channels and make predictions of their effects in digital twins of induced pluripotent stem cell-derived cardiac myocytes. The authors construct a simplified multilayer, 1-dimensional ring model with sufficient path length to enable the prediction of arrhythmogenic dispersion of repolarization. Finally, the authors validate the computational pipeline prediction of drug effects with data and quantify drug-induced propensity to repolarization abnormalities in cardiac tissue. The technology is high throughput, computationally efficient, and low cost toward personalized pharmacologic prediction.
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Affiliation(s)
- Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Anesthesiology and Pain Medicine, University of California-Davis, Davis, California, USA
| | - L Fernando Santana
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Pharmacology, University of California-Davis, Davis, California, USA.
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, California, USA; Department of Pharmacology, University of California-Davis, Davis, California, USA; Center for Precision Medicine, University of California-Davis, Davis, California, USA.
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5
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Ngo K, Yarov-Yarovoy V, Clancy CE, Vorobyov I. Harnessing AlphaFold to reveal state secrets: Prediction of hERG closed and inactivated states. bioRxiv 2024:2024.01.27.577468. [PMID: 38352360 PMCID: PMC10862728 DOI: 10.1101/2024.01.27.577468] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11.1 (hERG), comprising the primary cardiac repolarizing current, IKr. hERG is a notorious drug anti-target against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. However, the structural details of multiple conformational states have remained elusive. Here, we guided AlphaFold2 to predict plausible hERG inactivated and closed conformations, obtaining results consistent with myriad available experimental data. Drug docking simulations demonstrated hERG state-specific drug interactions aligning well with experimental results, revealing that most drugs bind more effectively in the inactivated state and are trapped in the closed state. Molecular dynamics simulations demonstrated ion conduction that aligned with earlier studies. Finally, we identified key molecular determinants of state transitions by analyzing interaction networks across closed, open, and inactivated states in agreement with earlier mutagenesis studies. Here, we demonstrate a readily generalizable application of AlphaFold2 as a novel method to predict discrete protein conformations and novel linkages from structure to function.
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Affiliation(s)
- Khoa Ngo
- Biophysics Graduate Group, University of California, Davis, CA
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
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6
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Emigh Cortez AM, DeMarco KR, Furutani K, Bekker S, Sack JT, Wulff H, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of hERG channel-drug interactions using Rosetta. Front Pharmacol 2023; 14:1244166. [PMID: 38035013 PMCID: PMC10682396 DOI: 10.3389/fphar.2023.1244166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome, which predisposes individuals to potentially deadly arrhythmias. However, not all hERG-blocking drugs are proarrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type and mutant variants (Y652A, F656A, and Y652A/F656 A) and a closed-state wild-type channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug-channel interactions that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.
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Affiliation(s)
- Aiyana M. Emigh Cortez
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- American River College, Sacramento, CA, United States
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
- Center for Precision Medicine and Data Sciences, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
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7
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Zachos NC, Vaughan H, Sarker R, Est-Witte S, Chakraborty M, Baetz NW, Yu H, Yarov-Yarovoy V, McNamara G, Green JJ, Tse CM, Donowitz M. A Novel Peptide Prevents Enterotoxin- and Inflammation-Induced Intestinal Fluid Secretion by Stimulating Sodium-Hydrogen Exchanger 3 Activity. Gastroenterology 2023; 165:986-998.e11. [PMID: 37429363 DOI: 10.1053/j.gastro.2023.06.028] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND & AIMS Acute diarrheal diseases are the second most common cause of infant mortality in developing countries. This is contributed to by lack of effective drug therapy that shortens the duration or lessens the volume of diarrhea. The epithelial brush border sodium (Na+)/hydrogen (H+) exchanger 3 (NHE3) accounts for a major component of intestinal Na+ absorption and is inhibited in most diarrheas. Because increased intestinal Na+ absorption can rehydrate patients with diarrhea, NHE3 has been suggested as a potential druggable target for drug therapy for diarrhea. METHODS A peptide (sodium-hydrogen exchanger 3 stimulatory peptide [N3SP]) was synthesized to mimic the part of the NHE3 C-terminus that forms a multiprotein complex that inhibits NHE3 activity. The effect of N3SP on NHE3 activity was evaluated in NHE3-transfected fibroblasts null for other plasma membrane NHEs, a human colon cancer cell line that models intestinal absorptive enterocytes (Caco-2/BBe), human enteroids, and mouse intestine in vitro and in vivo. N3SP was delivered into cells via a hydrophobic fluorescent maleimide or nanoparticles. RESULTS N3SP uptake stimulated NHE3 activity at nmol/L concentrations under basal conditions and partially reversed the reduced NHE3 activity caused by elevated adenosine 3',5'-cyclic monophosphate, guanosine 3',5'-cyclic monophosphate, and Ca2+ in cell lines and in in vitro mouse intestine. N3SP also stimulated intestinal fluid absorption in the mouse small intestine in vivo and prevented cholera toxin-, Escherichia coli heat-stable enterotoxin-, and cluster of differentiation 3 inflammation-induced fluid secretion in a live mouse intestinal loop model. CONCLUSIONS These findings suggest pharmacologic stimulation of NHE3 activity as an efficacious approach for the treatment of moderate/severe diarrheal diseases.
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Affiliation(s)
- Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Hannah Vaughan
- Translational Tissue Engineering Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rafiquel Sarker
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Savannah Est-Witte
- Translational Tissue Engineering Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Molee Chakraborty
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nicholas W Baetz
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hongzhe Yu
- Translational Tissue Engineering Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, California; Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, California
| | - George McNamara
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jordan J Green
- Translational Tissue Engineering Center, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chung-Ming Tse
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mark Donowitz
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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8
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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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9
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Li S, Nguyen PT, Vu S, Yarov-Yarovoy V, Zheng J. Opening of capsaicin receptor TRPV1 is stabilized equally by its four subunits. J Biol Chem 2023; 299:104828. [PMID: 37196769 PMCID: PMC10318505 DOI: 10.1016/j.jbc.2023.104828] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023] Open
Abstract
Capsaicin receptor TRPV1 is a nociceptor for vanilloid molecules, such as capsaicin and resiniferatoxin (RTX). Even though cryo-EM structures of TRPV1 in complex with these molecules are available, how their binding energetically favors the open conformation is not known. Here, we report an approach to control the number of bound RTX molecules (0-4) in functional rat TRPV1. The approach allowed direct measurements of each of the intermediate open states under equilibrium conditions at both macroscopic and single-molecule levels. We found that RTX binding to each of the four subunits contributes virtually the same activation energy, which we estimated to be 1.70 to 1.86 kcal/mol and found to arise predominately from destabilizing the closed conformation. We further showed that sequential bindings of RTX increase open probability without altering single-channel conductance, confirming that there is likely a single open-pore conformation for TRPV1 activated by RTX.
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Affiliation(s)
- Shisheng Li
- Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Phuong T Nguyen
- Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Simon Vu
- Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Jie Zheng
- Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, Davis, California, USA.
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10
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Ng LC, Harris BJ, Larmore M, Ta MC, Vien TN, Tokars VL, Yarov-Yarovoy V, DeCaen PG. Energetic landscape of polycystin channel gating. EMBO Rep 2023:e56783. [PMID: 37158562 DOI: 10.15252/embr.202356783] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Members of the polycystin family (PKD2 and PKD2L1) of transient receptor potential (TRP) channels conduct Ca2+ and depolarizing monovalent cations. Variants in PKD2 cause autosomal dominant polycystic kidney disease (ADPKD) in humans, whereas loss of PKD2L1 expression causes seizure susceptibility in mice. Understanding structural and functional regulation of these channels will provide the basis for interpreting their molecular dysregulation in disease states. However, the complete structures of polycystins are unresolved, as are the conformational changes regulating their conductive states. To provide a holistic understanding of the polycystin gating cycle, we use computational prediction tools to model missing PKD2L1 structural motifs and evaluate more than 150 mutations in an unbiased mutagenic functional screen of the entire pore module. Our results provide an energetic landscape of the polycystin pore, which enumerates gating sensitive sites and interactions required for opening, inactivation, and subsequent desensitization. These findings identify the external pore helices and specific cross-domain interactions as critical structural regulators controlling the polycystin ion channel conductive and nonconductive states.
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Affiliation(s)
- Leo Ct Ng
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brandon J Harris
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, USA
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Megan Larmore
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - My C Ta
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Thuy N Vien
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Valerie L Tokars
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 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
| | - Paul G DeCaen
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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11
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Kimball IH, Nguyen PT, Olivera BM, Sack JT, Yarov-Yarovoy V. Molecular determinants of μ-conotoxin KIIIA interaction with the human voltage-gated sodium channel NaV1.7. Front Pharmacol 2023; 14:1156855. [PMID: 37007002 PMCID: PMC10060530 DOI: 10.3389/fphar.2023.1156855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The voltage-gated sodium (NaV) channel subtype NaV1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between μ-Conotoxin KIIIA (KIIIA) and the human NaV1.7 channel (hNaV1.7). We developed a structural model of hNaV1.7 using Rosetta computational modeling and performed in silico docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNaV1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNaV1.7 model and the cryo-EM structure of KIIIA-hNaV1.2 revealed key similarities and differences between NaV channel subtypes with potential implications for the molecular mechanism of toxin block. The accuracy of our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations, suggests that Rosetta structural predictions will be useful for rational design of novel biologics targeting specific NaV channels.
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Affiliation(s)
- Ian H. Kimball
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Phuong T. Nguyen
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | | | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
- *Correspondence: Jon T. Sack, ; Vladimir Yarov-Yarovoy,
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
- *Correspondence: Jon T. Sack, ; Vladimir Yarov-Yarovoy,
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12
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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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13
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Ngo K, Lopez Mateos D, Han Y, Yarov-Yarovoy V, Clancy CE, Vorobyov IV. Simulations reveal molecular mechanisms of high affinity and selective binding of the tarantula venom protoxin-2 to the human Na V1.7 channel. Biophys J 2023; 122:179a. [PMID: 36782844 DOI: 10.1016/j.bpj.2022.11.1109] [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)
- Khoa Ngo
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Diego Lopez Mateos
- 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
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, 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
| | - Igor V 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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14
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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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15
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Han Y, Dawson JRD, DeMarco K, Rouen K, Ngo K, Bekker B, Yarov-Yarovoy V, Clancy CE, Xiang YK, Vorobyov IV. Elucidation of a dynamic interplay between guanine nucleotide and the ternary complex of a beta-adrenergic receptor, its agonist and stimulatory G protein. Biophys J 2023; 122:329a. [PMID: 36783658 DOI: 10.1016/j.bpj.2022.11.1839] [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)
- Yanxiao Han
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - John R D Dawson
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kevin DeMarco
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kyle Rouen
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Khoa Ngo
- University of California Davis, Davis, CA, USA
| | | | | | - Colleen E Clancy
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Yang K Xiang
- Pharmacology, University of California Davis, Davis, CA, USA
| | - Igor V Vorobyov
- Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
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16
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Ngo K, Rouen K, Dawson JRD, DeMarco K, Emigh Cortez AM, Maly J, Lopez Mateos D, Yarov-Yarovoy V, Clancy CE, Vorobyov IV. Computational assessment of molecular mechanisms underlying hERG K + channel conduction and affinity for drug binding. Biophys J 2023; 122:179a. [PMID: 36782843 DOI: 10.1016/j.bpj.2022.11.1108] [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)
- Khoa Ngo
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kyle Rouen
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - John R D Dawson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Kevin DeMarco
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Aiyana M 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
| | - Diego Lopez Mateos
- 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
| | - 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
| | - Igor V 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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17
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Nguyen PT, Nguyen HM, Wagner KM, Stewart R, Singh V, Thapa P, Tuan Ton A, Kondo RP, Ghetti A, Pennington MW, Hammock B, Griffith TN, Sack JT, Wulff H, Yarov-Yarovoy V. Computational design of peptides to target Na v1.7 channel with high potency and selectivity for the treatment of pain. Biophys J 2023; 122:309a. [PMID: 36783550 DOI: 10.1016/j.bpj.2022.11.1739] [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)
- Phuong T Nguyen
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Hai M Nguyen
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Karen M Wagner
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA; Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Robert Stewart
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Parashar Thapa
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | | | | | | | | | - Bruce Hammock
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA; Comprehensive Cancer Center, University of California Davis, Davis, CA, USA
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Jon T Sack
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA, USA
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18
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Harris BJ, Lopez Mateos D, Hareland G, Yarov-Yarovoy V. Using rosetta and alphafold to assess Jingzhaotoxin-III binding to hNa v1.5 and hK v2.1. Biophys J 2023; 122:102a. [PMID: 36782442 DOI: 10.1016/j.bpj.2022.11.737] [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)
- Brandon J Harris
- Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Diego Lopez Mateos
- Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Geir Hareland
- Biophysics Graduate Group, University of California Davis, Davis, CA, USA
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19
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Mateos DL, Yarov-Yarovoy V. Structural modeling of peptide toxin-ion channel interactions using RosettaDock. Proteins 2023. [PMID: 36729043 DOI: 10.1002/prot.26474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/09/2022] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Voltage-gated ion channels play essential physiological roles in action potential generation and propagation. Peptidic toxins from animal venoms target ion channels and provide useful scaffolds for the rational design of novel channel modulators with enhanced potency and subtype selectivity. Despite recent progress in obtaining experimental structures of peptide toxin-ion channel complexes, structural determination of peptide toxins bound to ion channels in physiologically important states remains challenging. Here we describe an application of RosettaDock approach to the structural modeling of peptide toxins interactions with ion channels. We tested this approach on 10 structures of peptide toxin-ion channel complexes and demonstrated that it can sample near-native structures in all tested cases. Our approach will be useful for improving the understanding of the molecular mechanism of natural peptide toxin modulation of ion channel gating and for the structural modeling of novel peptide-based ion channel modulators.
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Affiliation(s)
- Diego Lopez Mateos
- Department of Physiology and Membrane Biology, University of California Davis, Davis, California, USA.,Biophysics Graduate Group, University of California Davis, Davis, California, USA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, California, USA.,Biophysics Graduate Group, University of California Davis, Davis, California, USA.,Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, California, USA
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20
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Li S, Nguyen PT, Vu S, Yarov-Yarovoy V, Zheng J. TRPV1 Opening is Stabilized Equally by Its Four Subunits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525787. [PMID: 36747729 PMCID: PMC9900918 DOI: 10.1101/2023.01.26.525787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Capsaicin receptor TRPV1 is a nociceptor for vanilloid molecules such as capsaicin and resiniferatoxin (RTX). Even though cryo-EM structures of TRPV1 in complex with these molecules are available, how their binding energetically favors the open conformation is not known. Here we report an approach to control the number of bound RTX molecules (0-to-4) in functional mouse TRPV1. The approach allowed direct measurements of each of the intermediate open states under equilibrium conditions at both macroscopic and single-molecule levels. We found that RTX binding to each of the four subunits contributes virtually the same activation energy, which we estimated to be 1.86 kcal/mol and found to arise predominately from destabilizing the closed conformation. We further showed that sequential bindings of RTX increase open probability without altering single-channel conductance, confirming that there is likely a single open-pore conformation for TRPV1 activated by RTX.
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21
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Ren L, Thai PN, Gopireddy RR, Timofeyev V, Ledford HA, Woltz RL, Park S, Puglisi JL, Moreno CM, Santana LF, Conti AC, Kotlikoff MI, Xiang YK, Yarov-Yarovoy V, Zaccolo M, Zhang XD, Yamoah EN, Navedo MF, Chiamvimonvat N. Adenylyl cyclase isoform 1 contributes to sinoatrial node automaticity via functional microdomains. JCI Insight 2022; 7:e162602. [PMID: 36509290 PMCID: PMC9746826 DOI: 10.1172/jci.insight.162602] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Sinoatrial node (SAN) cells are the heart's primary pacemaker. Their activity is tightly regulated by β-adrenergic receptor (β-AR) signaling. Adenylyl cyclase (AC) is a key enzyme in the β-AR pathway that catalyzes the production of cAMP. There are current gaps in our knowledge regarding the dominant AC isoforms and the specific roles of Ca2+-activated ACs in the SAN. The current study tests the hypothesis that distinct AC isoforms are preferentially expressed in the SAN and compartmentalize within microdomains to orchestrate heart rate regulation during β-AR signaling. In contrast to atrial and ventricular myocytes, SAN cells express a diverse repertoire of ACs, with ACI as the predominant Ca2+-activated isoform. Although ACI-KO (ACI-/-) mice exhibit normal cardiac systolic or diastolic function, they experience SAN dysfunction. Similarly, SAN-specific CRISPR/Cas9-mediated gene silencing of ACI results in sinus node dysfunction. Mechanistically, hyperpolarization-activated cyclic nucleotide-gated 4 (HCN4) channels form functional microdomains almost exclusively with ACI, while ryanodine receptor and L-type Ca2+ channels likely compartmentalize with ACI and other AC isoforms. In contrast, there were no significant differences in T-type Ca2+ and Na+ currents at baseline or after β-AR stimulation between WT and ACI-/- SAN cells. Due to its central characteristic feature as a Ca2+-activated isoform, ACI plays a unique role in sustaining the rise of local cAMP and heart rates during β-AR stimulation. The findings provide insights into the critical roles of the Ca2+-activated isoform of AC in sustaining SAN automaticity that is distinct from contractile cardiomyocytes.
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Affiliation(s)
- Lu Ren
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Phung N. Thai
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
- Department of Veteran Affairs, Northern California Health Care System, Sacramento, California, USA
| | | | - Valeriy Timofeyev
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
| | - Hannah A. Ledford
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
| | - Ryan L. Woltz
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
- Department of Veteran Affairs, Northern California Health Care System, Sacramento, California, USA
| | - Seojin Park
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, Nevada, USA
- Prestige Biopharma Korea, Myongjigukje 7-ro, Gangseo-gu, Busan, South Korea
| | - Jose L. Puglisi
- College of Medicine. California North State University, Sacramento, California, USA
| | - Claudia M. Moreno
- Department of Physiology and Membrane Biology, UCD, Davis, California, USA
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Alana C. Conti
- Research & Development Service, John D. Dingell VA Medical Center, and
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, Michigan, USA
| | | | - Yang Kevin Xiang
- Department of Veteran Affairs, Northern California Health Care System, Sacramento, California, USA
- Department of Pharmacology, UCD, Davis, California, USA
| | | | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom
| | - Xiao-Dong Zhang
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
- Department of Veteran Affairs, Northern California Health Care System, Sacramento, California, USA
| | - Ebenezer N. Yamoah
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, Nevada, USA
| | | | - Nipavan Chiamvimonvat
- Department of Internal Medicine, Division of Cardiovascular Medicine, UCD, Davis, California, USA
- Department of Veteran Affairs, Northern California Health Care System, Sacramento, California, USA
- Department of Pharmacology, UCD, Davis, California, USA
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22
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Maly J, Emigh AM, DeMarco KR, Furutani K, Sack JT, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of the hERG potassium channel and associated drug interactions. Front Pharmacol 2022; 13:966463. [PMID: 36188564 PMCID: PMC9523588 DOI: 10.3389/fphar.2022.966463] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The voltage-gated potassium channel, KV11.1, encoded by the human Ether-à-go-go-Related Gene (hERG), is expressed in cardiac myocytes, where it is crucial for the membrane repolarization of the action potential. Gating of the hERG channel is characterized by rapid, voltage-dependent, C-type inactivation, which blocks ion conduction and is suggested to involve constriction of the selectivity filter. Mutations S620T and S641A/T within the selectivity filter region of hERG have been shown to alter the voltage dependence of channel inactivation. Because hERG channel blockade is implicated in drug-induced arrhythmias associated with both the open and inactivated states, we used Rosetta to simulate the effects of hERG S620T and S641A/T mutations to elucidate conformational changes associated with hERG channel inactivation and differences in drug binding between the two states. Rosetta modeling of the S641A fast-inactivating mutation revealed a lateral shift of the F627 side chain in the selectivity filter into the central channel axis along the ion conduction pathway and the formation of four lateral fenestrations in the pore. Rosetta modeling of the non-inactivating mutations S620T and S641T suggested a potential molecular mechanism preventing F627 side chain from shifting into the ion conduction pathway during the proposed inactivation process. Furthermore, we used Rosetta docking to explore the binding mechanism of highly selective and potent hERG blockers - dofetilide, terfenadine, and E4031. Our structural modeling correlates well with much, but not all, existing experimental evidence involving interactions of hERG blockers with key residues in hERG pore and reveals potential molecular mechanisms of ligand interactions with hERG in an inactivated state.
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Affiliation(s)
- Jan Maly
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Aiyana M. Emigh
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,Department of Pharmacology, University of California, Davis, Davis, CA, United States,*Correspondence: Igor Vorobyov, ; Vladimir Yarov-Yarovoy,
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States,*Correspondence: Igor Vorobyov, ; Vladimir Yarov-Yarovoy,
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23
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Mazola Y, Márquez Montesinos JCE, Ramírez D, Zúñiga L, Decher N, Ravens U, Yarov-Yarovoy V, González W. Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach. Pharmaceutics 2022; 14:pharmaceutics14071356. [PMID: 35890252 PMCID: PMC9318806 DOI: 10.3390/pharmaceutics14071356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Nav1.5 (and its current, INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of the flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.
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Affiliation(s)
- Yuliet Mazola
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
| | - José C. E. Márquez Montesinos
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Leandro Zúñiga
- Escuela de Medicina, Centro de Investigaciones Médicas, Universidad de Talca, Talca 3460000, Chile;
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35043 Marburg, Germany;
| | - Ursula Ravens
- Institut für Experimentelle Kardiovaskuläre Medizin, Universitäts-Herzzentrum Freiburg Bad Krotzingen, 79110 Freiburg im Breisgau, Germany;
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA;
| | - Wendy González
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Talca 3530000, Chile
- Correspondence:
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24
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George K, Lopez-Mateos D, Abd El-Aziz TM, Xiao Y, Kline J, Bao H, Raza S, Stockand JD, Cummins TR, Fornelli L, Rowe MP, Yarov-Yarovoy V, Rowe AH. Structural and Functional Characterization of a Novel Scorpion Toxin that Inhibits NaV1.8 via Interactions With the DI Voltage Sensor and DII Pore Module. Front Pharmacol 2022; 13:846992. [PMID: 35662692 PMCID: PMC9160825 DOI: 10.3389/fphar.2022.846992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/05/2022] [Indexed: 11/30/2022] Open
Abstract
Voltage-gated sodium channel NaV1.8 regulates transmission of pain signals to the brain. While NaV1.8 has the potential to serve as a drug target, the molecular mechanisms that shape NaV1.8 gating are not completely understood, particularly mechanisms that couple activation to inactivation. Interactions between toxin producing animals and their predators provide a novel approach for investigating NaV structure-function relationships. Arizona bark scorpions produce Na+ channel toxins that initiate pain signaling. However, in predatory grasshopper mice, toxins inhibit NaV1.8 currents and block pain signals. A screen of synthetic peptide toxins predicted from bark scorpion venom showed that peptide NaTx36 inhibited Na+ current recorded from a recombinant grasshopper mouse NaV1.8 channel (OtNaV1.8). Toxin NaTx36 hyperpolarized OtNaV1.8 activation, steady-state fast inactivation, and slow inactivation. Mutagenesis revealed that the first gating charge in the domain I (DI) S4 voltage sensor and an acidic amino acid (E) in the DII SS2 – S6 pore loop are critical for the inhibitory effects of NaTx36. Computational modeling showed that a DI S1 – S2 asparagine (N) stabilizes the NaTx36 – OtNaV1.8 complex while residues in the DI S3 – S4 linker and S4 voltage sensor form electrostatic interactions that allow a toxin glutamine (Q) to contact the first S4 gating charge. Surprisingly, the models predicted that NaTx36 contacts amino acids in the DII S5 – SS1 pore loop instead of the SS2 – S6 loop; the DII SS2 – S6 loop motif (QVSE) alters the conformation of the DII S5 – SS1 pore loop, enhancing allosteric interactions between toxin and the DII S5 – SS1 pore loop. Few toxins have been identified that modify NaV1.8 gating. Moreover, few toxins have been described that modify sodium channel gating via the DI S4 voltage sensor. Thus, NaTx36 and OtNaV1.8 provide tools for investigating the structure-activity relationship between channel activation and inactivation gating, and the connection to alternative pain phenotypes.
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Affiliation(s)
- Kiran George
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Diego Lopez-Mateos
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center San Antonio, San Antonio, TX, United States
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
- Amsaal Venom Farm L.L.C., Abu Dhabi, United Arab Emirates
| | - Yucheng Xiao
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Jake Kline
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Hong Bao
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Syed Raza
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - James D. Stockand
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center San Antonio, San Antonio, TX, United States
| | - Theodore R. Cummins
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Matthew P. Rowe
- Department of Biology, University of Oklahoma, Norman, OK, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
| | - Ashlee H. Rowe
- Department of Biology, University of Oklahoma, Norman, OK, United States
- Graduate Program in Cellular and Behavioral Neurobiology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Ashlee H. Rowe,
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25
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Nguyen PT, Yarov-Yarovoy V. Towards Structure-Guided Development of Pain Therapeutics Targeting Voltage-Gated Sodium Channels. Front Pharmacol 2022; 13:842032. [PMID: 35153801 PMCID: PMC8830516 DOI: 10.3389/fphar.2022.842032] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/12/2022] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated sodium (NaV) channels are critical molecular determinants of action potential generation and propagation in excitable cells. Normal NaV channel function disruption can affect physiological neuronal signaling and lead to increased sensitivity to pain, congenital indifference to pain, uncoordinated movement, seizures, or paralysis. Human genetic studies have identified human NaV1.7 (hNaV1.7), hNaV1.8, and hNaV1.9 channel subtypes as crucial players in pain signaling. The premise that subtype selective NaV inhibitors can reduce pain has been reinforced through intensive target validation and therapeutic development efforts. However, an ideal therapeutic has yet to emerge. This review is focused on recent progress, current challenges, and future opportunities to develop NaV channel targeting small molecules and peptides as non-addictive therapeutics to treat pain.
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Affiliation(s)
- Phuong T Nguyen
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States.,Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
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26
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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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27
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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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28
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Lopez Mateos D, Yarov-Yarovoy V. Modeling of peptide toxin: ion channel interactions using RosettaDock. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.255] [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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29
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Woltz RL, Srivatsa A, DeMarco K, Lopez Mateos D, Nguyen PT, Zhang XD, Vorobyov IV, Yarov-Yarovoy V, Chiamvimonvat N. Developing a stable full atom molecular dynamics model starting from a cyro-EM structure of a K+ channel bound to regulatory protein and varying PIP2 concentrations to understand regulation. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.891] [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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30
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Emigh Cortez A, DeMarco K, Furutani K, Sack JT, Clancy CE, Vorobyov IV, Yarov-Yarovoy V. Predicting arrhythmogenicity: structural modeling of safe and unsafe hERG blockers using Rosetta. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.817] [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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31
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Harris BJ, Nguyen PT, Yarov-Yarovoy V. High-resolution modeling of small molecule-ion channel interactions with Rosetta's GALigandDock. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1776] [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: 11/30/2022] Open
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32
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Nguyen PT, Nguyen HM, Wagner KM, Stewart RG, Singh V, Thapa P, Chen YJ, Lillya MW, Ton AT, Kondo R, Ghetti A, Pennington MW, Hammock B, Griffith TN, Sack JT, Wulff H, Yarov-Yarovoy V. Computational design of peptides to target Na V1.7 channel with high potency and selectivity for the treatment of pain. eLife 2022; 11:81727. [PMID: 36576241 PMCID: PMC9831606 DOI: 10.7554/elife.81727] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The voltage-gated sodium NaV1.7 channel plays a key role as a mediator of action potential propagation in C-fiber nociceptors and is an established molecular target for pain therapy. ProTx-II is a potent and moderately selective peptide toxin from tarantula venom that inhibits human NaV1.7 activation. Here we used available structural and experimental data to guide Rosetta design of potent and selective ProTx-II-based peptide inhibitors of human NaV1.7 channels. Functional testing of designed peptides using electrophysiology identified the PTx2-3127 and PTx2-3258 peptides with IC50s of 7 nM and 4 nM for hNaV1.7 and more than 1000-fold selectivity over human NaV1.1, NaV1.3, NaV1.4, NaV1.5, NaV1.8, and NaV1.9 channels. PTx2-3127 inhibits NaV1.7 currents in mouse and human sensory neurons and shows efficacy in rat models of chronic and thermal pain when administered intrathecally. Rationally designed peptide inhibitors of human NaV1.7 channels have transformative potential to define a new class of biologics to treat pain.
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Affiliation(s)
- Phuong T Nguyen
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States
| | - Hai M Nguyen
- Department of Pharmacology, University of California DavisDavisUnited States
| | - Karen M Wagner
- Department of Entomology and Nematology & Comprehensive Cancer Center, University of California DavisDavisUnited States
| | - Robert G Stewart
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States
| | - Vikrant Singh
- Department of Pharmacology, University of California DavisDavisUnited States
| | - Parashar Thapa
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States
| | - Yi-Je Chen
- Department of Pharmacology, University of California DavisDavisUnited States
| | - Mark W Lillya
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States
| | | | | | | | | | - Bruce Hammock
- Department of Entomology and Nematology & Comprehensive Cancer Center, University of California DavisDavisUnited States
| | - Theanne N Griffith
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States
| | - Jon T Sack
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States,Department of Anesthesiology and Pain Medicine, University of California DavisDavisUnited States
| | - Heike Wulff
- Department of Pharmacology, University of California DavisDavisUnited States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California DavisDavisUnited States,Department of Anesthesiology and Pain Medicine, University of California DavisDavisUnited States,Biophysics Graduate Group, University of California DavisDavisUnited States
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33
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Franco FP, Xu P, Harris BJ, Yarov-Yarovoy V, Leal WS. Single amino acid residue mediates reciprocal specificity in two mosquito odorant receptors. eLife 2022; 11:82922. [PMID: 36511779 PMCID: PMC9799979 DOI: 10.7554/elife.82922] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The southern house mosquito, Culex quinquefasciatus, utilizes two odorant receptors, CquiOR10 and CquiOR2, narrowly tuned to oviposition attractants and well conserved among mosquito species. They detect skatole and indole, respectively, with reciprocal specificity. We swapped the transmembrane (TM) domains of CquiOR10 and CquiOR2 and identified TM2 as a specificity determinant. With additional mutations, we showed that CquiOR10A73L behaved like CquiOR2. Conversely, CquiOR2L74A recapitulated CquiOR10 specificity. Next, we generated structural models of CquiOR10 and CquiOR10A73L using RoseTTAFold and AlphaFold and docked skatole and indole using RosettaLigand. These modeling studies suggested space-filling constraints around A73. Consistent with this hypothesis, CquiOR10 mutants with a bulkier residue (Ile, Val) were insensitive to skatole and indole, whereas CquiOR10A73G retained the specificity to skatole and showed a more robust response than the wildtype receptor CquiOR10. On the other hand, Leu to Gly mutation of the indole receptor CquiOR2 reverted the specificity to skatole. Lastly, CquiOR10A73L, CquiOR2, and CquiOR2L74I were insensitive to 3-ethylindole, whereas CquiOR2L74A and CquiOR2L74G gained activity. Additionally, CquiOR10A73G gave more robust responses to 3-ethylindole than CquiOR10. Thus, we suggest the specificity of these receptors is mediated by a single amino acid substitution, leading to finely tuned volumetric space to accommodate specific oviposition attractants.
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Affiliation(s)
- Flavia P Franco
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Pingxi Xu
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - Brandon J Harris
- Department of Physiology and Membrane Biology, University of California, DavisDavisUnited States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, DavisDavisUnited States,Department of Anesthesiology and Pain Medicine, University of California, DavisDavisUnited States
| | - Walter S Leal
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
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34
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Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Ó Conchúir S, Roy Burman SS, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 2021; 12:6947. [PMID: 34845212 PMCID: PMC8630030 DOI: 10.1038/s41467-021-27222-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/02/2021] [Indexed: 01/14/2023] Open
Abstract
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Steven M Lewis
- Cyrus Biotechnology, 1201 Second Ave, Suite 900, Seattle, WA, 98101, USA
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA
| | - Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kyle Barlow
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ziv Ben-Aharon
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel
| | - Daniel Farrell
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Jason Fell
- Genome Center, University of California, Davis, CA, 95616, USA
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - William A Hansen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeliazko Jeliazkov
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany
| | - Justyna D Krys
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Ajasja Ljubetič
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Amanda L Loshbaugh
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jack Maguire
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA
| | - Morgan L Nance
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Phuong T Nguyen
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frank Teets
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Johanna K S Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Andrew Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, 37235, USA
| | - Brahm J Yachnin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA, 02115, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | | | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08904, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason W Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Institute for Drug Discovery, Medical School, Leipzig University, 04103, Leipzig, Germany
| | - William Schief
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, 92037, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Hebrew University, Hadassah Medical School, POB 12272, Jerusalem, 91120, Israel
| | - Justin B Siegel
- Genome Center, University of California, Davis, CA, 95616, USA
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, 95616, USA
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200, Copenhagen N., Denmark
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Brian Kuhlman
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Andrew Leaver-Fay
- Department of Bioochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27516, USA
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
- Department of Computer Science, New York University, New York, NY, 10003, USA.
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35
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Ledford HA, Ren L, Thai PN, Park S, Timofeyev V, Sirish P, Xu W, Emigh AM, Priest JR, Perez MV, Ashley EA, Yarov-Yarovoy V, Yamoah EN, Zhang XD, Chiamvimonvat N. Disruption of protein quality control of the human ether-à-go-go related gene K + channel results in profound long QT syndrome. Heart Rhythm 2021; 19:281-292. [PMID: 34634443 DOI: 10.1016/j.hrthm.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 09/20/2021] [Accepted: 10/04/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Long QT syndrome (LQTS) is a hereditary disease that predisposes patients to life-threatening cardiac arrhythmias and sudden cardiac death. Our previous study of the human ether-à-go-go related gene (hERG)-encoded K+ channel (Kv11.1) supports an association between hERG and RING finger protein 207 (RNF207) variants in aggravating the onset and severity of LQTS, specifically T613M hERG (hERGT613M) and RNF207 frameshift (RNF207G603fs) mutations. However, the underlying mechanistic underpinning remains unknown. OBJECTIVE The purpose of the present study was to test the role of RNF207 in the function of hERG-encoded K+ channel subunits. METHODS Whole-cell patch-clamp experiments were performed in human embryonic kidney (HEK 293) cells and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) together with immunofluorescent confocal and high resolution microscopy, auto-ubiquitinylation assays, and co-immunoprecipitation experiments to test the functional interactions between hERG and RNF207. RESULTS Here, we demonstrated that RNF207 serves as an E3 ubiquitin ligase and targets misfolded hERGT613M proteins for degradation. RNF207G603fs exhibits decreased activity and hinders the normal degradation pathway; this increases the levels of hERGT613M subunits and their dominant-negative effect on the wild-type subunits, ultimately resulting in decreased current density. Similar findings are shown for hERGA614V, a known dominant-negative mutant subunit. Finally, the presence of RNF207G603fs with hERGT613M results in significantly prolonged action potential durations and reduced hERG current in human-induced pluripotent stem cell-derived cardiomyocytes. CONCLUSION Our study establishes RNF207 as an interacting protein serving as a ubiquitin ligase for hERG-encoded K+ channel subunits. Normal function of RNF207 is critical for the quality control of hERG subunits and consequently cardiac repolarization. Moreover, our study provides evidence for protein quality control as a new paradigm in life-threatening cardiac arrhythmias in patients with LQTS.
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Affiliation(s)
- Hannah A Ledford
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California
| | - Lu Ren
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California
| | - Phung N Thai
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California
| | - Seojin Park
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California; Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, Nevada
| | - Valeriy Timofeyev
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California; Department of Veterans Affairs, Northern California Health Care System, Mather, California
| | - Wilson Xu
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California
| | - Aiyana M Emigh
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, California
| | - James R Priest
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California
| | - Marco V Perez
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California
| | - Euan A Ashley
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, California
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, California
| | - Ebenezer N Yamoah
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, Nevada
| | - Xiao-Dong Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California; Department of Veterans Affairs, Northern California Health Care System, Mather, California
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, California; Department of Veterans Affairs, Northern California Health Care System, Mather, California.
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36
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Ledford HA, Park S, Muir D, Woltz RL, Ren L, Nguyen PT, Sirish P, Wang W, Sihn CR, George AL, Knollmann BC, Yamoah EN, Yarov-Yarovoy V, Zhang XD, Chiamvimonvat N. Different arrhythmia-associated calmodulin mutations have distinct effects on cardiac SK channel regulation. J Gen Physiol 2021; 152:211546. [PMID: 33211795 PMCID: PMC7681919 DOI: 10.1085/jgp.202012667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/25/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Calmodulin (CaM) plays a critical role in intracellular signaling and regulation of Ca2+-dependent proteins and ion channels. Mutations in CaM cause life-threatening cardiac arrhythmias. Among the known CaM targets, small-conductance Ca2+-activated K+ (SK) channels are unique, since they are gated solely by beat-to-beat changes in intracellular Ca2+. However, the molecular mechanisms of how CaM mutations may affect the function of SK channels remain incompletely understood. To address the structural and functional effects of these mutations, we introduced prototypical human CaM mutations in human induced pluripotent stem cell–derived cardiomyocyte-like cells (hiPSC-CMs). Using structural modeling and molecular dynamics simulation, we demonstrate that human calmodulinopathy-associated CaM mutations disrupt cardiac SK channel function via distinct mechanisms. CaMD96V and CaMD130G mutants reduce SK currents through a dominant-negative fashion. By contrast, specific mutations replacing phenylalanine with leucine result in conformational changes that affect helix packing in the C-lobe, which disengage the interactions between apo-CaM and the CaM-binding domain of SK channels. Distinct mutant CaMs may result in a significant reduction in the activation of the SK channels, leading to a decrease in the key Ca2+-dependent repolarization currents these channels mediate. The findings in this study may be generalizable to other interactions of mutant CaMs with Ca2+-dependent proteins within cardiac myocytes.
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Affiliation(s)
- Hannah A Ledford
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA
| | - Seojin Park
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV
| | - Duncan Muir
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA
| | - Ryan L Woltz
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA
| | - Lu Ren
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA
| | - Phuong T Nguyen
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, Davis, CA
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA
| | - Wenying Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV
| | - Choong-Ryoul Sihn
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Björn C Knollmann
- Vanderbilt Center for Arrhythmia Research and Therapeutics, Department of Medicine, School of Medicine, Vanderbilt University, Nashville, TN
| | - Ebenezer N Yamoah
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, Davis, CA
| | - Xiao-Dong Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA.,Department of Veterans Affairs, Northern California Health Care System, Mather, CA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA.,Department of Veterans Affairs, Northern California Health Care System, Mather, CA
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37
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DeMarco KR, Yang PC, Singh V, Furutani K, Dawson JRD, Jeng MT, Fettinger JC, Bekker S, Ngo VA, Noskov SY, Yarov-Yarovoy V, Sack JT, Wulff H, Clancy CE, Vorobyov I. Molecular determinants of pro-arrhythmia proclivity of d- and l-sotalol via a multi-scale modeling pipeline. J Mol Cell Cardiol 2021; 158:163-177. [PMID: 34062207 PMCID: PMC8906354 DOI: 10.1016/j.yjmcc.2021.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/03/2021] [Accepted: 05/24/2021] [Indexed: 11/20/2022]
Abstract
Drug isomers may differ in their proarrhythmia risk. An interesting example is the drug sotalol, an antiarrhythmic drug comprising d- and l- enantiomers that both block the hERG cardiac potassium channel and confer differing degrees of proarrhythmic risk. We developed a multi-scale in silico pipeline focusing on hERG channel – drug interactions and used it to probe and predict the mechanisms of pro-arrhythmia risks of the two enantiomers of sotalol. Molecular dynamics (MD) simulations predicted comparable hERG channel binding affinities for d- and l-sotalol, which were validated with electrophysiology experiments. MD derived thermodynamic and kinetic parameters were used to build multi-scale functional computational models of cardiac electrophysiology at the cell and tissue scales. Functional models were used to predict inactivated state binding affinities to recapitulate electrocardiogram (ECG) QT interval prolongation observed in clinical data. Our study demonstrates how modeling and simulation can be applied to predict drug effects from the atom to the rhythm for dl-sotalol and also increased proarrhythmia proclivity of d- vs. l-sotalol when accounting for stereospecific beta-adrenergic receptor blocking.
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Affiliation(s)
- Kevin R DeMarco
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Tokushima 770-8514, Japan
| | - John R D Dawson
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Biophysics Graduate Group, University of California Davis, Davis, CA 95616, USA
| | - Mao-Tsuen Jeng
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA
| | - James C Fettinger
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Science and Engineering, American River College, Sacramento, CA 95841, USA
| | - Van A Ngo
- Centre for Molecular Simulation and Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulation and Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, CA 95616, USA
| | - Jon T Sack
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Anesthesiology and Pain Medicine, University of California Davis, Davis, CA 95616, USA
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, University of California Davis, Davis, CA 95616, USA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California Davis, Davis, CA 95616, USA; Department of Pharmacology, University of California Davis, Davis, CA 95616, USA.
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38
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Kisiela DI, Magala P, Interlandi G, Carlucci LA, Ramos A, Tchesnokova V, Basanta B, Yarov-Yarovoy V, Avagyan H, Hovhannisyan A, Thomas WE, Stenkamp RE, Klevit RE, Sokurenko EV. Toggle switch residues control allosteric transitions in bacterial adhesins by participating in a concerted repacking of the protein core. PLoS Pathog 2021; 17:e1009440. [PMID: 33826682 PMCID: PMC8064603 DOI: 10.1371/journal.ppat.1009440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/23/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Critical molecular events that control conformational transitions in most allosteric proteins are ill-defined. The mannose-specific FimH protein of Escherichia coli is a prototypic bacterial adhesin that switches from an ‘inactive’ low-affinity state (LAS) to an ‘active’ high-affinity state (HAS) conformation allosterically upon mannose binding and mediates shear-dependent catch bond adhesion. Here we identify a novel type of antibody that acts as a kinetic trap and prevents the transition between conformations in both directions. Disruption of the allosteric transitions significantly slows FimH’s ability to associate with mannose and blocks bacterial adhesion under dynamic conditions. FimH residues critical for antibody binding form a compact epitope that is located away from the mannose-binding pocket and is structurally conserved in both states. A larger antibody-FimH contact area is identified by NMR and contains residues Leu-34 and Val-35 that move between core-buried and surface-exposed orientations in opposing directions during the transition. Replacement of Leu-34 with a charged glutamic acid stabilizes FimH in the LAS conformation and replacement of Val-35 with glutamic acid traps FimH in the HAS conformation. The antibody is unable to trap the conformations if Leu-34 and Val-35 are replaced with a less bulky alanine. We propose that these residues act as molecular toggle switches and that the bound antibody imposes a steric block to their reorientation in either direction, thereby restricting concerted repacking of side chains that must occur to enable the conformational transition. Residues homologous to the FimH toggle switches are highly conserved across a diverse family of fimbrial adhesins. Replacement of predicted switch residues reveals that another E. coli adhesin, galactose-specific FmlH, is allosteric and can shift from an inactive to an active state. Our study shows that allosteric transitions in bacterial adhesins depend on toggle switch residues and that an antibody that blocks the switch effectively disables adhesive protein function. To bind their ligands, allosteric proteins shift between ‘inactive’ and ‘active’ states, but molecular details of the conformational changes during the transition are often unclear. We describe a monoclonal antibody against the mannose-specific bacterial adhesin, FimH, that blocks the conformational transition in both directions. The antibody-trapped LAS and HAS conformations of FimH are unable to mediate bacterial adhesion under dynamic shear conditions. We propose that the conformational trapping involves a steric block of the core-to-surface switching of certain residues which is critical for the allosteric transitions. Furthermore, we demonstrate that the allosteric switches are structurally and functionally conserved across a broad spectrum of bacterial fimbrial adhesins.
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Affiliation(s)
- Dagmara I. Kisiela
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Pearl Magala
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Gianluca Interlandi
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Laura A. Carlucci
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Angelo Ramos
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Veronika Tchesnokova
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, California, United States of America
| | - Hovhannes Avagyan
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Anahit Hovhannisyan
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Wendy E. Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Ronald E. Stenkamp
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Department of Biological Structure, University of Washington, Seattle, Washington, United States of America
| | - Rachel E. Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail: (REK); (EVS)
| | - Evgeni V. Sokurenko
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (REK); (EVS)
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39
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Woltz RL, Srivatsa A, Nguyen PT, DeMarco K, Zhang XD, Vorobyov IV, Yarov-Yarovoy V, Chiamvimonvat N. The Use of Enhanced Sampling Molecular Dynamics (ES-MD) to Determine PIP2 Binding in SK2-Calmodulin Complex. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1514] [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: 10/22/2022] Open
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40
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Maly J, Emigh AM, DeMarco K, Sack JT, Vorobyov IV, Clancy CE, Yarov-Yarovoy V. Structural Modeling of the hERG Channel in an Inactivated State and Associated Drug Interactions. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1595] [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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41
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Gonzalez W, Nuñez-Vivanco G, Ramírez D, Kiper AK, Rinne S, Bedoya M, Arévalo B, Márquez-Montesinos J, Reyes-Parada M, Yarov-Yarovoy V, Decher N. A “Receptophore Model” for Local Anesthetics Binding Site in Cardiac Ion Channels. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1616] [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: 10/22/2022] Open
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42
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Harris BJ, Nguyen PT, Yarov-Yarovoy V. Structural Modeling of NaV-Ligand Interactions with Rosetta’s Galiganddock. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1112] [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: 11/30/2022] Open
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43
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Emigh AM, DeMarco KR, Furutani K, Sack JT, Clancy CE, Vorobyov IV, Yarov-Yarovoy V. Predicting Arrhythmogenicity: Structural Modeling of Safe and Unsafe Herg Blockers. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1385] [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: 10/22/2022] Open
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44
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Dawson JR, DeMarco KR, Yang PC, Bekker S, Yarov-Yarovoy V, Vorobyov IV. Assessing State Dependent Beta-Adrenergic Receptor - Ligand Interactions for Multiscale Modeling. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.959] [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: 11/25/2022] Open
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45
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DeMarco KR, Yang PC, Furutani K, Dawson JR, Bekker S, Ngo VA, Noskov SY, Yarov-Yarovoy V, Sack JT, Clancy CE, Vorobyov I. Molecular Determinants of D and L-Sotalol Stereoselective Proarrhythmia Procilivties. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1605] [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: 10/22/2022] Open
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46
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Srivatsa AV, Woltz RL, Nguyen PT, DeMarco K, Zhang XD, Vorobyov IV, Yarov-Yarovoy V, Chiamvimonvat N. Molecular Dynamic Simulations Suggest Novel PIP2 Binding Sites for SK2 Channel Regulation. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1511] [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: 10/22/2022] Open
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47
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Lopez Mateos D, Yarov-Yarovoy V. Structural Modeling of Peptide Toxin - Ion Channel Interactions. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1066] [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: 10/22/2022] Open
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48
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Unger EK, Keller JP, Altermatt M, Liang R, Matsui A, Dong C, Hon OJ, Yao Z, Sun J, Banala S, Flanigan ME, Jaffe DA, Hartanto S, Carlen J, Mizuno GO, Borden PM, Shivange AV, Cameron LP, Sinning S, Underhill SM, Olson DE, Amara SG, Temple Lang D, Rudnick G, Marvin JS, Lavis LD, Lester HA, Alvarez VA, Fisher AJ, Prescher JA, Kash TL, Yarov-Yarovoy V, Gradinaru V, Looger LL, Tian L. Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning. Cell 2020; 183:1986-2002.e26. [PMID: 33333022 PMCID: PMC8025677 DOI: 10.1016/j.cell.2020.11.040] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [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: 11/23/2019] [Revised: 06/22/2020] [Accepted: 11/20/2020] [Indexed: 12/28/2022]
Abstract
Serotonin plays a central role in cognition and is the target of most pharmaceuticals for psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will require better understanding of serotonergic circuitry, which has been hampered by our inability to monitor serotonin release and transport with high spatial and temporal resolution. We developed and applied a binding-pocket redesign strategy, guided by machine learning, to create a high-performance, soluble, fluorescent serotonin sensor (iSeroSnFR), enabling optical detection of millisecond-scale serotonin transients. We demonstrate that iSeroSnFR can be used to detect serotonin release in freely behaving mice during fear conditioning, social interaction, and sleep/wake transitions. We also developed a robust assay of serotonin transporter function and modulation by drugs. We expect that both machine-learning-guided binding-pocket redesign and iSeroSnFR will have broad utility for the development of other sensors and in vitro and in vivo serotonin detection, respectively.
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Affiliation(s)
- Elizabeth K Unger
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Jacob P Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA
| | - Michael Altermatt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ruqiang Liang
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Aya Matsui
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Chunyang Dong
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Olivia J Hon
- Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Zi Yao
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Junqing Sun
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Samba Banala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA
| | - Meghan E Flanigan
- Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - David A Jaffe
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Samantha Hartanto
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Jane Carlen
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Grace O Mizuno
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Phillip M Borden
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA
| | - Amol V Shivange
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay P Cameron
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Steffen Sinning
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Suzanne M Underhill
- Laboratory of Molecular and Cellular Neurobiology, National Institute on Mental Health, NIH, Bethesda, MD 20892, USA
| | - David E Olson
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Susan G Amara
- Laboratory of Molecular and Cellular Neurobiology, National Institute on Mental Health, NIH, Bethesda, MD 20892, USA
| | - Duncan Temple Lang
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Gary Rudnick
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Veronica A Alvarez
- Laboratory on Neurobiology of Compulsive Behaviors, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Andrew J Fisher
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Thomas L Kash
- Bowles Center for Alcohol Studies, Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Vladimir Yarov-Yarovoy
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20174, USA.
| | - Lin Tian
- Departments of Biochemistry and Molecular Medicine, Chemistry, Statistics, Molecular and Cellular Biology, and Physiology and Membrane Biology, the Center for Neuroscience, and Graduate Programs in Molecular, Cellular, and Integrative Physiology, Biochemistry, Molecular, Cellular and Developmental Biology and Neuroscience, University of California, Davis, Davis, CA 95616, USA.
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Vu S, Singh V, Wulff H, Yarov-Yarovoy V, Zheng J. New capsaicin analogs as molecular rulers to define the permissive conformation of the mouse TRPV1 ligand-binding pocket. eLife 2020; 9:62039. [PMID: 33164749 PMCID: PMC7671684 DOI: 10.7554/elife.62039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/08/2020] [Indexed: 12/23/2022] Open
Abstract
The capsaicin receptor TRPV1 is an outstanding representative of ligand-gated ion channels in ligand selectivity and sensitivity. However, molecular interactions that stabilize the ligand-binding pocket in its permissive conformation, and how many permissive conformations the ligand-binding pocket may adopt, remain unclear. To answer these questions, we designed a pair of novel capsaicin analogs to increase or decrease the ligand size by about 1.5 Å without altering ligand chemistry. Together with capsaicin, these ligands form a set of molecular rulers for investigating ligand-induced conformational changes. Computational modeling and functional tests revealed that structurally these ligands alternate between drastically different binding poses but stabilize the ligand-binding pocket in nearly identical permissive conformations; functionally, they all yielded a stable open state despite varying potencies. Our study suggests the existence of an optimal ligand-binding pocket conformation for capsaicin-mediated TRPV1 activation gating, and reveals multiple ligand-channel interactions that stabilize this permissive conformation.
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Affiliation(s)
- Simon Vu
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, School of Medicine, Davis, United States
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, School of Medicine, Davis, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California Davis, School of Medicine, Davis, United States
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50
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Turner M, Anderson DE, Bartels P, Nieves-Cintron M, Coleman AM, Henderson PB, Man KNM, Tseng PY, Yarov-Yarovoy V, Bers DM, Navedo MF, Horne MC, Ames JB, Hell JW. α-Actinin-1 promotes activity of the L-type Ca 2+ channel Ca v1.2. EMBO J 2020; 39:e106171. [PMID: 33433005 DOI: 10.15252/embj.2020106171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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