1
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Mills KR, Torabifard H. Computational approaches to investigate fluoride binding, selectivity and transport across the membrane. Methods Enzymol 2024; 696:109-154. [PMID: 38658077 DOI: 10.1016/bs.mie.2024.01.006] [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: 04/26/2024]
Abstract
The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States
| | - Hedieh Torabifard
- Department of Chemistry & Biochemistry, The University of Texas at Dallas, Richardson, TX, United States.
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2
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Zheng W, Rawson S, Shen Z, Tamilselvan E, Smith HE, Halford J, Shen C, Murthy SE, Ulbrich MH, Sotomayor M, Fu TM, Holt JR. TMEM63 proteins function as monomeric high-threshold mechanosensitive ion channels. Neuron 2023; 111:3195-3210.e7. [PMID: 37543036 PMCID: PMC10592209 DOI: 10.1016/j.neuron.2023.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/12/2023] [Accepted: 07/08/2023] [Indexed: 08/07/2023]
Abstract
OSCA/TMEM63s form mechanically activated (MA) ion channels in plants and animals, respectively. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. Here, we uncover an unanticipated monomeric configuration of TMEM63 proteins. Structures of TMEM63A and TMEM63B (referred to as TMEM63s) revealed a single highly restricted pore. Functional analyses demonstrated that TMEM63s are bona fide mechanosensitive ion channels, characterized by small conductance and high thresholds. TMEM63s possess evolutionary variations in the intracellular linker IL2, which mediates dimerization in OSCAs. Replacement of OSCA1.2 IL2 with TMEM63A IL2 or mutations to key variable residues resulted in monomeric OSCA1.2 and MA currents with significantly higher thresholds. Structural analyses revealed substantial conformational differences in the mechano-sensing domain IL2 and gating helix TM6 between TMEM63s and OSCA1.2. Our studies reveal that mechanosensitivity in OSCA/TMEM63 channels is affected by oligomerization and suggest gating mechanisms that may be shared by OSCA/TMEM63, TMEM16, and TMC channels.
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Affiliation(s)
- Wang Zheng
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Harper E Smith
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Julia Halford
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Chen Shen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Swetha E Murthy
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maximilian H Ulbrich
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany; Internal Medicine IV, University of Freiburg Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.
| | - Jeffrey R Holt
- Departments of Otolaryngology & Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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3
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Zhang J, Song D, Schackert FK, Li J, Xiang S, Tian C, Gong W, Carloni P, Alfonso-Prieto M, Shi C. Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR. SCIENCE ADVANCES 2023; 9:eadg9709. [PMID: 37611110 PMCID: PMC10446490 DOI: 10.1126/sciadv.adg9709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of membrane proteins in liposomes at the atomic level and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we report our study on the fluoride channel Fluc-Ec1 in phospholipid bilayers based on ssNMR and molecular dynamics simulations. Previously unidentified fluoride binding sites in the aqueous vestibules were experimentally verified by 19F-detected ssNMR. One of the two fluoride binding sites in the polar track was identified as a water molecule by 1H-detected ssNMR. Meanwhile, a dynamic hotspot at loop 1 was observed by comparing the spectra of wild-type Fluc-Ec1 in variant buffer conditions or with its mutants. Therefore, we propose that fluoride conduction in the Fluc channel occurs via a "water-mediated knock-on" permeation mechanism and that loop 1 is a key molecular determinant for channel gating.
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Affiliation(s)
- Jin Zhang
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Dan Song
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Florian Karl Schackert
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Juan Li
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Shengqi Xiang
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Changlin Tian
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Weimin Gong
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Chaowei Shi
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Center for BioAnalytical Chemistry, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, 230027 Hefei, P. R. China
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4
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Mills KR, Torabifard H. Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLC F Antiporter. J Chem Inf Model 2023; 63:2445-2455. [PMID: 37053383 DOI: 10.1021/acs.jcim.2c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLCF F-/H+ antiporter protein, a member of the CLC superfamily of anion-transport proteins. Though previous studies have examined this F- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLCF, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first studies of the CLCF F-/H+ antiporter and is the first computational investigation to model the full transport process, proposing a mechanism which couples the F- export with the H+ import.
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Affiliation(s)
- Kira R Mills
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Hedieh Torabifard
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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5
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Yadav PR, Basha SH. Impact of F80M and F83M mutations on the functionality of fluoride ion channel elucidated in microsecond level molecular dynamic simulation. J Biomol Struct Dyn 2022; 40:10899-10904. [PMID: 34463212 DOI: 10.1080/07391102.2021.1951356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fluoride ion channels of the Fluc family plays a critically important role in combating environmental fluoride toxicity. As per the crystal structure of these fluoride ion channels, the pore region is densely packed with a series of hydrogen bond donating residues arranged in a ladder fashion creating an ion conducting pathway. In earlier studies, it was revealed that although the ion conducting pathway polarity is highly conserved, however the functionality of the channel protein depends on several residues at particular positions. While, a threonine at end of the pore is critically important in forming initial interactions, two phenylalanines at the central region coordinate F- transportation through the channel. It was also revealed that these two phenylalanines cannot be substituted by any other aromatic, polar or non-polar residues without hindering the functionality with exception of methionine. In another study, it was revealed that these two phenylalanines F80 and F83 when mutated with methionine; F80M lead to active state, while the F83M has lead to inactivity of F- anion conductivity. However, the exact atomic level detailing on how exactly these mutations have impacted the conductivity remained elusive. In this scenario, in this present study, we have modeled these two mutations and performed a microsecond level simulation on each mutation compared with wild type towards understanding the atomic level detailing revealing several insights on what exactly happening at these residues responsible for the selective conductivity of F- ions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pulala Raghuveer Yadav
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
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6
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Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022; 24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
The presence of mineral fluoride (F- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F- is more abundant than other halides in the Earth crust (e.g. in some soils, the F- concentration can reach up to 1 mg gsoil -1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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7
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Liu W, Yuan S, Jin M, Xian M. Biocatalytic synthesis of 2-fluoro-3-hydroxypropionic acid. Front Bioeng Biotechnol 2022; 10:969012. [PMID: 36061447 PMCID: PMC9428585 DOI: 10.3389/fbioe.2022.969012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Fluorine has become an important element for the design of synthetic molecules for use in medicine, agriculture, and materials. The introduction of fluorine atoms into organic compound molecules can often give these compounds new functions and make them have better performance. Despite the many advantages provided by fluorine for tuning key molecular properties, it is rarely found in natural metabolism. We seek to expand the molecular space available for discovery through the development of new biosynthetic strategies that cross synthetic with natural compounds. Towards this goal, 2-fluoro-3-hydroxypropionic acid (2-F-3-HP) was first synthesized using E. coli coexpressing methylmalonyl CoA synthase (MatBrp), methylmalonyl CoA reductase (MCR) and malonate transmembrane protein (MadLM). The concentration of 2-F-3-HP reached 50.0 mg/L by whole-cell transformation after 24 h. 2-F-3-HP can be used as the substrate to synthesize other fluorides, such as poly (2-fluoro-3-hydroxypropionic acid) (FP3HP). Being entirely biocatalytic, our procedure provides considerable advantages in terms of environmental and safety impacts over reported chemical methods.
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Affiliation(s)
- Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- *Correspondence: Mo Xian, ; Wei Liu,
| | - Shan Yuan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Jin
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- *Correspondence: Mo Xian, ; Wei Liu,
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8
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Ion permeation, selectivity, and electronic polarization in fluoride channels. Biophys J 2022; 121:1336-1347. [PMID: 35151630 PMCID: PMC9034187 DOI: 10.1016/j.bpj.2022.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/16/2022] Open
Abstract
Fluoride channels (Flucs) export toxic F- from the cytoplasm. Crystallography and mutagenesis have identified several conserved residues crucial for fluoride transport, but the permeation mechanism at the molecular level has remained elusive. Herein, we have applied constant-pH molecular dynamics and free-energy-sampling methods to investigate fluoride permeation through a Fluc protein from Escherichia coli. We find that fluoride is facile to permeate in its charged form, i.e., F-, by traversing through a non-bonded network. The extraordinary F- selectivity is gained by the hydrogen-bonding capability of the central binding site and the Coulombic filter at the channel entrance. The F- permeation rate calculated using an electronically polarizable force field is significantly more accurate compared with the experimental value than that calculated using a more standard additive force field, suggesting an essential role for electronic polarization in the F--Fluc interactions.
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9
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Abstract
TMEM16A Ca2+-activated chloride channels are involved in multiple cellular functions and are proposed targets for diseases such as hypertension, stroke, and cystic fibrosis. This therapeutic endeavor, however, suffers from paucity of selective and potent modulators. Here, exploiting a synthetic small molecule with a biphasic effect on the TMEM16A channel, anthracene-9-carboxylic acid (A9C), we shed light on sites of the channel amenable for pharmacological intervention. Mutant channels with the intracellular gate constitutively open were generated. These channels were entirely insensitive to extracellular A9C when intracellular Ca2+ was omitted. However, when physiological Ca2+ levels were reestablished, the mutants regained sensitivity to A9C. Thus, intracellular Ca2+ is mandatory for the channel response to an extracellular modulator. The underlying mechanism is a conformational change in the outer pore that enables A9C to enter the pore to reach its binding site. The explanation of this structural rearrangement highlights a critical site for pharmacological intervention and reveals an aspect of Ca2+ gating in the TMEM16A channel.
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10
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McIlwain BC, Gundepudi R, Koff BB, Stockbridge RB. The fluoride permeation pathway and anion recognition in Fluc family fluoride channels. eLife 2021; 10:69482. [PMID: 34250906 PMCID: PMC8315801 DOI: 10.7554/elife.69482] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Fluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride-binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology, and liposome-based assays, we identified additional binding sites along the permeation pathway. We used this information to develop an oriented system for planar lipid bilayer electrophysiology and observed anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion-binding sites that are fully assembled only as the substrate approaches.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Roja Gundepudi
- Program in Biophysics, University of Michigan, Ann Arbor, United States
| | - B Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States.,Program in Biophysics, University of Michigan, Ann Arbor, United States
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11
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The application of Poisson distribution statistics in ion channel reconstitution to determine oligomeric architecture. Methods Enzymol 2021; 652:321-340. [PMID: 34059289 DOI: 10.1016/bs.mie.2021.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During reconstitution, membrane proteins are randomly inserted into liposomes according to Poisson distribution statistics. When the protein to lipid ratios in the reconstitution mixture are varied systematically, the characteristics of this statistical capture permit inferences about the proteins themselves, such as the number of subunits that assemble into a single functional unit. This chapter describes the Poisson distribution as applied to the reconstitution of membrane proteins into proteoliposomes and focuses on an application whereby this statistical behavior is used to determine the number of ion channel subunits that assemble into a functional pore. Practical considerations for performing these experiments are emphasized. Harnessing Poisson dilution statistics provides a function-based method to determine ion channel oligomerization, complementing other biophysical, biochemical, or structural approaches.
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12
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Abstract
Microorganisms contend with numerous and unusual chemical threats and have evolved a catalog of resistance mechanisms in response. One particularly ancient, pernicious threat is posed by fluoride ion (F-), a common xenobiotic in natural environments that causes broad-spectrum harm to metabolic pathways. This review focuses on advances in the last ten years toward understanding the microbial response to cytoplasmic accumulation of F-, with a special emphasis on the structure and mechanisms of the proteins that microbes use to export fluoride: the CLCF family of F-/H+ antiporters and the Fluc/FEX family of F- channels.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Michal T Ruprecht
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; .,Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Lee HJ, Jeong H, Hyun J, Ryu B, Park K, Lim HH, Yoo J, Woo JS. Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel. SCIENCE ADVANCES 2020; 6:eaba4996. [PMID: 32923625 PMCID: PMC7455182 DOI: 10.1126/sciadv.aba4996] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/15/2020] [Indexed: 05/28/2023]
Abstract
Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). We determined the cryo-electron microscopy structures of human connexin 31.3 (Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G at 2.3-, 2.5-, and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in open conformation, Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion-binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. We also found that the hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions. Our study provides structural insights into the permeant selectivity of Cx31.3 hemichannel.
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Affiliation(s)
- Hyuk-Joon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyeongseop Jeong
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Korea Basic Science Institute, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Korea Basic Science Institute, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0496, Japan
| | - Bumhan Ryu
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kunwoong Park
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 41062 Daegu, Republic of Korea
| | - Hyun-Ho Lim
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 41062 Daegu, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon, Republic of Korea
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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14
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Zhekova HR, Sakuma T, Johnson R, Concilio SC, Lech PJ, Zdravkovic I, Damergi M, Suksanpaisan L, Peng KW, Russell SJ, Noskov S. Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). J Chem Inf Model 2020; 60:1652-1665. [PMID: 32134653 DOI: 10.1021/acs.jcim.9b01114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human sodium iodide symporter (hNIS) is a theranostic reporter gene which concentrates several clinically approved SPECT and PET radiotracers and plays an essential role for the synthesis of thyroid hormones as an iodide transporter in the thyroid gland. Development of hNIS mutants which could enhance translocation of the desired imaging ions is currently underway. Unfortunately, it is hindered by lack of understanding of the 3D organization of hNIS and its relation to anion transport. There are no known crystal structures of hNIS in any of its conformational states. Homology modeling can be very effective in such situations; however, the low sequence identity between hNIS and relevant secondary transporters with available experimental structures makes the choice of a template and the generation of 3D models nontrivial. Here, we report a combined application of homology modeling and molecular dynamics refining of the hNIS structure in its semioccluded state. The modeling was based on templates from the LeuT-fold protein family and was done with emphasis on the refinement of the substrate-ion binding pocket. The consensus model developed in this work is compared to available biophysical and biochemical experimental data for a number of different LeuT-fold proteins. Some functionally important residues contributing to the formation of putative binding sites and permeation pathways for the cotransported Na+ ions and I- substrate were identified. The model predictions were experimentally tested by generation of mutant versions of hNIS and measurement of relative (to WT hNIS) 125I- uptake of 35 hNIS variants.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Toshie Sakuma
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Ryan Johnson
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Susanna C Concilio
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States.,Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Patrycja J Lech
- Imanis Life Sciences, Rochester, Minnesota 55901, United States
| | - Igor Zdravkovic
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Mirna Damergi
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Kah-Whye Peng
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Stephen J Russell
- Imanis Life Sciences, Rochester, Minnesota 55901, United States.,Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota 55902, United States
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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15
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An Interfacial Sodium Ion is an Essential Structural Feature of Fluc Family Fluoride Channels. J Mol Biol 2020; 432:1098-1108. [PMID: 31945374 DOI: 10.1016/j.jmb.2020.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/17/2022]
Abstract
Fluc family fluoride channels are assembled as primitive antiparallel homodimers. Crystallographic studies revealed a cation bound at the center of the protein, where it is coordinated at the dimer interface by main chain carbonyl oxygen atoms from the midmembrane breaks in two corresponding transmembrane helices. Here, we show that this cation is a stably bound sodium ion, and although it is not a transported substrate, its presence is required for the channel to adopt an open, fluoride-conducting conformation. The interfacial site is selective for sodium over other cations, except for Li+, which competes with Na+ for binding, but does not support channel activity. The strictly structural role fulfilled by this sodium provides new context to understand the structures, mechanisms, and evolutionary origins of widespread Na+-coupled transporters.
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16
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Johnston NR, Strobel SA. Nitrate and Phosphate Transporters Rescue Fluoride Toxicity in Yeast. Chem Res Toxicol 2019; 32:2305-2319. [PMID: 31576749 DOI: 10.1021/acs.chemrestox.9b00315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organisms are exposed to fluoride in the air, water, and soil. Yeast and other microbes utilize fluoride channels as a method to prevent intracellular fluoride accumulation and mediate fluoride toxicity. Consequently, deletion of fluoride exporter genes (FEX) in S. cerevisiae resulted in over 1000-fold increased fluoride sensitivity. We used this FEX knockout strain to identify genes, that when overexpressed, are able to partially relieve the toxicity of fluoride exposure. Overexpression of five genes, SSU1, YHB1, IPP1, PHO87, and PHO90, increase fluoride tolerance by 2- to 10-fold. Overexpression of these genes did not provide improved fluoride resistance in wild-type yeast, suggesting that the mechanism is specific to low fluoride toxicity in yeast. Ssu1p and Yhb1p both function in nitrosative stress response, which is induced upon fluoride exposure along with metal influx. Ipp1p, Pho87p, and Pho90p increase intracellular orthophosphate. Consistent with this observation, fluoride toxicity is also partially mitigated by the addition of high levels of phosphate to the growth media. Fluoride inhibits phosphate import upon stress induction and causes nutrient starvation and organelle disruption, as supported by gene induction monitored through RNA-Seq. The combination of observations suggests that transmembrane nutrient transporters are among the most sensitized proteins during fluoride-instigated stress.
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Affiliation(s)
- Nichole R Johnston
- From the Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520
| | - Scott A Strobel
- From the Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520.,Department of Chemistry , Yale University , New Haven , Connecticut 06520
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17
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Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
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Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
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18
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Zhu J, Xing A, Wu Z, Tao J, Ma Y, Wen B, Zhu X, Fang W, Wang Y. CsFEX, a Fluoride Export Protein Gene from Camellia sinensis, Alleviates Fluoride Toxicity in Transgenic Escherichia coli and Arabidopsis thaliana. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5997-6006. [PMID: 31056906 DOI: 10.1021/acs.jafc.9b00509] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A fluoride export gene ( CsFEX) was newly found and isolated from Camellia sinensis, and its functions in detoxifying F were investigated in transgenic Escherichia coli and Arabidopsis thaliana. CsFEX contains two crcB domains, which is the typical structure in plants. The expression of CsFEX in C. sinensis is tissue-specific and related to maturity of leaves, and its expression is significantly induced by F treatments in different tissues of C. sinensis, particularly in leaves. Additionally, the growth of C. sinensis, E. coli, and A. thaliana can all be inhibited by F treatment. However, the growth of CsFEX-overexpression E. coli was increased with lower F content under F treatment compared to the control. Similarly, the germination and growth of CsFEX-overexpression A. thaliana were enhanced with lower F content under F treatment compared to the wild type. CsFEX relieves F toxicity in the transgenic E. coli and A. thaliana by alleviating F accumulation.
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Affiliation(s)
- Jiaojiao Zhu
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Anqi Xing
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Zichen Wu
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Jing Tao
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Yuanchun Ma
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Bo Wen
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Xujun Zhu
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Wanping Fang
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
| | - Yuhua Wang
- College of Horticulture , Nanjing Agricultural University , Nanjing , Jiangsu 210095 , People's Republic of China
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19
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Banerjee A, Roychoudhury A. Structural introspection of a putative fluoride transporter in plants. 3 Biotech 2019; 9:103. [PMID: 30800614 DOI: 10.1007/s13205-019-1629-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/10/2019] [Indexed: 12/11/2022] Open
Abstract
The xenobiotic fluoride is a detrimental toxin which is exported by a double-barrelled fluoride channel (Fluc) in prokaryotes and a single-barrelled fluoride exporter (FEX) in lower eukaryotes. The presence of FEX gene in higher plant species has not been reported till date. In this communication, we have identified FEXs across nine plant species belonging to five different families. Homology modelling predicted the sequential and structural conservation of crucial residues in plant FEXs. It was predicted that the N-terminal segments were the main target sites for phosphorylation. Other post-translational modifications included Arg methylation, Lys acetylation and Cys S-nitrosylation, all of which contribute to protein stability and function. FEXs were predicted to contain lipid moieties which anchor the transporters to the plasma membrane. The crystallizability along with associated properties of plant FEXs was also analyzed to facilitate future experimental analyses. The predicted RNA structure of OsFEX formed several pseudoknots, though no riboswitches could be detected from our prediction. The analysis of upstream regions of FEX in representative plants represented that this gene could be responsive to phytohormone-mediated signaling. This is the first novel report highlighting that FEX genes in plants are probably expressed in a tissue-specific pattern and possibly via a phytohormone-dependent pathway to encode functional FEX proteins during fluoride stress.
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20
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Last NB, Stockbridge RB, Wilson AE, Shane T, Kolmakova-Partensky L, Koide A, Koide S, Miller C. A CLC-type F -/H + antiporter in ion-swapped conformations. Nat Struct Mol Biol 2018; 25:601-606. [PMID: 29941917 PMCID: PMC6044475 DOI: 10.1038/s41594-018-0082-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 11/09/2022]
Abstract
Fluoride/proton antiporters of the CLCF family combat F- toxicity in bacteria by exporting this halide from the cytoplasm. These transporters belong to the widespread CLC superfamily but display transport properties different from those of the well-studied Cl-/H+ antiporters. Here, we report a structural and functional investigation of these F--transport proteins. Crystal structures of a CLCF homolog from Enterococcus casseliflavus are captured in two conformations with simultaneous accessibility of F- and H+ ions via separate pathways on opposite sides of the membrane. Manipulation of a key glutamate residue critical for H+ and F- transport reverses the anion selectivity of transport; replacement of the glutamate with glutamine or alanine completely inhibits F- and H+ transport while allowing for rapid uncoupled flux of Cl-. The structural and functional results lead to a 'windmill' model of CLC antiport wherein F- and H+ simultaneously move through separate ion-specific pathways that switch sidedness during the transport cycle.
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Affiliation(s)
- Nicholas B Last
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Randy B Stockbridge
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Ashley E Wilson
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Tania Shane
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | | | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA.
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21
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Riederer EA, Focke PJ, Georgieva ER, Akyuz N, Matulef K, Borbat PP, Freed JH, Blanchard SC, Boudker O, Valiyaveetil FI. A facile approach for the in vitro assembly of multimeric membrane transport proteins. eLife 2018; 7:36478. [PMID: 29889023 PMCID: PMC6025958 DOI: 10.7554/elife.36478] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
Membrane proteins such as ion channels and transporters are frequently homomeric. The homomeric nature raises important questions regarding coupling between subunits and complicates the application of techniques such as FRET or DEER spectroscopy. These challenges can be overcome if the subunits of a homomeric protein can be independently modified for functional or spectroscopic studies. Here, we describe a general approach for in vitro assembly that can be used for the generation of heteromeric variants of homomeric membrane proteins. We establish the approach using GltPh, a glutamate transporter homolog that is trimeric in the native state. We use heteromeric GltPh transporters to directly demonstrate the lack of coupling in substrate binding and demonstrate how heteromeric transporters considerably simplify the application of DEER spectroscopy. Further, we demonstrate the general applicability of this approach by carrying out the in vitro assembly of VcINDY, a Na+-coupled succinate transporter and CLC-ec1, a Cl-/H+ antiporter.
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Affiliation(s)
- Erika A Riederer
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Paul J Focke
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Kimberly Matulef
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, Unites States.,National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, United States
| | | | - Olga Boudker
- Weill Cornell Medicine, New York, United States.,Howard Hughes Medical Institute, Maryland, United States
| | - Francis I Valiyaveetil
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, United States
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22
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Ariz-Extreme I, Hub JS. Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc. PLoS One 2018; 13:e0196751. [PMID: 29771936 PMCID: PMC5957342 DOI: 10.1371/journal.pone.0196751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/18/2018] [Indexed: 11/25/2022] Open
Abstract
Approximately 90% of the structures in the Protein Data Bank (PDB) were obtained by X-ray crystallography or electron microscopy. Whereas the overall quality of structure is considered high, thanks to a wide range of tools for structure validation, uncertainties may arise from density maps of small molecules, such as organic ligands, ions or water, which are non-covalently bound to the biomolecules. Even with some experience and chemical intuition, the assignment of such disconnected electron densities is often far from obvious. In this study, we suggest the use of molecular dynamics (MD) simulations and free energy calculations, which are well-established computational methods, to aid in the assignment of ambiguous disconnected electron densities. Specifically, estimates of (i) relative binding affinities, for instance between an ion and water, (ii) absolute binding free energies, i.e., free energies for transferring a solute from bulk solvent to a binding site, and (iii) stability assessments during equilibrium simulations may reveal the most plausible assignments. We illustrate this strategy using the crystal structure of the fluoride specific channel (Fluc), which contains five disconnected electron densities previously interpreted as four fluoride and one sodium ion. The simulations support the assignment of the sodium ion. In contrast, calculations of relative and absolute binding free energies as well as stability assessments during free MD simulations suggest that four of the densities represent water molecules instead of fluoride. The assignment of water is compatible with the loss of these densities in the non-conductive F82I/F85I mutant of Fluc. We critically discuss the role of the ion force fields for the calculations presented here. Overall, these findings indicate that MD simulations and free energy calculations are helpful tools for modeling water and ions into crystallographic density maps.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Jochen S. Hub
- Institute for Microbiology and Genetics, University of Goettingen, Göttingen, Germany
- * E-mail:
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23
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Abstract
Crystallization of dual-topology fluoride (Fluc) channels requires small, soluble crystallization chaperones known as monobodies, which act as primary crystal lattice contacts. Previous structures of Flucs have been solved in the presence of monobodies that inhibit fluoride currents in single-channel electrophysiological recordings. These structures have revealed two-fold symmetric, doubly bound arrangements, with one monobody on each side of the membrane. The combined electrophysiological and structural observations raise the possibility that chaperone binding allosterically closes the channel, altering the structure from its conducting form. To address this, we identify and solve the structure with a different monobody that only partially blocks fluoride currents. The structure of the channel-monobody complex is asymmetric, with monobody bound to one side of the channel only. The channel conformation is nearly identical on the bound and uncomplexed sides, and to all previously solved structures, providing direct structural evidence that monobody binding does not induce local structural changes. Inhibitory crystallization chaperones bind on each side of the membrane Crystal structure of channel with one side free of chaperone binding S8 chaperone-bound channel is competent for fluoride transport Chaperones inhibit channels via a “cork-in-bottle” mechanism of physical occlusion
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24
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Turman DL, Cheloff AZ, Corrado AD, Nathanson JT, Miller C. Molecular Interactions between a Fluoride Ion Channel and Synthetic Protein Blockers. Biochemistry 2018; 57:1212-1218. [PMID: 29393634 DOI: 10.1021/acs.biochem.7b01272] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluoride ion channels of the Fluc family selectively export F- ions to rescue unicellular organisms from acute F- toxicity. Crystal structures of bacterial Fluc channels in complex with synthetic monobodies, fibronectin-derived soluble β-sandwich fold proteins, show 2-fold symmetric homodimers with an antiparallel transmembrane topology. Monobodies also block Fluc F- current via a pore blocking mechanism. However, little is known about the energetic contributions of individual monobody residues to the affinity of the monobody-channel complex or whether the structural paratope corresponds to functional reality. This study seeks to structurally identify and compare residues interacting with Fluc between two highly similar monobodies and subjects them to mutagenesis and functional measurements of equilibrium affinities via a fluorescence anisotropy binding assay to determine their energetic contributions. The results indicate that the functional and structural paratopes strongly agree and that many Tyr residues at the interface, while playing a key role in affinity, can be substituted with Phe and Trp without large disruptions.
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Affiliation(s)
- Daniel L Turman
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Abraham Z Cheloff
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Alexis D Corrado
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Jacob T Nathanson
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University , 415 South Street, Waltham, Massachusetts 02453, United States
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25
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Last NB, Sun S, Pham MC, Miller C. Molecular determinants of permeation in a fluoride-specific ion channel. eLife 2017; 6:31259. [PMID: 28952925 PMCID: PMC5636608 DOI: 10.7554/elife.31259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/26/2017] [Indexed: 12/28/2022] Open
Abstract
Fluoride ion channels of the Fluc family combat toxicity arising from accumulation of environmental F-. Although crystal structures are known, the densely packed pore region has precluded delineation of the ion pathway. Here we chart out the Fluc pore and characterize its chemical requirements for transport. A ladder of H-bond donating residues creates a ‘polar track’ demarking the ion-conduction pathway. Surprisingly, while track polarity is well conserved, polarity is nonetheless functionally dispensable at several positions. A threonine at one end of the pore engages in vital interactions through its β-branched methyl group. Two critical central phenylalanines that directly coordinate F- through a quadrupolar-ion interaction cannot be functionally substituted by aromatic, non-polar, or polar sidechains. The only functional replacement is methionine, which coordinates F- through its partially positive γ-methylene in mimicry of phenylalanine’s quadrupolar interaction. These results demonstrate the unusual chemical requirements for selectively transporting the strongly H-bonding F- anion.
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Affiliation(s)
- Nicholas B Last
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Senmiao Sun
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Minh C Pham
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
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26
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Macdonald CB, Stockbridge RB. A topologically diverse family of fluoride channels. Curr Opin Struct Biol 2017; 45:142-149. [PMID: 28514705 DOI: 10.1016/j.sbi.2017.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 01/13/2023]
Abstract
Dual-topology proteins are likely evolutionary antecedents to a common motif in membrane protein structures, the inverted repeat. A family of fluoride channels, the Flucs, which protect microorganisms, fungi, and plants against cytoplasmic fluoride accumulation, has representatives of all topologies along this evolutionary trajectory, including dual-topology homodimers, antiparallel heterodimers, and, in eukaryotes, fused two-domain proteins with an inverted repeat motif. Recent high-resolution crystal structures of dual-topology homodimers, coupled with extensive functional information about both the homodimers and two-domain Flucs, provide a case study of the co-evolution of fold and function.
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Affiliation(s)
- Christian B Macdonald
- Program in Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Randy B Stockbridge
- Program in Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
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27
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Berbasova T, Nallur S, Sells T, Smith KD, Gordon PB, Tausta SL, Strobel SA. Fluoride export (FEX) proteins from fungi, plants and animals are 'single barreled' channels containing one functional and one vestigial ion pore. PLoS One 2017; 12:e0177096. [PMID: 28472134 PMCID: PMC5417652 DOI: 10.1371/journal.pone.0177096] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/21/2017] [Indexed: 01/31/2023] Open
Abstract
The fluoride export protein (FEX) in yeast and other fungi provides tolerance to fluoride (F-), an environmentally ubiquitous anion. FEX efficiently eliminates intracellular fluoride that otherwise would accumulate at toxic concentrations. The FEX homolog in bacteria, Fluc, is a 'double-barreled' channel formed by dimerization of two identical or similar subunits. FEX in yeast and other eukaryotes is a monomer resulting from covalent fusion of the two subunits. As a result, both potential fluoride pores are created from different parts of the same protein. Here we identify FEX proteins from two multicellular eukaryotes, a plant Arabidopsis thaliana and an animal Amphimedon queenslandica, by demonstrating significant fluoride tolerance when these proteins are heterologously expressed in the yeast Saccharomyces cerevisiae. Residues important for eukaryotic FEX function were determined by phylogenetic sequence alignment and functional analysis using a yeast growth assay. Key residues of the fluoride channel are conserved in only one of the two potential fluoride-transporting pores. FEX activity is abolished upon mutation of residues in this conserved pore, suggesting that only one of the pores is functional. The same topology is conserved for the newly identified FEX proteins from plant and animal. These data suggest that FEX family of fluoride channels in eukaryotes are 'single-barreled' transporters containing one functional pore and a second non-functional vestigial remnant of a homologous gene fusion event.
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Affiliation(s)
- Tetyana Berbasova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Sunitha Nallur
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Taylor Sells
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Kathryn D. Smith
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Patricia B. Gordon
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Susan Lori Tausta
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Scott A. Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Chemical Biology Institute, Yale University, West Haven, Connecticut, United States of America
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28
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Chavan T, Maduke M, Swartz K. Protein ligands for studying ion channel proteins. J Gen Physiol 2017; 149:407-411. [PMID: 28270405 PMCID: PMC5379924 DOI: 10.1085/jgp.201711776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chavan et al. highlight work showing that a monobody can inhibit a fluoride channel using a mechanism similar to that of a scorpion toxin blocker of potassium channels.
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Affiliation(s)
- Tanmay Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Kenton Swartz
- Molecular Physiology and Biophysics Section, John Edward Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
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Turman DL, Stockbridge RB. Mechanism of single- and double-sided inhibition of dual topology fluoride channels by synthetic monobodies. J Gen Physiol 2017; 149:511-522. [PMID: 28258203 PMCID: PMC5379923 DOI: 10.1085/jgp.201611747] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/03/2017] [Indexed: 11/30/2022] Open
Abstract
Fibronectin domain monobodies bind to both sides of Fluc Fl− channels in a negatively cooperative way, but crystal structures show two monobodies binding simultaneously. Turman and Stockbridge resolve this contradiction by showing that monobodies block channel pores by means of a negatively charged loop. The Fluc family of proteins comprises small, electrodiffusive fluoride channels, which prevent accumulation of toxic F− ions in microorganisms. Recent crystal structures have confirmed their unusual architecture, in which a pair of antiparallel subunits convenes to form a dimer with a twofold symmetry axis parallel to the plane of the membrane. These structures have also revealed the interactions between Fluc channels and several different fibronectin domain monobodies that inhibit Fluc-mediated F− currents; in all structures, each channel binds to two monobodies symmetrically, one on either side of the membrane. However, these structures do not reveal the mechanism of monobody inhibition. Moreover, the results appear to diverge from a recent electrophysiological study indicating that monobody binding is negatively cooperative; that is, a bound monobody on one side of a Fluc channel decreases the affinity of an oppositely bound monobody by ∼10-fold. In this study, we reconcile these observations by probing the mechanism of monobody binding and its negative cooperativity using electrophysiological experiments in planar lipid bilayers. Our results indicate that monobody inhibition occurs via a pore-blocking mechanism and that negative cooperativity arises from electrostatic repulsion between the oppositely bound monobodies. A single glutamate residue, on a loop of the monobody that extends into the channel interior, is responsible for negatively cooperative binding. This glutamate side chain also confers voltage dependence and sensitivity to the concentration of trans-F− ion to monobody binding. Neutralization by mutation to glutamine abolishes these electrostatic effects. Monobodies that are amenable to cocrystallization with Fluc channels lack an analogous negatively charged side chain and bind independently to opposite sides of the channel. Thus, this work reveals the source of voltage dependence and negative cooperativity of monobody binding to Fluc channels along with the pore-blocking mechanism.
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Affiliation(s)
- Daniel L Turman
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454
| | - Randy B Stockbridge
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109 .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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