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Bondarenko V, Chen Q, Tillman TS, Xu Y, Tang P. Unconventional PDZ Recognition Revealed in α7 nAChR-PICK1 Complexes. ACS Chem Neurosci 2024; 15:2070-2079. [PMID: 38691676 PMCID: PMC11099923 DOI: 10.1021/acschemneuro.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
PDZ domains are modular domains that conventionally bind to C terminal or internal motifs of target proteins to control cellular functions through the regulation of protein complex assemblies. Almost all reported structures of PDZ-target protein complexes rely on fragments or peptides as target proteins. No intact target protein complexed with PDZ was structurally characterized. In this study, we used NMR spectroscopy and other biochemistry and biophysics tools to uncover insights into structural coupling between the PDZ domain of protein interacting with C-kinase 1 (PICK1) and α7 nicotinic acetylcholine receptors (α7 nAChR). Notably, the intracellular domains of both α7 nAChR and PICK1 PDZ exhibit a high degree of plasticity in their coupling. Specifically, the MA helix of α7 nAChR interacts with residues lining the canonical binding site of the PICK1 PDZ, while flexible loops also engage in protein-protein interactions. Both hydrophobic and electrostatic interactions mediate the coupling. Overall, the resulting structure of the α7 nAChR-PICK1 complex reveals an unconventional PDZ binding mode, significantly expanding the repertoire of functionally important PDZ interactions.
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Affiliation(s)
- Vasyl Bondarenko
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tommy S. Tillman
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Physics and Astronomy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Depatment
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Computational and Systems Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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2
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Bondarenko V, Chen Q, Singewald K, Haloi N, Tillman TS, Howard RJ, Lindahl E, Xu Y, Tang P. Structural Elucidation of Ivermectin Binding to α7nAChR and the Induced Channel Desensitization. ACS Chem Neurosci 2023; 14:1156-1165. [PMID: 36821490 PMCID: PMC10020961 DOI: 10.1021/acschemneuro.2c00783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The α7 nicotinic acetylcholine receptor (α7nAChR) mediates signaling in the central nervous system and cholinergic anti-inflammatory pathways. Ivermectin is a positive allosteric modulator of a full-length α7nAChR and an agonist of the α7nAChR construct containing transmembrane (TMD) and intracellular (ICD) domains, but structural insights of the binding have not previously been determined. Here, combining nuclear magnetic resonance as a primary experimental tool with Rosetta comparative modeling and molecular dynamics simulations, we have revealed details of ivermectin binding to the α7nAChR TMD + ICD and corresponding structural changes in an ivermectin-induced desensitized state. Ivermectin binding was stabilized predominantly by hydrophobic interactions from interfacial residues between adjacent subunits near the extracellular end of the TMD, where the inter-subunit gap was substantially expanded in comparison to the apo structure. The ion-permeation pathway showed a profile distinctly different from the resting-state profile but similar to profiles of desensitized α7nAChR. The ICD also exhibited structural changes, including reorientation of the MX and h3 helices relative to the channel axis. The resulting structures of the α7nAChR TMD + ICD in complex with ivermectin provide opportunities for discovering new modulators of therapeutic potential and exploring the structural basis of cytoplasmic signaling under different α7nAChR functional states.
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Affiliation(s)
- Vasyl Bondarenko
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin Singewald
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nandan Haloi
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Tommy S. Tillman
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rebecca J. Howard
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Erik Lindahl
- Department
of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden
- Department
of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, PO Box 1031, SE-17121 Solna, Sweden
| | - Yan Xu
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Physics and Astronomy, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department
of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Pharmacology and Chemical Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department
of Computational and Systems Biology, University
of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Godellas NE, Grosman C. Probing function in ligand-gated ion channels without measuring ion transport. J Gen Physiol 2022; 154:213244. [PMID: 35612603 DOI: 10.1085/jgp.202213082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/28/2022] [Indexed: 12/11/2022] Open
Abstract
Although the functional properties of ion channels are most accurately assessed using electrophysiological approaches, a number of experimental situations call for alternative methods. Here, working on members of the pentameric ligand-gated ion channel (pLGIC) superfamily, we focused on the practical implementation of, and the interpretation of results from, equilibrium-type ligand-binding assays. Ligand-binding studies of pLGICs are by no means new, but the lack of uniformity in published protocols, large disparities between the results obtained for a given parameter by different groups, and a general disregard for constraints placed on the experimental observations by simple theoretical considerations suggested that a thorough analysis of this classic technique was in order. To this end, we present a detailed practical and theoretical study of this type of assay using radiolabeled α-bungarotoxin, unlabeled small-molecule cholinergic ligands, the human homomeric α7-AChR, and extensive calculations in the framework of a realistic five-binding-site reaction scheme. Furthermore, we show examples of the practical application of this method to tackle two longstanding questions in the field: our results suggest that ligand-binding affinities are insensitive to binding-site occupancy and that mutations to amino-acid residues in the transmembrane domain are unlikely to affect the channel's affinities for ligands that bind to the extracellular domain.
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Affiliation(s)
- Nicole E Godellas
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Claudio Grosman
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL
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4
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Bondarenko V, Wells MM, Chen Q, Tillman TS, Singewald K, Lawless MJ, Caporoso J, Brandon N, Coleman JA, Saxena S, Lindahl E, Xu Y, Tang P. Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor. Nat Commun 2022; 13:793. [PMID: 35145092 PMCID: PMC8831596 DOI: 10.1038/s41467-022-28400-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
The intracellular domain (ICD) of Cys-loop receptors mediates diverse functions. To date, no structure of a full-length ICD is available due to challenges stemming from its dynamic nature. Here, combining nuclear magnetic resonance (NMR) and electron spin resonance experiments with Rosetta computations, we determine full-length ICD structures of the human α7 nicotinic acetylcholine receptor in a resting state. We show that ~57% of the ICD residues are in highly flexible regions, primarily in a large loop (loop L) with the most mobile segment spanning ~50 Å from the central channel axis. Loop L is anchored onto the MA helix and virtually forms two smaller loops, thereby increasing its stability. Previously known motifs for cytoplasmic binding, regulation, and signaling are found in both the helices and disordered flexible regions, supporting the essential role of the ICD conformational plasticity in orchestrating a broad range of biological processes. The intracellular domain (ICD) of Cys-loop receptors mediates many of their functions, but no complete structure of a Cys-loop receptor ICD is available to date. Here, the authors combine NMR and ESR spectroscopy to determine the full-length ICD structures of the human α7 nicotinic acetylcholine receptor (α7nAChR).
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Affiliation(s)
- Vasyl Bondarenko
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Marta M Wells
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Qiang Chen
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tommy S Tillman
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Joel Caporoso
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Nicole Brandon
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| | - Yan Xu
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Pei Tang
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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5
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Xiang D, Xu X, Zhou Q, Yan R, Chen M, Guo Y, Zhu G. The expression of soluble functional α7-nicotinic acetylcholine receptors in E. coli and its high-affinity binding to neonicotinoid pesticides. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:237-241. [PMID: 32284132 DOI: 10.1016/j.pestbp.2020.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/06/2020] [Accepted: 02/01/2020] [Indexed: 06/11/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels mediating fast cholinergic synaptic transmission in nervous system. In insects, nAChRs are the target sites for several naturally occurring and synthetic compounds, including the neonicotinoid insecticides. So far, one of the major strategies to explore the interaction of nAChR and ligands is based on the heterologous expression of nAChR, which is tough, and needs to be explored. In this study, we expressed and purified extracellular domain of rat a7 subunit (Rα7-ECD), the binding site of the ligands in E. coli and determined the interactions and kinetic constants of neonicotinoid insecticides with Rα7-ECD. The recombinant Rα7-ECD is water-soluble and appears to be correctly folded. The interactions of three neonicotinoid pesticides with Rα7-ECD were assessed by surface plasmon resonance (SPR) biosensor. The results revealed a fast association and fast disassociation binding mode of Rα7-ECD/pesticides complexes with the KD value of clothianidin (6.414E-9 M) > imidacloprid (9.030E-9 M) > acetamiprid (2.874E-6 M), respectively. This study demonstrated that the nAChR expressed from E. coli was functional, and SPR biosensor technology would be a good alternative for characterizing members of nAChR receptor family.
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Affiliation(s)
- Dandan Xiang
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
| | - Xiaojun Xu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
| | - Qiaoling Zhou
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of life sciences, China Jiliang University, Hangzhou 310018, China; Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
| | - Ru Yan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of life sciences, China Jiliang University, Hangzhou 310018, China; Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
| | - Mengli Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of life sciences, China Jiliang University, Hangzhou 310018, China; Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China.
| | - Yirong Guo
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310029, China
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6
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Tillman TS, Choi Z, Xu Y, Tang P. Functional Tolerance to Cysteine Mutations in Human α7 Nicotinic Acetylcholine Receptors. ACS Chem Neurosci 2020; 11:242-247. [PMID: 31951367 DOI: 10.1021/acschemneuro.9b00647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (α7 nAChR) is involved in various intracellular signaling pathways that mediate addiction, chronic pain, and other diseases, but its intracellular domain structures remain undetermined. The presence of 17 native cysteines in α7 nAChR provides opportunities for extracting structural information through site-directed labeling of chemical probes in strategic locations, but it also creates uncertainties in channel function when those native cysteines must be mutated. Using site-directed mutagenesis and two-electrode voltage clamp electrophysiology measurements, we found that α7 nAChR's function was well tolerated for mutations of all 13 cysteines as long as two pairs of disulfide-bond cysteines remained in the extracellular domain. Furthermore, surface plasmon resonance measurements showed that the cysteine mutations did not affect α7 nAChR binding to the intracellular protein PICK1. The study suggests that a high native cysteine content does not necessarily preclude the use of single cysteine labeling for acquiring structural information on functional proteins.
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Affiliation(s)
- Tommy S. Tillman
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zachary Choi
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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7
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Bondarenko V, Wells MM, Chen Q, Singewald KC, Saxena S, Xu Y, Tang P. 19F Paramagnetic Relaxation-Based NMR for Quaternary Structural Restraints of Ion Channels. ACS Chem Biol 2019; 14:2160-2165. [PMID: 31525026 DOI: 10.1021/acschembio.9b00692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å, which challenges the high and low measurement limits of conventional nuclear magnetic resonance (NMR) and double electron-electron resonance electron spin resonance spectroscopies. Here, we report the use of 19F paramagnetic relaxation enhancement (PRE) NMR in combination with 19F/paramagnetic labeling to equivalent sites in different subunits of a protein complex in micelles to determine intersubunit distances. The feasibility of this strategy was evaluated on a pentameric ligand-gated ion channel, for which we found excellent agreement of the 19F PRE NMR results with previous structural information. The study suggests that 19F PRE NMR is a viable tool in extracting distance restraints to define quaternary structures.
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Affiliation(s)
- Vasyl Bondarenko
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marta M. Wells
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin C. Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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8
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Chen Q, Xu Y, Tang P. X-Ray Crystallographic Studies for Revealing Binding Sites of General Anesthetics in Pentameric Ligand-Gated Ion Channels. Methods Enzymol 2018; 603:21-47. [PMID: 29673527 DOI: 10.1016/bs.mie.2018.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
X-ray crystallography is a powerful tool in structural biology and can offer insight into structured-based understanding of general anesthetic action on various relevant molecular targets, including pentameric ligand-gated ion channels (pLGICs). In this chapter, we outline the procedures for expression and purification of pLGICs. Optimization of crystallization conditions, especially to achieve high-resolution structures of pLGICs bound with general anesthetics, is also presented. Case studies of pLGICs bound with the volatile general anesthetic isoflurane, 2-bromoethanol, and the intravenous general anesthetic ketamine are revisited.
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Affiliation(s)
- Qiang Chen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yan Xu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pei Tang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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