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D'Avanzo N, Miles AJ, Powl AM, Nichols CG, Wallace BA, O'Reilly AO. The T1-tetramerisation domain of Kv1.2 rescues expression and preserves function of a truncated NaChBac sodium channel. FEBS Lett 2022; 596:772-783. [PMID: 35015304 PMCID: PMC9303580 DOI: 10.1002/1873-3468.14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Cytoplasmic domains frequently promote functional assembly of multimeric ion channels. To investigate structural determinants of this process, we generated the ‘T1‐chimera’ construct of the NaChBac sodium channel by truncating its C‐terminal domain and splicing the T1‐tetramerisation domain of the Kv1.2 channel to the N terminus. Purified T1‐chimera channels were tetrameric, conducted Na+ when reconstituted into proteoliposomes, and were functionally blocked by the drug mibefradil. Both the T1‐chimera and full‐length NaChBac had comparable expression levels in the membrane, whereas a NaChBac mutant lacking a cytoplasmic domain had greatly reduced membrane expression. Our findings support a model whereby bringing the transmembrane regions into close proximity enables their tetramerisation. This phenomenon is found with other channels, and thus, our findings substantiate this as a common assembly mechanism.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Pharmacology and Physiology, Université de Montréal, Canada
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrew M Powl
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, UK
| | - Andrias O O'Reilly
- School of Biological & Environmental Sciences, Liverpool John Moores University, UK
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2
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The role of circular dichroism spectroscopy in the era of integrative structural biology. Curr Opin Struct Biol 2019; 58:191-196. [DOI: 10.1016/j.sbi.2019.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022]
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3
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Zhang H, Wei W, Huang M, Umar Z, Feng Y. Definition of a Family of Nonmobile Colistin Resistance (NMCR-1) Determinants Suggests Aquatic Reservoirs for MCR-4. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900038. [PMID: 31179218 PMCID: PMC6548957 DOI: 10.1002/advs.201900038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Polymyxins, a family of cationic antimicrobial peptides, are recognized as a last-resort clinical option used in the treatment of lethal infections with carbapenem-resistant pathogens. A growing body of mobile colistin resistance (MCR) determinants renders colistin ineffective in the clinical and human sectors, posing a challenge to human health and food security. However, the origin and reservoir of the MCR family enzymes is poorly understood. Herein, a new family of nonmobile colistin resistance (from nmcr-1 to nmcr-1.8) from the aquatic bacterium Shewanella is reported. NMCR-1 (541aa) displays 62.78% identity to MCR-4. Genetic and structural analyses reveal that NMCR-1 shares a similar catalytic mechanism and functional motifs, both of which are required for MCR action and its resultant phenotypic resistance to polymyxin. Phylogeny and domain-swapping demonstrate that NMCR-1 is a progenitor of MCR-4 rather than MCR-1/2. Additionally, the experiment of bacterial growth and viability reveals that NMCR-1 promotes fitness cost as MCR-1/4 does in the recipient Escherichia coli. In summary, the finding suggests that the aquatic bacterium Shewanella (and even its associated aquaculture) is a reservoir for MCR-4 mobile colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zeeshan Umar
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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4
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McDonald SK, Levitz TS, Valiyaveetil FI. A Shared Mechanism for the Folding of Voltage-Gated K + Channels. Biochemistry 2019; 58:1660-1671. [PMID: 30793887 DOI: 10.1021/acs.biochem.9b00068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we probe the folding of KvAP, a voltage-gated K+ (Kv) channel. The KvAP channel, though of archaebacterial origin, is structurally and functionally similar to eukaryotic Kv channels. An advantage of the KvAP channel is that it can be folded in vitro from an extensively unfolded state and the folding can be controlled by temperature. We utilize these properties of the KvAP channel to separately study the membrane insertion and the tetramerization stages during folding. We use two quantitative assays: a Cys PEGylation assay to monitor membrane insertion and a cross-linking assay to monitor tetramerization. We show that during folding the KvAP polypeptide is rapidly inserted into the lipid bilayer with a "native-like" topology. We identify a segment at the C-terminus that is important for multimerization of the KvAP channel. We show that this C-terminal domain forms a dimer, which raises the possibility that the tetramerization of the KvAP channel proceeds through a dimer of dimers pathway. Our studies show that the in vitro folding of the KvAP channel mirrors aspects of the cellular assembly pathway for voltage-gated K+ channels and therefore suggest that evolutionarily distinct Kv channels share a common folding pathway. The pathway for the folding and assembly of a Kv channel is of central importance as defects in this pathway have been implicated in the etiology of several disease states. Our studies indicate that the KvAP channel provides an experimentally tractable system for elucidating the folding mechanism of Kv channels.
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Affiliation(s)
- Sarah K McDonald
- Program in Chemical Biology, Department of Physiology and Pharmacology , Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239 , United States
| | - Talya S Levitz
- Program in Chemical Biology, Department of Physiology and Pharmacology , Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239 , United States
| | - Francis I Valiyaveetil
- Program in Chemical Biology, Department of Physiology and Pharmacology , Oregon Health & Science University , 3181 Southwest Sam Jackson Park Road , Portland , Oregon 97239 , United States
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5
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Zhang H, Hou M, Xu Y, Srinivas S, Huang M, Liu L, Feng Y. Action and mechanism of the colistin resistance enzyme MCR-4. Commun Biol 2019; 2:36. [PMID: 30701201 PMCID: PMC6347640 DOI: 10.1038/s42003-018-0278-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/17/2018] [Indexed: 12/29/2022] Open
Abstract
Colistin is the last-resort antibiotic against lethal infections with multidrug-resistant bacterial pathogens. A rainbow coalition of mobile colistin resistance (mcr) genes raises global health concerns. Here, we describe the action and mechanism of colistin resistance imparted by MCR-4, a recently-identified member from the broader MCR family. We found that MCR-4 originates from the silenced variant of Shewanella frigidimarina via progressive evolution and forms a phylogenetically-distinct group from the well-studied MCR-1/2 family. Domain-swapping experiments further confirmed that MCR-1 and MCR-4 transmembrane and catalytic domains are not functionally-interchangeable. However, structural and functional analyses demonstrated that MCR-4 possesses a similar PE lipid substrate-recognizable cavity and exploits an almost-identical ping-pong catalysis mechanism. MCR-4 also can alleviate colistin-triggered accumulation of reactive oxygen species (ROS). Taken together, this finding constitutes a functional proof that MCR-4 proceeds in a distinct evolutionary path to fulfill a consistent molecular mechanism, resulting in phenotypic colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Mengyun Hou
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Yongchang Xu
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Swaminath Srinivas
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Man Huang
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Lizhang Liu
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058 China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
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6
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Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophys J 2018; 115:1920-1930. [PMID: 30366630 DOI: 10.1016/j.bpj.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023] Open
Abstract
Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the presence of a novel motif consisting of an extensive network of salt bridges involving residues in the voltage sensor, S4-S5 linker, pore, and C-terminal domains. This motif has been proposed to be responsible for maintaining an open conformation that enables ion translocation through the channel. In this study, we have used long-time molecular dynamics calculations without artificial restraints to demonstrate that the interaction network of full-length NavMs indeed prevents a rapid collapse and closure of the gate, in marked difference to earlier studies of the pore-only construct in which the gate had to be restrained to remain open. Interestingly, a frequently discussed "hydrophobic gating" mechanism at nanoscopic level is also observed in our simulations, in which the discontinuous water wire close to the gate region leads to an energetic barrier for ion conduction. In addition, we demonstrate the effects of in silico mutations of several of the key residues in the motif on the open channel's stability and functioning, correlating them with existing functional studies on this channel and homologous disease-associated mutations in human sodium channels; we also examine the effects of truncating/removing the voltage sensor and C-terminal domains in maintaining an open gate.
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Affiliation(s)
- Song Ke
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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7
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Gamal El-Din TM, Lenaeus MJ, Catterall WA. Structural and Functional Analysis of Sodium Channels Viewed from an Evolutionary Perspective. Handb Exp Pharmacol 2018; 246:53-72. [PMID: 29043505 DOI: 10.1007/164_2017_61] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels initiate and propagate action potentials in excitable cells. They respond to membrane depolarization through opening, followed by fast inactivation that terminates the sodium current. This ON-OFF behavior of voltage-gated sodium channels underlays the coding of information and its transmission from one location in the nervous system to another. In this review, we explore and compare structural and functional data from prokaryotic and eukaryotic channels to infer the effects of evolution on sodium channel structure and function.
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Affiliation(s)
- Tamer M Gamal El-Din
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA.
| | - Michael J Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
| | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA, 98195-7280, USA
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8
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Xu Y, Zhong LL, Srinivas S, Sun J, Huang M, Paterson DL, Lei S, Lin J, Li X, Tang Z, Feng S, Shen C, Tian GB, Feng Y. Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study. EBioMedicine 2018; 34:139-157. [PMID: 30061009 PMCID: PMC6116419 DOI: 10.1016/j.ebiom.2018.07.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mobilized resistance to colistin is evolving rapidly and its global dissemination poses a severe threat to human health and safety. Transferable colistin resistance gene, mcr-3, first identified in Shandong, China, has already been found in several countries in multidrug-resistant human infections. Here we track the spread of mcr-3 within 13 provinces in China and provide a complete characterization of its evolution, structure and function. METHODS A total of 6497 non-duplicate samples were collected from thirteen provinces in China, from 2016 to 2017 and then screened for the presence of mcr-3 gene by PCR amplification. mcr-3-positive isolates were analyzed for antibiotic resistance and by southern blot hybridization, transfer analysis and plasmid typing. We then examined the molecular evolution of MCR-3 through phylogenetic analysis. Furthermore, we also characterized the structure and function of MCR-3 through circular dichroism analyses, inductively coupled plasma mass spectrometry (ICP-MS), liquid chromatography mass spectrometry (LC/MS), confocal microscopy and chemical rescue tests. FINDINGS 49 samples (49/6497 = 0.75%) were mcr-3 positive, comprising 40 samples (40/4144 = 0.97%) from 2017 and 9 samples (9/2353 = 0.38%) from 2016. Overall, mcr-3-positive isolates were distributed in animals and humans in 8 of the 13 provinces. Three mcr-3-positive IncP-type and one mcr-1-bearing IncHI2-like plasmids were identified and characterized. MCR-3 clusters with PEA transferases from Aeromonas and other bacteria and forms a phylogenetic entity that is distinct from the MCR-1/2/P(M) family, the largest group of transferable colistin resistance determinants. Despite that the two domains of MCR-3 not being exchangeable with their counterparts in MCR-1/2, structure-guided functional mapping of MCR-3 defines a conserved PE-lipid recognizing cavity prerequisite for its enzymatic catalysis and its resultant phenotypic resistance to colistin. We therefore propose that MCR-3 uses a possible "ping-pong" mechanism to transfer the moiety of PEA from its donor PE to the 1(or 4')-phosphate of lipid A via an adduct of MCR-3-bound PEA. Additionally, the expression of MCR-3 in E. coli prevents the colistin-triggered formation of reactive oxygen species (ROS) and interferes bacterial growth and viability. INTERPRETATION Our results provide an evolutionary, structural and functional definition of MCR-3 and its epidemiology in China, paving the way for smarter policies, better surveillance and effective treatments.
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Affiliation(s)
- Yongchang Xu
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lan-Lan Zhong
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Man Huang
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - David L Paterson
- Centre for Clinical Research, Royal Brisbane and Women's Hospital, University of Queensland, Building 71/918, Brisbane QLD 4029, Australia
| | - Sheng Lei
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingxia Lin
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Zichen Tang
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan 471023, China
| | - Siyuan Feng
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Cong Shen
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guo-Bao Tian
- Zhongshan School of Medicine, Key Laboratory of Tropical Diseases Control of Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Youjun Feng
- Department of Medical Microbiology & Parasitology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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9
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Wei W, Srinivas S, Lin J, Tang Z, Wang S, Ullah S, Kota VG, Feng Y. Defining ICR-Mo, an intrinsic colistin resistance determinant from Moraxella osloensis. PLoS Genet 2018; 14:e1007389. [PMID: 29758020 PMCID: PMC5983563 DOI: 10.1371/journal.pgen.1007389] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 05/02/2018] [Indexed: 11/19/2022] Open
Abstract
Polymyxin is the last line of defense against severe infections caused by carbapenem-resistant gram-negative pathogens. The emergence of transferable MCR-1/2 polymyxin resistance greatly challenges the renewed interest in colistin (polymyxin E) for clinical treatments. Recent studies have suggested that Moraxella species are a putative reservoir for MCR-1/2 genetic determinants. Here, we report the functional definition of ICR-Mo from M. osloensis, a chromosomally encoded determinant of colistin resistance, in close relation to current MCR-1/2 family. ICR-Mo transmembrane protein was prepared and purified to homogeneity. Taken along with an in vitro enzymatic detection, MALDI-TOF mass spectrometry of bacterial lipid A pools determined that the ICR-Mo enzyme might exploit a possible "ping-pong" mechanism to accept the phosphoethanolamine (PEA) moiety from its donor phosphatidylethanolamine (PE) and then transfer it to the 1(or 4')-phosphate position of lipid A via an ICR-Mo-bound PEA adduct. Structural decoration of LPS-lipid A by ICR-Mo renders the recipient strain of E. coli resistant to polymyxin. Domain swapping assays indicate that the two domains of ICR-Mo cannot be functionally-exchanged with its counterparts in MCR-1/2 and EptA, validating its phylogenetic position in a distinct set of MCR-like genes. Structure-guided functional mapping of ICR-Mo reveals a PE lipid substrate recognizing cavity having a role in enzymatic catalysis and the resultant conference of antibiotic resistance. Expression of icr-Mo in E. coli significantly prevents the formation of reactive oxygen species (ROS) induced by colistin. Taken together, our results define a member of a group of intrinsic colistin resistance genes phylogenetically close to the MCR-1/2 family, highlighting the evolution of transferable colistin resistance.
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Affiliation(s)
- Wenhui Wei
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, United States of America
| | - Jingxia Lin
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zichen Tang
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Saif Ullah
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Vishnu Goutham Kota
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Department of Medical Microbiology & Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Xu Y, Wei W, Lei S, Lin J, Srinivas S, Feng Y. An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance. mBio 2018; 9:e02317-17. [PMID: 29636432 PMCID: PMC5893884 DOI: 10.1128/mbio.02317-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/08/2018] [Indexed: 12/30/2022] Open
Abstract
Polymyxins, a family of cationic antimicrobial cyclic peptides, act as a last line of defense against severe infections by Gram-negative pathogens with carbapenem resistance. In addition to the intrinsic resistance to polymyxin E (colistin) conferred by Neisseria eptA, the plasmid-borne mobilized colistin resistance gene mcr-1 has been disseminated globally since the first discovery in Southern China, in late 2015. However, the molecular mechanisms for both intrinsic and transferable resistance to colistin remain largely unknown. Here, we aim to address this gap in the knowledge of these proteins. Structural and functional analyses of EptA and MCR-1 and -2 have defined a conserved 12-residue cavity that is required for the entry of the lipid substrate, phosphatidylethanolamine (PE). The in vitro and in vivo data together have allowed us to visualize the similarities in catalytic activity shared by EptA and MCR-1 and -2. The expression of either EptA or MCR-1 or -2 is shown to remodel the surface of enteric bacteria (e.g., Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, etc.), rendering them resistant to colistin. The parallels in the PE substrate-binding cavities among EptA, MCR-1, and MCR-2 provide a comprehensive understanding of both intrinsic and transferable colistin resistance. Domain swapping between EptA and MCR-1 and -2 reveals that the two domains (transmembrane [TM] region and phosphoethanolamine [PEA] transferase) are not functionally exchangeable. Taken together, the results represent a common mechanism for intrinsic and transferable PEA resistance to polymyxin, a last-resort antibiotic against multidrug-resistant pathogens.IMPORTANCE EptA and MCR-1 and -2 remodel the outer membrane, rendering bacteria resistant to colistin, a final resort against carbapenem-resistant pathogens. Structural and functional analyses of EptA and MCR-1 and -2 reveal parallel PE lipid substrate-recognizing cavities, which explains intrinsic and transferable colistin resistance in gut bacteria. A similar mechanism is proposed for the catalytic activities of EptA and MCR-1 and -2. Together, they constitute a common mechanism for intrinsic and transferable polymyxin resistance.
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Affiliation(s)
- Yongchang Xu
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenhui Wei
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sheng Lei
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingxia Lin
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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11
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Xu Y, Lin J, Cui T, Srinivas S, Feng Y. Mechanistic insights into transferable polymyxin resistance among gut bacteria. J Biol Chem 2018; 293:4350-4365. [PMID: 29462787 DOI: 10.1074/jbc.ra117.000924] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/05/2018] [Indexed: 12/15/2022] Open
Abstract
Polymyxins such as colistin are antibiotics used as a final line of defense in the management of infections with multidrug-resistant Gram-negative bacteria. Although natural resistance to polymyxins is rare, the discovery of a mobilized colistin resistance gene (mcr-1) in gut bacteria has raised significant concern. As an intramembrane enzyme, MCR-1 catalyzes the transfer of phosphoethanolamine (PEA) to the 1 (or 4')-phosphate group of the lipid A moiety of lipopolysaccharide, thereby conferring colistin resistance. However, the structural and biochemical mechanisms used by this integral membrane enzyme remain poorly understood. Here, we report the modeled structure of the full-length MCR-1 membrane protein. Together with molecular docking, our structural and functional dissection of the complex of MCR-1 with its phosphatidylethanolamine (PE) substrate suggested the presence of a 12 residue-containing cavity for substrate entry, which is critical for both enzymatic activity and its resultant phenotypic resistance to colistin. More importantly, two periplasm-facing helices (PH2 and PH2') of the trans-membrane domain were essential for MCR-1 activity. MALDI-TOF MS and thin-layer chromatography assays provide both in vivo and in vitro evidence that MCR-1 catalyzes the transfer of PEA from the PE donor substrate to its recipient substrate lipid A. Also, the chemical modification of lipid A species was detected in clinical species of bacteria carrying mcr-1 Our results provide mechanistic insights into transferable MCR-1 polymyxin resistance, raising the prospect of rational design of small molecules that reverse bacterial polymyxin resistance, as a last-resort clinical option to combat pathogens with carbapenem resistance.
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Affiliation(s)
- Yongchang Xu
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingxia Lin
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Tao Cui
- the School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shannxi 710072, China, and
| | - Swaminath Srinivas
- the Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Youjun Feng
- From the Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China, .,the College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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12
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Global versus local mechanisms of temperature sensing in ion channels. Pflugers Arch 2018; 470:733-744. [PMID: 29340775 DOI: 10.1007/s00424-017-2102-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Ion channels turn diverse types of inputs, ranging from neurotransmitters to physical forces, into electrical signals. Channel responses to ligands generally rely on binding to discrete sensor domains that are coupled to the portion of the channel responsible for ion permeation. By contrast, sensing physical cues such as voltage, pressure, and temperature arises from more varied mechanisms. Voltage is commonly sensed by a local, domain-based strategy, whereas the predominant paradigm for pressure sensing employs a global response in channel structure to membrane tension changes. Temperature sensing has been the most challenging response to understand and whether discrete sensor domains exist for pressure and temperature has been the subject of much investigation and debate. Recent exciting advances have uncovered discrete sensor modules for pressure and temperature in force-sensitive and thermal-sensitive ion channels, respectively. In particular, characterization of bacterial voltage-gated sodium channel (BacNaV) thermal responses has identified a coiled-coil thermosensor that controls channel function through a temperature-dependent unfolding event. This coiled-coil thermosensor blueprint recurs in other temperature sensitive ion channels and thermosensitive proteins. Together with the identification of ion channel pressure sensing domains, these examples demonstrate that "local" domain-based solutions for sensing force and temperature exist and highlight the diversity of both global and local strategies that channels use to sense physical inputs. The modular nature of these newly discovered physical signal sensors provides opportunities to engineer novel pressure-sensitive and thermosensitive proteins and raises new questions about how such modular sensors may have evolved and empowered ion channel pores with new sensibilities.
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13
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Mutagenesis of the NaChBac sodium channel discloses a functional role for a conserved S6 asparagine. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:665-674. [PMID: 28825121 PMCID: PMC5599482 DOI: 10.1007/s00249-017-1246-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/21/2017] [Accepted: 07/29/2017] [Indexed: 12/11/2022]
Abstract
Asparagine is conserved in the S6 transmembrane segments of all voltage-gated sodium, calcium, and TRP channels identified to date. A broad spectrum of channelopathies including cardiac arrhythmias, epilepsy, muscle diseases, and pain disorders is associated with its mutation. To investigate its effects on sodium channel functional properties, we mutated the simple prokaryotic sodium channel NaChBac. Electrophysiological characterization of the N225D mutant reveals that this conservative substitution shifts the voltage-dependence of inactivation by 25 mV to more hyperpolarized potentials. The mutant also displays greater thermostability, as determined by synchrotron radiation circular dichroism spectroscopy studies of purified channels. Based on our analyses of high-resolution structures of NaChBac homologues, we suggest that the side-chain amine group of asparagine 225 forms one or more hydrogen bonds with different channel elements and that these interactions are important for normal channel function. The N225D mutation eliminates these hydrogen bonds and the structural consequences involve an enhanced channel inactivation.
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14
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Kumagai PS, Araujo APU, Lopes JLS. Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy. Biophys Rev 2017; 9:517-527. [PMID: 28825203 DOI: 10.1007/s12551-017-0314-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/03/2017] [Indexed: 10/25/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.
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Affiliation(s)
- Patricia S Kumagai
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana P U Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jose L S Lopes
- Departamento Física Aplicada, Instituto de Física,, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
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15
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Sula A, Wallace BA. Interpreting the functional role of a novel interaction motif in prokaryotic sodium channels. J Gen Physiol 2017; 149:613-622. [PMID: 28522439 PMCID: PMC5460950 DOI: 10.1085/jgp.201611740] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/01/2017] [Indexed: 01/17/2023] Open
Abstract
Sula and Wallace explore evidence supporting a role for a novel interaction motif in the gating of prokaryotic sodium channels. Voltage-gated sodium channels enable the translocation of sodium ions across cell membranes and play crucial roles in electrical signaling by initiating the action potential. In humans, mutations in sodium channels give rise to several neurological and cardiovascular diseases, and hence they are targets for pharmaceutical drug developments. Prokaryotic sodium channel crystal structures have provided detailed views of sodium channels, which by homology have suggested potentially important functionally related structural features in human sodium channels. A new crystal structure of a full-length prokaryotic channel, NavMs, in a conformation we proposed to represent the open, activated state, has revealed a novel interaction motif associated with channel opening. This motif is associated with disease when mutated in human sodium channels and plays an important and dynamic role in our new model for channel activation.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, England, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, England, UK
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16
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Advantages of synchrotron radiation circular dichroism spectroscopy to study intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:599-606. [PMID: 28258312 DOI: 10.1007/s00249-017-1202-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
The unordered secondary structural content of an intrinsically disordered protein (IDP) is susceptible to conformational changes induced by many different external factors, such as the presence of organic solvents, removal of water, changes in temperature, binding to partner molecules, and interaction with lipids and/or other ligands. In order to characterize the high-flexibility nature of an IDP, circular dichroism (CD) spectroscopy is a particularly useful method due to its capability of monitoring both subtle and remarkable changes in different environments, relative ease in obtaining measurements, the small amount of sample required, and the capability for sample recovery (sample not damaged) and others. Using synchrotron radiation as the light source for CD spectroscopy represents the state-of-the-art version of this technique with feasibility of accessing the lower wavelength UV region, and therefore presenting a series of advantages over conventional circular dichroism (cCD) to monitor a protein conformational behavior, check protein stability, detect ligand binding, and many others. In this paper, we have performed a comparative study using cCD and SRCD methods for investigating the secondary structure and the conformational behavior of natively unfolded proteins: MEG-14 and soybean trypsin inhibitor. We show that the SRCD technique greatly improves the analysis and accuracy of the studies on the conformations of IDPs.
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17
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Sula A, Booker J, Ng LCT, Naylor CE, DeCaen PG, Wallace BA. The complete structure of an activated open sodium channel. Nat Commun 2017; 8:14205. [PMID: 28205548 PMCID: PMC5316852 DOI: 10.1038/ncomms14205] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
Voltage-gated sodium channels (Navs) play essential roles in excitable tissues, with their activation and opening resulting in the initial phase of the action potential. The cycling of Navs through open, closed and inactivated states, and their closely choreographed relationships with the activities of other ion channels lead to exquisite control of intracellular ion concentrations in both prokaryotes and eukaryotes. Here we present the 2.45 Å resolution crystal structure of the complete NavMs prokaryotic sodium channel in a fully open conformation. A canonical activated conformation of the voltage sensor S4 helix, an open selectivity filter leading to an open activation gate at the intracellular membrane surface and the intracellular C-terminal domain are visible in the structure. It includes a heretofore unseen interaction motif between W77 of S3, the S4–S5 interdomain linker, and the C-terminus, which is associated with regulation of opening and closing of the intracellular gate. Voltage-gated sodium (Nav) channels are crucial for action potential initiation in excitable cells. Here the authors present the complete structure of prokaryotic NavMs in a fully open state, providing structural insight into the opening and closure of the channel's intracellular gate.
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Affiliation(s)
- Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Jennifer Booker
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Leo C T Ng
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, Illinois 60611, USA
| | - Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
| | - Paul G DeCaen
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 E Superior, Chicago, Illinois 60611, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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18
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Ezquerra-Romano I, Ezquerra A. Highway to thermosensation: a traced review, from the proteins to the brain. Rev Neurosci 2017; 28:45-57. [PMID: 27754972 DOI: 10.1515/revneuro-2016-0039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/07/2016] [Indexed: 01/09/2023]
Abstract
Temperature maintenance and detection are essential for the survival and perpetuation of any species. This review is focused on thermosensation; thus a detailed and traced explanation of the anatomical and physiological characteristics of each component of this sensation is given. First, the proteins that react to temperature changes are identified; next, the nature of the neurons involved in thermosensation is described; and then, the pathways from the skin through the spinal cord to the brain are outlined. Finally, the areas of the brain and their interconnections where thermoperception arises are explained. Transduction of the external and internal temperature information is essentially mediated by the transient receptor potential ion channels (TRPs). These proteins are embedded in the neurons' membrane and they hyper- or de-polarize neurons in function of the intrinsic voltage and the temperature changes. There are distinct TRP sensors for different temperature ranges. Interestingly, the primary afferent neurons have either cold or hot receptors, so they are dedicated separately to cold or hot sensation. The information is transmitted by different pathways from the skin to the brain, where it either remains separated or is integrated to generate a response. It seems that both the determination of how thermoperception is produced and how we interact with the world are dependent on the particular arrangement and nature of the components, the way of transduction of information and the communication between these elements.
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19
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Penny CJ, Rahman T, Sula A, Miles AJ, Wallace BA, Patel S. Isolated pores dissected from human two-pore channel 2 are functional. Sci Rep 2016; 6:38426. [PMID: 27941820 PMCID: PMC5150636 DOI: 10.1038/srep38426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/08/2016] [Indexed: 01/30/2023] Open
Abstract
Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels.
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Affiliation(s)
- Christopher J Penny
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Andrew J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7HX, UK
| | - Sandip Patel
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
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20
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Arrigoni C, Rohaim A, Shaya D, Findeisen F, Stein RA, Nurva SR, Mishra S, Mchaourab HS, Minor DL. Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation. Cell 2016; 164:922-36. [PMID: 26919429 DOI: 10.1016/j.cell.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/22/2015] [Accepted: 01/28/2016] [Indexed: 02/07/2023]
Abstract
Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel.
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Affiliation(s)
- Cristina Arrigoni
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ahmed Rohaim
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - David Shaya
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Felix Findeisen
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Shailika Reddy Nurva
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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21
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Hussain R, Siligardi G. Characterisation of Conformational and Ligand Binding Properties of Membrane Proteins Using Synchrotron Radiation Circular Dichroism (SRCD). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:43-59. [PMID: 27553234 PMCID: PMC6126569 DOI: 10.1007/978-3-319-35072-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Membrane proteins are notoriously difficult to crystallise for use in X-ray crystallographic structural determination, or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour in solution. The advantage of synchrotron radiation circular dichroism (SRCD) measured with synchrotron beamlines compared to the CD from benchtop instruments is the extended spectral far-UV region that increases the accuracy of secondary structure estimations, in particular under high ionic strength conditions. Membrane proteins are often available in small quantities, and for this SRCD measured at the Diamond B23 beamline has successfully facilitated molecular recognition studies. This was done by probing the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells (1-5 cm) of small volume capacity (70 μl-350 μl). In this chapter we describe the use of SRCD to qualitatively and quantitatively screen ligand binding interactions (exemplified by Sbma, Ace1 and FsrC proteins); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by FsrC); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by inositol transporters) as well as the stability of membrane proteins (exemplified by GalP, Ace1). The importance of the in solution characterisation of the conformational behaviour and ligand binding properties of proteins in both far- andnear-UV regions and the use of high-throughput CD (HT-CD) using 96- and 384-well multiplates to study the folding effects in various protein crystallisation buffers are also discussed.
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Affiliation(s)
- Rohanah Hussain
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
| | - Giuliano Siligardi
- grid.18785.330000 0004 1764 0696Diamond Light Source, Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
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22
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Miller WC, Miles AJ, Wallace BA. Structure of the C-terminal domain of the prokaryotic sodium channel orthologue NsvBa. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:807-814. [PMID: 27106836 DOI: 10.1007/s00249-016-1125-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 01/13/2023]
Abstract
Crystallographic and electrophysiological studies have recently provided insight into the structure, function, and drug binding of prokaryotic sodium channels. These channels exhibit significant sequence identities, especially in their transmembrane regions, with human voltage-gated sodium channels. However, rather than being single polypeptides with four homologous domains, they are tetramers of single domain polypeptides, with a C-terminal domain (CTD) composed of an inter-subunit four helix coiled coil. The structures of the CTDs differ between orthologues. In NavBh and NavMs, the C-termini form a disordered region adjacent to the final transmembrane helix, followed by a coiled-coil region, as demonstrated by synchrotron radiation circular dichroism (SRCD) and double electron-electron resonance electron paramagnetic resonance spectroscopic measurements. In contrast, in the crystal structure of the NavAe orthologue, the entire C-terminus is comprised of a helical region followed by a coiled coil. In this study, we have examined the CTD of the NsvBa from Bacillus alcalophilus, which unlike other orthologues is predicted by different methods to have different types of structures: either a disordered region adjacent to the transmembrane region, followed by a helical coiled coil, or a fully helical CTD. To discriminate between the two possible structures, we have used SRCD spectroscopy to experimentally determine the secondary structure of the C-terminus of this orthologue and used the results as the basis for modeling the open and closed conformations of the channel.
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Affiliation(s)
- W C Miller
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- School of Biological Sciences, University of Kent, Canterbury, UK
| | - A J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK.
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23
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Abstract
Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.
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Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
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24
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Bagnéris C, Naylor CE, McCusker EC, Wallace BA. Structural model of the open-closed-inactivated cycle of prokaryotic voltage-gated sodium channels. ACTA ACUST UNITED AC 2014; 145:5-16. [PMID: 25512599 PMCID: PMC4278185 DOI: 10.1085/jgp.201411242] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In excitable cells, the initiation of the action potential results from the opening of voltage-gated sodium channels. These channels undergo a series of conformational changes between open, closed, and inactivated states. Many models have been proposed for the structural transitions that result in these different functional states. Here, we compare the crystal structures of prokaryotic sodium channels captured in the different conformational forms and use them as the basis for examining molecular models for the activation, slow inactivation, and recovery processes. We compare structural similarities and differences in the pore domains, specifically in the transmembrane helices, the constrictions within the pore cavity, the activation gate at the cytoplasmic end of the last transmembrane helix, the C-terminal domain, and the selectivity filter. We discuss the observed differences in the context of previous models for opening, closing, and inactivation, and present a new structure-based model for the functional transitions. Our proposed prokaryotic channel activation mechanism is then compared with the activation transition in eukaryotic sodium channels.
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Affiliation(s)
- Claire Bagnéris
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - Emily C McCusker
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England, UK
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25
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Payandeh J, Minor DL. Bacterial voltage-gated sodium channels (BacNa(V)s) from the soil, sea, and salt lakes enlighten molecular mechanisms of electrical signaling and pharmacology in the brain and heart. J Mol Biol 2014; 427:3-30. [PMID: 25158094 DOI: 10.1016/j.jmb.2014.08.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/11/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
Voltage-gated sodium channels (Na(V)s) provide the initial electrical signal that drives action potential generation in many excitable cells of the brain, heart, and nervous system. For more than 60years, functional studies of Na(V)s have occupied a central place in physiological and biophysical investigation of the molecular basis of excitability. Recently, structural studies of members of a large family of bacterial voltage-gated sodium channels (BacNa(V)s) prevalent in soil, marine, and salt lake environments that bear many of the core features of eukaryotic Na(V)s have reframed ideas for voltage-gated channel function, ion selectivity, and pharmacology. Here, we analyze the recent advances, unanswered questions, and potential of BacNa(V)s as templates for drug development efforts.
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Affiliation(s)
- Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA 94080, USA.
| | - Daniel L Minor
- Cardiovascular Research Institute, Departments of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Role of the C-terminal domain in the structure and function of tetrameric sodium channels. Nat Commun 2014; 4:2465. [PMID: 24051986 PMCID: PMC3791462 DOI: 10.1038/ncomms3465] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022] Open
Abstract
Voltage-gated sodium channels have essential roles in electrical signalling. Prokaryotic sodium channels are tetramers consisting of transmembrane (TM) voltage-sensing and pore domains, and a cytoplasmic carboxy-terminal domain. Previous crystal structures of bacterial sodium channels revealed the nature of their TM domains but not their C-terminal domains (CTDs). Here, using electron paramagnetic resonance (EPR) spectroscopy combined with molecular dynamics, we show that the CTD of the NavMs channel from Magnetococcus marinus includes a flexible region linking the TM domains to a four-helix coiled-coil bundle. A 2.9 Å resolution crystal structure of the NavMs pore indicates the position of the CTD, which is consistent with the EPR-derived structure. Functional analyses demonstrate that the coiled-coil domain couples inactivation with channel opening, and is enabled by negatively charged residues in the linker region. A mechanism for gating is proposed based on the structure, whereby splaying of the bottom of the pore is possible without requiring unravelling of the coiled-coil. Prokaryotic voltage-gated sodium channels possess dynamically disordered cytoplasmic C-terminal domains. Bagnéris et al. present the structure of the Magnetococcus marinus NavMs pore and C-terminal domain and reveal its role in coupling channel inactivation and opening.
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Two Alternative Conformations of a Voltage-Gated Sodium Channel. J Mol Biol 2013; 425:4074-88. [DOI: 10.1016/j.jmb.2013.06.036] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 11/21/2022]
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Shaya D, Findeisen F, Abderemane-Ali F, Arrigoni C, Wong S, Nurva SR, Loussouarn G, Minor DL. Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels. J Mol Biol 2013; 426:467-83. [PMID: 24120938 DOI: 10.1016/j.jmb.2013.10.010] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/20/2013] [Accepted: 10/05/2013] [Indexed: 12/18/2022]
Abstract
Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.
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Affiliation(s)
- David Shaya
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Felix Findeisen
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Fayal Abderemane-Ali
- Institut National de la Santé et de la Recherche Médicale, UMR 1087, F-44000 Nantes, France; Centre National de la Recherche Scientifique, UMR 6291, F-44000 Nantes, France; L'institut du thorax, L'UNAM, Université de Nantes, F-44000 Nantes, France
| | - Cristina Arrigoni
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Stephanie Wong
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Shailika Reddy Nurva
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA
| | - Gildas Loussouarn
- Institut National de la Santé et de la Recherche Médicale, UMR 1087, F-44000 Nantes, France; Centre National de la Recherche Scientifique, UMR 6291, F-44000 Nantes, France; L'institut du thorax, L'UNAM, Université de Nantes, F-44000 Nantes, France
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158-9001, USA; Departments of Biochemistry and Biophysics and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158-9001, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158-9001, USA; Physical Biosciences Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Siligardi G, Hussain R, Patching SG, Phillips-Jones MK. Ligand- and drug-binding studies of membrane proteins revealed through circular dichroism spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:34-42. [PMID: 23811229 DOI: 10.1016/j.bbamem.2013.06.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 11/15/2022]
Abstract
A great number of membrane proteins have proven difficult to crystallise for use in X-ray crystallographic structural determination or too complex for NMR structural studies. Circular dichroism (CD) is a fast and relatively easy spectroscopic technique to study protein conformational behaviour. In this review examples of the applications of CD and synchrotron radiation CD (SRCD) to membrane protein ligand binding interaction studies are discussed. The availability of SRCD has been an important advancement in recent progress, most particularly because it can be used to extend the spectral region in the far-UV region (important for increasing the accuracy of secondary structure estimations) and for working with membrane proteins available in only small quantities for which SRCD has facilitated molecular recognition studies. Such studies have been accomplished by probing in the near-UV region the local tertiary structure of aromatic amino acid residues upon addition of chiral or non-chiral ligands using long pathlength cells of small volume capacity. In particular, this review describes the most recent use of the technique in the following areas: to obtain quantitative data on ligand binding (exemplified by the FsrC membrane sensor kinase receptor); to distinguish between functionally similar drugs that exhibit different mechanisms of action towards membrane proteins (exemplified by secretory phospholipase A2); and to identify suitable detergent conditions to observe membrane protein-ligand interactions using stabilised proteins (exemplified by the antiseptic transporter SugE). Finally, the importance of characterising in solution the conformational behaviour and ligand binding properties of proteins in both far- and near-UV regions is discussed. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; School of Biological Sciences, University of Liverpool, Liverpool, UK.
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D'Avanzo N, McCusker EC, Powl AM, Miles AJ, Nichols CG, Wallace BA. Differential lipid dependence of the function of bacterial sodium channels. PLoS One 2013; 8:e61216. [PMID: 23579615 PMCID: PMC3620320 DOI: 10.1371/journal.pone.0061216] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/08/2013] [Indexed: 12/13/2022] Open
Abstract
The lipid bilayer is important for maintaining the integrity of cellular compartments and plays a vital role in providing the hydrophobic and charged interactions necessary for membrane protein structure, conformational flexibility and function. To directly assess the lipid dependence of activity for voltage-gated sodium channels, we compared the activity of three bacterial sodium channel homologues (NaChBac, NavMs, and NavSp) by cumulative (22)Na(+) uptake into proteoliposomes containing a 3∶1 ratio of 1-palmitoyl 2-oleoyl phosphatidylethanolamine and different "guest" glycerophospholipids. We observed a unique lipid profile for each channel tested. NavMs and NavSp showed strong preference for different negatively-charged lipids (phosphatidylinositol and phosphatidylglycerol, respectively), whilst NaChBac exhibited a more modest variation with lipid type. To investigate the molecular bases of these differences we used synchrotron radiation circular dichroism spectroscopy to compare structures in liposomes of different composition, and molecular modeling and electrostatics calculations to rationalize the functional differences seen. We then examined pore-only constructs (with voltage sensor subdomains removed) and found that in these channels the lipid specificity was drastically reduced, suggesting that the specific lipid influences on voltage-gated sodium channels arise primarily from their abilities to interact with the voltage-sensing subdomains.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Physiology and GEPROM (Group d'étude des Proteins Membranaires), Université de Montréal, Montréal, Québec, Canada
- Department of Cell Biology and Physiology and Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Emily C. McCusker
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Andrew M. Powl
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Andrew J. Miles
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Colin G. Nichols
- Department of Cell Biology and Physiology and Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (CN); (BW)
| | - B. A. Wallace
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
- * E-mail: (CN); (BW)
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McCusker EC, Bagnéris C, Naylor CE, Cole AR, D'Avanzo N, Nichols CG, Wallace BA. Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Nat Commun 2013; 3:1102. [PMID: 23033078 PMCID: PMC3493636 DOI: 10.1038/ncomms2077] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/20/2012] [Indexed: 02/03/2023] Open
Abstract
Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al. report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel. Voltage-gated sodium channels are vital membrane proteins essential for electrical signalling; in humans, they are key targets for the development of pharmaceutical drugs. Here we report the crystal structure of an open-channel conformation of NavMs, the bacterial channel pore from the marine bacterium Magnetococcus sp. (strain MC-1). It differs from the recently published crystal structure of a closed form of a related bacterial sodium channel (NavAb) by having its internal cavity accessible to the cytoplasmic surface as a result of a bend/rotation about a central residue in the carboxy-terminal transmembrane segment. This produces an open activation gate of sufficient diameter to allow hydrated sodium ions to pass through. Comparison of the open and closed structures provides new insight into the features of the functional states present in the activation cycles of sodium channels and the mechanism of channel opening and closing.
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Affiliation(s)
- Emily C McCusker
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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Powl AM, Miles AJ, Wallace BA. Transmembrane and extramembrane contributions to membrane protein thermal stability: studies with the NaChBac sodium channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:889-95. [PMID: 22226848 DOI: 10.1016/j.bbamem.2011.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/30/2011] [Accepted: 12/20/2011] [Indexed: 11/16/2022]
Abstract
The thermal stabilities of the extramembranous and transmembranous regions of the bacterial voltage-gated sodium channel NaChBac have been characterised using thermal-melt synchrotron radiation circular dichroism (SRCD) spectroscopy. A series of constructs, ranging from the full-length protein containing both the C-terminal cytoplasmic and the transmembranous domains, to proteins with decreasing amounts of the cytoplasmic domain, were examined in order to separately define the roles of these two types of domains in the stability and processes of unfolding of a membrane protein. The sensitivity of the SRCD measurements over a wide range of wavelengths and temperatures has meant that subtle but reproducible conformational changes could be detected with accuracy. The residues in the C-terminal extramembranous domain were highly susceptible to thermal denaturation, but for the most part the transmembrane residues were not thermally-labile and retained their helical character even at very elevated temperatures. The process of thermal unfolding involved an initial irreversible unfolding of the highly labile distal extramembranous C-terminal helical region, which was accompanied by a reversible unfolding of a small number of helical residues in the transmembrane domain. This was then followed by the irreversible unfolding of a limited number of additional transmembrane helical residues at greatly elevated temperatures. Hence this study has been able to determine the different contributions and roles of the transmembrane and extramembrane residues in the processes of thermal denaturation of this multipass integral membrane protein.
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Affiliation(s)
- Andrew M Powl
- Department of Crystallography, University of London, London, UK
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33
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AcrB contamination in 2-D crystallization of membrane proteins: Lessons from a sodium channel and a putative monovalent cation/proton antiporter. J Struct Biol 2011; 176:419-24. [DOI: 10.1016/j.jsb.2011.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 11/19/2022]
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Abstract
![]()
In excitable cells, the main mediators of sodium conductance
across
membranes are voltage-gated sodium channels (NaVs). Eukaryotic
NaVs are essential elements in neuronal signaling and muscular
contraction and in humans have been causally related to a variety
of neurological and cardiovascular channelopathies. They are complex
heavily glycosylated intrinsic membrane proteins present in only trace
quantities that have proven to be challenging objects of study. However,
in recent years, a number of simpler prokaryotic sodium channels have
been identified, with NaChBac from Bacillus halodurans being the most well-characterized to date. The availability of a
bacterial NaV that is amenable to heterologous expression
and functional characterization in both bacterial and mammalian systems
has provided new opportunities for structure–function studies.
This review describes features of NaChBac as an exemplar of this class
of bacterial channels, compares prokaryotic and eukaryotic NaVs with respect to their structural organization, pharmacological
profiling, and functional kinetics, and discusses how voltage-gated
ion channels may have evolved to deal with the complex functional
demands of higher organisms.
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Affiliation(s)
- Kalypso Charalambous
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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35
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McCusker EC, D'Avanzo N, Nichols CG, Wallace BA. Simplified bacterial "pore" channel provides insight into the assembly, stability, and structure of sodium channels. J Biol Chem 2011; 286:16386-91. [PMID: 21454659 PMCID: PMC3091244 DOI: 10.1074/jbc.c111.228122] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Eukaryotic sodium channels are important membrane proteins involved in ion
permeation, homeostasis, and electrical signaling. They are long, multidomain
proteins that do not express well in heterologous systems, and hence,
structure/function and biochemical studies on purified sodium channel proteins
have been limited. Bacteria produce smaller, homologous tetrameric single domain
channels specific for the conductance of sodium ions. They consist of N-terminal
voltage sensor and C-terminal pore subdomains. We designed a functional
pore-only channel consisting of the final two transmembrane helices, the
intervening P-region, and the C-terminal extramembranous region of the sodium
channel from the marine bacterium Silicibacter pomeroyi. This
sodium “pore” channel forms a tetrameric, folded structure that is
capable of supporting sodium flux in phospholipid vesicles. The pore-only
channel is more thermally stable than its full-length counterpart, suggesting
that the voltage sensor subdomain may destabilize the full-length channel. The
pore subdomains can assemble, fold, and function independently from the voltage
sensor and exhibit similar ligand-blocking characteristics as the intact
channel. The availability of this simple pore-only construct should enable
high-level expression for the testing of potential new ligands and enhance our
understanding of the structural features that govern sodium selectivity and
permeability.
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Affiliation(s)
- Emily C McCusker
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
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36
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Christov C, González-Bulnes P, Malhaire F, Karabencheva T, Goudet C, Pin JP, Llebaria A, Giraldo J. Integrated Synthetic, Pharmacological, and Computational Investigation of cis-2-(3,5-Dichlorophenylcarbamoyl)cyclohexanecarboxylic Acid Enantiomers As Positive Allosteric Modulators of Metabotropic Glutamate Receptor Subtype 4. ChemMedChem 2010; 6:131-40. [DOI: 10.1002/cmdc.201000378] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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37
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Whitmore L, Woollett B, Miles AJ, Klose DP, Janes RW, Wallace BA. PCDDB: the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata. Nucleic Acids Res 2010; 39:D480-6. [PMID: 21071417 PMCID: PMC3013654 DOI: 10.1093/nar/gkq1026] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk.
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Affiliation(s)
- Lee Whitmore
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
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