1
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Avalos-Hernandez A, Juarez-Navarro K, Ruiz-Baca E, Meneses-Morales I, Espino-Saldaña E, Martinez-Torres A, Lopez-Rodriguez A. Unlocking cellular traffic jams: olive oil-mediated rescue of CNG mutant channels. Front Pharmacol 2024; 15:1408156. [PMID: 39119605 PMCID: PMC11306028 DOI: 10.3389/fphar.2024.1408156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024] Open
Abstract
One of the reasons to suggest olive oil consumption for a healthy life is its potential to induce robust lipidomic remodeling through membrane modification by dietary lipids. This remodeling might, in turn, modulate essential lipid-protein interactions while maintaining accurate transmembrane protein/domain orientation. Oleic acid, the primary compound in olive oil, has been suggested as a modulator of ion channel function. In this study, we explored whether this lipid could rescue the trafficking of mutated transmembrane proteins. In our initial approach, we supplemented the cell culture medium of HEK-293 cells expressing cyclic nucleotide channels tagged using green fluorescent protein (CNG-GFP) with olive oil or oleic acid. In addition to wild-type channels, we also expressed R272Q and R278W mutant channels, two non-functional intracellularly retained channels related to retinopathies. We used fluorescence microscopy and patch-clamp in the inside-out configuration to assess changes in the cell localization and function of the tested channels. Our results demonstrated that olive oil and oleic acid facilitated the transport of cyclic nucleotide-gated R272Q mutant channels towards the plasma membrane, rendering them electrophysiologically functional. Thus, our findings reveal a novel property of olive oil as a membrane protein traffic inductor.
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Affiliation(s)
| | - Karina Juarez-Navarro
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Estela Ruiz-Baca
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Ivan Meneses-Morales
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Mexico
| | - Edith Espino-Saldaña
- Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México. Campus Juriquilla, Juriquilla, Mexico
| | - Ataulfo Martinez-Torres
- Laboratorio de Neurobiología Molecular y Celular, Instituto de Neurobiología, Universidad Nacional Autónoma de México. Campus Juriquilla, Juriquilla, Mexico
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2
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Lee HS, Kim YC, Wang Z, Brenner JS, Muzykantov VR, Myerson JW, Composto RJ. Controlling spatial distribution of functional lipids in a supported lipid bilayer prepared from vesicles. J Colloid Interface Sci 2024; 664:1042-1055. [PMID: 38522178 PMCID: PMC11100466 DOI: 10.1016/j.jcis.2024.03.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/16/2024] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
Conjugating biomolecules, such as antibodies, to bioconjugate moieties on lipid surfaces is a powerful tool for engineering the surface of diverse biomaterials, including cells and nanoparticles. We developed supported lipid bilayers (SLBs) presenting well-defined spatial distributions of functional moieties as models for precisely engineered functional biomolecular-lipid surfaces. We used quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy (AFM) to determine how vesicles containing a mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[azido(polyethylene glycol)-2000] (DSPE-PEG-N3) form SLBs as a function of the lipid phase transition temperature (Tm). Above the DPPC Tm, DPPC/DSPE-PEG-N3 vesicles form SLBs with functional azide moieties on SiO2 substrates via vesicle fusion. Below this Tm, DPPC/DSPE-PEG-N3 vesicles attach to SiO2 intact. Intact DPPC/DSPE-PEG-N3 vesicles on the SiO2 surfaces fuse and rupture to form SLBs when temperature is brought above the DPPC Tm. AFM studies show uniform and complete DPPC/DSPE-PEG-N3 SLB coverage of SiO2 surfaces for different DSPE-PEG-N3 concentrations. As the DSPE-PEG-N3 concentration increases from 0.01 to 6 mol%, the intermolecular spacing of DSPE-PEG-N3 in the SLBs decreases from 4.6 to 1.0 nm. The PEG moiety undergoes a mushroom to brush transition as DSPE-PEG-N3 concentration varies from 0.1 to 2.0 mol%. Via copper-free click reaction, IgG was conjugated to SLB surfaces with 4.6 nm or 1.3 nm inter-DSPE-PEG-N3 spacing. QCM-D and AFM data show; 1) uniform and complete IgG layers of similar mass and thickness on the two types of SLB; 2) a higher-viscosity/less rigid IgG layer on the SLB with 4.6 nm inter-DSPE-PEG-N3 spacing. Our studies provide a blueprint for SLBs modeling spatial control of functional macromolecules on lipid surfaces, including surfaces of lipid nanoparticles and cells.
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Affiliation(s)
- Hyun-Su Lee
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Ye Chan Kim
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Zhicheng Wang
- Division of Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Jacob S Brenner
- Division of Pulmonary and Critical Care Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Vladimir R Muzykantov
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Jacob W Myerson
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Russell J Composto
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States; Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, United States; Laboratory for Research on the Structure of Matter, University of Pennsylvania, Philadelphia, PA 19104, United States.
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3
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Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nat Commun 2024; 15:1848. [PMID: 38418487 PMCID: PMC10901782 DOI: 10.1038/s41467-024-46027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics are examined. We demonstrate that SoPIP2;1's structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Austin T Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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Peluso P, Chankvetadze B. Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research. J Pharm Biomed Anal 2024; 238:115836. [PMID: 37939549 DOI: 10.1016/j.jpba.2023.115836] [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] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB-CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, 07100 Sassari, Italy.
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Ave 3, 0179 Tbilisi, Georgia
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5
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Wawrzkiewicz-Jałowiecka A, Fuliński A. Brownian Aging as One of the Mechanistic Components That Shape the Single-Channel Ionic Currents through Biological and Synthetic Membranes. MEMBRANES 2023; 13:879. [PMID: 37999365 PMCID: PMC10673163 DOI: 10.3390/membranes13110879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/26/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Semipermeable membranes enable the separation of a given system from its environment. In biological terms, they are responsible for cells' identity. In turn, the functioning of ion channels is crucial for the control of ionic fluxes across the membranes and, consequently, for the exchange of chemical and electrical signals. This paper presents a model and simulations of currents through ionic nanochannels in an attempt to better understand the physical mechanism(s) of open/closed (O/C) sequences, i.e., random interruptions of ionic flows through channels observed in all known biochannels and in some synthetic nanopores. We investigate whether aging, i.e., the changes in Brownian motion characteristics with the lapse of time, may be at least one of the sources of the O/C sequences (in addition to the gating machinery in biochannels). The simulations based on the approximated nanostructure of ion channels confirm this postulation. The results also show the possibility of changing the O/C characteristics through an appropriate alteration of the channel surroundings. This observation may be valuable in technical uses of nanochannels in synthetic membranes and allow for a better understanding of the reason for the differences between the biochannels' activity in diverse biological membranes. Proposals of experimental verification of this aging O/C hypothesis are also presented.
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Affiliation(s)
- Agata Wawrzkiewicz-Jałowiecka
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Strzody 9, 44-100 Gliwice, Poland
| | - Andrzej Fuliński
- Institute of Theoretical Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
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6
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Mishra S, Rout M, Singh MK, Dehury B, Pati S. Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all-atoms molecular dynamics simulations. J Cell Biochem 2023; 124:1848-1869. [PMID: 37942587 DOI: 10.1002/jcb.30493] [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] [Received: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Advances in structural biology have bestowed insights into the pleiotropic effects of neurokinin 1 receptors (NK1R) in diverse patho-physiological processes, thereby highlighting the potential therapeutic value of antagonists directed against NK1R. Herein, we investigate the mode of antagonist recognition to discern the obscure atomic facets germane for the function and molecular determinants of NK1R. To commence discernment of potent antagonists and the conformational changes in NK1R, induced upon antagonist binding, state-of-the-art classical all-atoms molecular dynamics (MD) simulations in lipid mimetic bilayers have been utilized. MD simulations of structural ensembles reveals the involvement of TM5 and TM6 in tight anchoring of antagonists through a network of interhelical hydrogen-bonds, while, the extracellular loop 2 (ECL2) governs the overall size and nature of the pocket, thereby modulating NK1R. Consistent comparison between experiments and MD simulation results discerns the predominant role of TM3, TM4, and TM6 in lipid-NK1R interaction. Correlation between hydrophobic index and helicity of TM domains elucidates their importance in maintaining the structural stability in addition to regulating NK1R antagonism. Taken together, we anticipate that our computational study marks a comprehensive structural basis of NK1R antagonism in lipid bilayers, which may facilitate designing of new therapeutics against associated diseases targeting human neurokinin receptors.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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7
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Nguyen ATP, Weigle AT, Shukla D. Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549977. [PMID: 37502896 PMCID: PMC10370204 DOI: 10.1101/2023.07.20.549977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
With the diversity of lipid-protein interactions, any observed membrane protein dynamics or functions directly depend on the lipid bilayer selection. However, the implications of lipid bilayer choice are seldom considered unless characteristic lipid-protein interactions have been previously reported. Using molecular dynamics simulation, we characterize the effects of membrane embedding on plant aquaporin SoPIP2;1, which has no reported high-affinity lipid interactions. The regulatory impacts of a realistic lipid bilayer, and nine different homogeneous bilayers, on varying SoPIP2;1 dynamics were examined. We demonstrate that SoPIP2;1s structure, thermodynamics, kinetics, and water transport are altered as a function of each membrane construct's ensemble properties. Notably, the realistic bilayer provides stabilization of non-functional SoPIP2;1 metastable states. Hydrophobic mismatch and lipid order parameter calculations further explain how lipid ensemble properties manipulate SoPIP2;1 behavior. Our results illustrate the importance of careful bilayer selection when studying membrane proteins. To this end, we advise cautionary measures when performing membrane protein molecular dynamics simulations.
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Affiliation(s)
- Anh T P Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
| | - Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, IL 61801
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, IL 61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, IL 61801
- Department of Plant Biology, University of Illinois at Urbana-Champaign, IL 61801
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8
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Gu RX, de Groot BL. Central cavity dehydration as a gating mechanism of potassium channels. Nat Commun 2023; 14:2178. [PMID: 37069187 PMCID: PMC10110622 DOI: 10.1038/s41467-023-37531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The hydrophobic gating model, in which ion permeation is inhibited by the hydrophobicity, rather than a physical occlusion of the nanopore, functions in various ion channels including potassium channels. Available research focused on the energy barriers for ion/water conduction due to the hydrophobicity, whereas how hydrophobic gating affects the function and structure of channels remains unclear. Here, we use potassium channels as examples and conduct molecular dynamics simulations to investigate this problem. Our simulations find channel activities (ion currents) highly correlated with cavity hydration level, implying insufficient hydration as a barrier for ion permeation. Enforced cavity dehydration successfully induces conformational transitions between known channel states, further implying cavity dewetting as a key step in the gating procedure of potassium channels utilizing different activation mechanisms. Our work reveals how the cavity dewetting is coupled to structural changes of potassium channels and how it affects channel activity. The conclusion may also apply to other ion channels.
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Affiliation(s)
- Ruo-Xu Gu
- School of Life Sciences and Biotechnology, Shanghai Jia Tong University, 800 Dongchuan Road, 200240, Shanghai, China
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
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9
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Minniberger S, Abdolvand S, Braunbeck S, Sun H, Plested AJR. Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. J Mol Biol 2023; 435:167970. [PMID: 36682679 DOI: 10.1016/j.jmb.2023.167970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became available recently by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as positioning of the side-chains in the SF is still missing. Here, in an attempt to obtain high-resolution information about glutamate receptor SFs, we incorporated partial SF sequences of the AMPA and kainate receptors into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, previously unobserved structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.
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Affiliation(s)
- Sonja Minniberger
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sebastian Braunbeck
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Han Sun
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institute of Chemistry, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.
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10
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Morán-Zendejas R, Rodríguez-Menchaca AA. The anti-tumor drug 2-hydroxyoleic acid regulates the oncogenic potassium channel Kv10.1. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2023. [DOI: 10.1186/s43088-023-00354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abstract
Background
2-hydroxyoleic acid (2OHOA) is a synthetic fatty acid with antitumor properties that alters membrane composition and structure, which in turn influences the functioning of membrane proteins and cell signaling. In this study, we propose a novel antitumoral mechanism of 2OHOA accomplished through the regulation of Kv10.1 channels. We evaluated the effects of 2OHOA on Kv10.1 channels expressed in HEK-293 cells by using electrophysiological techniques and a cell proliferation assay.
Results
2OHOA increased Kv10.1 channel currents in a voltage-dependent manner, shifted its conductance-voltage relationship towards negative potentials, and accelerated its activation kinetics. Moreover, 2OHOA reduced proliferation of cells that exogenously (HEK-293) and endogenously (MCF-7) expressed Kv10.1 channels. It is worth noting that the antiproliferative effect of 2OHOA was maintained in HEK-293 cells expressing a non-conducting mutant of Kv10.1 channel (Kv10.1-F456A), while it did not affect HEK-293 cells not expressing Kv10.1 channels, suggesting that 2OHOA interferes with a non-conducting function of Kv10.1 channels involved in cell proliferation. Finally, we found that 2OHOA can act synergistically with astemizole, a Kv10.1 channel blocker, to decrease cell proliferation more efficiently.
Conclusion
Our data suggest that 2OHOA decreases cell proliferation, at least in part, by regulating Kv10.1 channels.
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11
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Quiroz-Acosta T, Bermeo K, Arenas I, Garcia DE. Inactivation of potassium channels by ceramide in rat pancreatic β-cells. Arch Biochem Biophys 2023; 735:109520. [PMID: 36646267 DOI: 10.1016/j.abb.2023.109520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/29/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Lipid regulation of ion channels is a fundamental mechanism in physiological processes as of neurotransmitter release and hormone secretion. Ceramide is a bioactive lipid proposed as a regulator of several voltage-gated ion channels including potassium channels (Kv). It is generated either de novo or by sphingomyelin (SM) hydrolysis in membranes of mammalian cells. In pancreatic β-cells, ceramide is the main sphingolipid associated with lipotoxicity and likely involved in cell dysfunction. Despite of the wealth of information regarding regulation of potassium channels by ceramides, the regulation of Kv channels by accumulated ceramide in native pancreatic β-cells has not been investigated. To do so, we used either the C2-ceramide, a cell-permeable short-chain analogue, or a sphingomyelinase (SMase C), a hydrolase causing ceramide to elevate from an endogenous production, in pancreatic β-cells of rat. C2-ceramide markedly accelerates steady-state current inactivation according to kinetic changes in the channel machinery. Interestingly, only C2-ceramide accelerates current inactivation while SMase C decreases both, peak-current and step-current amplitude supporting differential effects of ceramide derivatives. A specific inhibitor of the Kv2.1 channel (GxTX-1E), readily inhibits a fraction of the Kv channel current while no further inhibition by C2-ceramide superfusion can be observed supporting Kv2.1 channel involvement in the ceramide inhibition. Thus, intramembrane ceramide accumulation, as a lipidic metabolite released under cell-stress conditions, may alter pancreatic β-cell repolarization and secretion. These results may provide a new insight regarding lipid-protein regulation and advance our understanding in ceramide actions on Kv channels in pancreatic β-cells.
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Affiliation(s)
- Tayde Quiroz-Acosta
- Department of Physiology, Faculty of Medicine, Universidad Nacional Autónoma de México, UNAM, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - Karina Bermeo
- Department of Physiology, Faculty of Medicine, Universidad Nacional Autónoma de México, UNAM, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - Isabel Arenas
- Department of Physiology, Faculty of Medicine, Universidad Nacional Autónoma de México, UNAM, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - David E Garcia
- Department of Physiology, Faculty of Medicine, Universidad Nacional Autónoma de México, UNAM, Circuito Exterior S/N, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México.
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12
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Kurauskas V, Tonelli M, Henzler-Wildman K. Full opening of helix bundle crossing does not lead to NaK channel activation. J Gen Physiol 2022; 154:213659. [PMID: 36326620 PMCID: PMC9640265 DOI: 10.1085/jgp.202213196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
A critical part of ion channel function is the ability to open and close in response to stimuli and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels suggested a general steric gating mechanism located at the helix bundle crossing (HBC), recent functional studies on several channels indicate that the helix bundle crossing is wide-open even in functionally nonconductive channels. Two NaK channel variants were crystallized in very different open and closed conformations, which served as important models of the HBC gating hypothesis. However, neither of these NaK variants is conductive in liposomes unless phenylalanine 92 is mutated to alanine (F92A). Here, we use NMR to probe distances at near-atomic resolution of the two NaK variants in lipid bicelles. We demonstrate that in contrast to the crystal structures, both NaK variants are in a fully open conformation, akin to Ca2+-bound MthK channel structure where the HBC is widely open. While we were not able to determine what a conductive NaK structure is like, our further inquiry into the gating mechanism suggests that the selectivity filter and pore helix are coupled to the M2 helix below and undergo changes in the structure when F92 is mutated. Overall, our data show that NaK exhibits coupling between the selectivity filter and HBC, similar to K+ channels, and has a more complex gating mechanism than previously thought, where the full opening of HBC does not lead to channel activation.
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Affiliation(s)
- Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
- Correspondence to Katherine Henzler-Wildman:
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13
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Aupič J, Lapenta F, Janoš P, Magistrato A. Intrinsically disordered ectodomain modulates ion permeation through a metal transporter. Proc Natl Acad Sci U S A 2022; 119:e2214602119. [PMID: 36409899 PMCID: PMC9889885 DOI: 10.1073/pnas.2214602119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
The function of many channels and transporters is enriched by the conformational plasticity of intrinsically disordered regions (IDRs). Copper transporter 1 (Ctr1) is the main entry point for Cu(I) ions in eukaryotes and contains IDRs both at its N-terminal (Nterm) and C-terminal ends. The former delivers copper ions from the extracellular matrix to the selectivity filter in the Ctr1 lumen. However, the molecular mechanism of this process remains elusive due to Nterm's disordered nature. Here, we combine advanced molecular dynamics simulations and circular dichroism experiments to show that Cu(I) ions and a lipidic environment drive the insertion of the Nterm into the Ctr1 selectivity filter, causing its opening. Through a lipid-aided conformational switch of one of the transmembrane helices, the conformational change of the selectivity filter propagates down to the cytosolic gate of Ctr1. Taken together, our results elucidate how conformational variability of IDRs modulates ion transport.
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Affiliation(s)
- Jana Aupič
- National Research Council of Italy - Materials Foundry Istituto Officina dei Materiali c/o International School for Advanced Studies,34136Trieste, Italy
| | - Fabio Lapenta
- Laboratory for Environmental and Life Sciences, University of Nova Gorica,5000Nova Gorica, Slovenia
| | - Pavel Janoš
- National Research Council of Italy - Materials Foundry Istituto Officina dei Materiali c/o International School for Advanced Studies,34136Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy - Materials Foundry Istituto Officina dei Materiali c/o International School for Advanced Studies,34136Trieste, Italy
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14
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Schmidpeter PAM, Wu D, Rheinberger J, Riegelhaupt PM, Tang H, Robinson CV, Nimigean CM. Anionic lipids unlock the gates of select ion channels in the pacemaker family. Nat Struct Mol Biol 2022; 29:1092-1100. [PMID: 36352139 PMCID: PMC10022520 DOI: 10.1038/s41594-022-00851-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/25/2022] [Indexed: 11/11/2022]
Abstract
Lipids play important roles in regulating membrane protein function, but the molecular mechanisms used are elusive. Here we investigated how anionic lipids modulate SthK, a bacterial pacemaker channel homolog, and HCN2, whose activity contributes to pacemaking in the heart and brain. Using SthK allowed the reconstitution of purified channels in controlled lipid compositions for functional and structural assays that are not available for the eukaryotic channels. We identified anionic lipids bound tightly to SthK and their exact binding locations and determined that they potentiate channel activity. Cryo-EM structures in the most potentiating lipids revealed an open state and identified a nonannular lipid bound with its headgroup near an intersubunit salt bridge that clamps the intracellular channel gate shut. Breaking this conserved salt bridge abolished lipid modulation in SthK and eukaryotic HCN2 channels, indicating that anionic membrane lipids facilitate channel opening by destabilizing these interactions. Our findings underline the importance of state-dependent protein-lipid interactions.
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Affiliation(s)
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Department of Structural Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | | | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
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15
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Clarke A, Groschner K, Stockner T. Exploring TRPC3 Interaction with Cholesterol through Coarse-Grained Molecular Dynamics Simulations. Biomolecules 2022; 12:890. [PMID: 35883446 PMCID: PMC9313397 DOI: 10.3390/biom12070890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transient receptor potential canonical 3 (TRPC3) channel belongs to the superfamily of transient receptor potential (TRP) channels which mediate Ca2+ influx into the cell. These channels constitute essential elements of cellular signalling and have been implicated in a wide range of diseases. TRPC3 is primarily gated by lipids and its surface expression has been shown to be dependent on cholesterol, yet a comprehensive exploration of its interaction with this lipid has thus far not emerged. Here, through 80 µs of coarse-grained molecular dynamics simulations, we show that cholesterol interacts with multiple elements of the transmembrane machinery of TRPC3. Through our approach, we identify an annular binding site for cholesterol on the pre-S1 helix and a non-annular site at the interface between the voltage-sensor-like domain and pore domains. Here, cholesterol interacts with exposed polar residues and possibly acts to stabilise the domain interface.
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Affiliation(s)
- Amy Clarke
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr., 13A, 1090 Vienna, Austria;
| | - Klaus Groschner
- Gottfried Schatz Research Center, Division of Biophysics, Medical University of Graz, 8010 Graz, Austria;
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstr., 13A, 1090 Vienna, Austria;
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16
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Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake. Int J Mol Sci 2022; 23:ijms23136913. [PMID: 35805918 PMCID: PMC9278134 DOI: 10.3390/ijms23136913] [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] [Received: 05/19/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
S-TGA-1 and PGP-Me are native archaeal lipids associated with the bacteriorhodopsin (bR) trimer and contribute to protein stabilization and native dynamics for proton transfer. However, little is known about the underlying molecular mechanism of how these lipids regulate bR trimerization and efficient photocycling. Here, we explored the specific binding of S-TGA-1 and PGP-Me with the bR trimer and elucidated how specific interactions modulate the bR trimeric structure and proton release and uptake using long-term atomistic molecular dynamic simulations. Our results showed that S-TGA-1 and PGP-Me are essential for stabilizing the bR trimer and maintaining the coherent conformational dynamics necessary for proton transfer. The specific binding of S-TGA-1 with W80 and K129 regulates proton release on the extracellular surface by forming a “Glu-shared” model. The interaction of PGP-Me with K40 ensures proton uptake by accommodating the conformation of the helices to recruit enough water molecules on the cytoplasmic side. The present study results could fill in the theoretical gaps of studies on the functional role of archaeal lipids and could provide a reference for other membrane proteins containing similar archaeal lipids.
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17
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Borcik CG, Eason IR, Yekefallah M, Amani R, Han R, Vanderloop BH, Wylie BJ. A Cholesterol Dimer Stabilizes the Inactivated State of an Inward-Rectifier Potassium Channel. Angew Chem Int Ed Engl 2022; 61:e202112232. [PMID: 34985791 PMCID: PMC8957755 DOI: 10.1002/anie.202112232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 12/15/2022]
Abstract
Cholesterol oligomers reside in multiple membrane protein X-ray crystal structures. Yet, there is no direct link between these oligomers and a biological function. Here we present the structural and functional details of a cholesterol dimer that stabilizes the inactivated state of an inward-rectifier potassium channel KirBac1.1. K+ efflux assays confirm that high cholesterol concentration reduces K+ conductance. We then determine the structure of the cholesterol-KirBac1.1 complex using Xplor-NIH simulated annealing calculations driven by solid-state NMR distance measurements. These calculations identified an α-α cholesterol dimer docked to a cleft formed by adjacent subunits of the homotetrameric protein. We compare these results to coarse grain molecular dynamics simulations. This is one of the first examples of a cholesterol oligomer performing a distinct biological function and structural characterization of a conserved promiscuous lipid binding region.
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Affiliation(s)
- Collin G Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Isaac R Eason
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Reza Amani
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ruixian Han
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Boden H Vanderloop
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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18
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Borcik CG, Eason IR, Yekefallah M, Amani R, Han R, Vanderloop BH, Wylie BJ. A Cholesterol Dimer Stabilizes the Inactivated State of an Inward‐Rectifier Potassium Channel. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Collin G. Borcik
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
| | - Isaac R. Eason
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
| | - Reza Amani
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
| | - Ruixian Han
- Department of Biochemistry University of Wisconsin-Madison Madison WI 53706 USA
| | - Boden H. Vanderloop
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
| | - Benjamin J. Wylie
- Department of Chemistry and Biochemistry Texas Tech University Lubbock TX 79409 USA
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19
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Jäger M, Koslowski T, Wolf S. Predicting Ion Channel Conductance via Dissipation-Corrected Targeted Molecular Dynamics and Langevin Equation Simulations. J Chem Theory Comput 2021; 18:494-502. [PMID: 34928150 DOI: 10.1021/acs.jctc.1c00426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, here we applied dissipation-corrected targeted molecular dynamics in combination with Langevin equation simulations to potassium diffusion through the gramicidin A channel as a test system. Performing a nonequilibrium principal component analysis on backbone dihedral angles, we find coupled protein-ion dynamics to occur during ion transfer. The dissipation-corrected free energy profiles correspond well to predictions from other biased simulation methods. The incorporation of an external electric field in Langevin simulations enables the prediction of macroscopic observables in the form of I-V characteristics.
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Affiliation(s)
- Miriam Jäger
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - Thorsten Koslowski
- Institute of Physical Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
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20
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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21
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Pipatpolkai T, Quetschlich D, Stansfeld PJ. From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels. J Mol Biol 2021; 433:167105. [PMID: 34139216 PMCID: PMC8361781 DOI: 10.1016/j.jmb.2021.167105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/05/2022]
Abstract
Potassium (K+) ion channels are crucial in numerous cellular processes as they hyperpolarise a cell through K+ conductance, returning a cell to its resting potential. K+ channel mutations result in multiple clinical complications such as arrhythmia, neonatal diabetes and migraines. Since 1995, the regulation of K+ channels by phospholipids has been heavily studied using a range of interdisciplinary methods such as cellular electrophysiology, structural biology and computational modelling. As a result, K+ channels are model proteins for the analysis of protein-lipid interactions. In this review, we will focus on the roles of lipids in the regulation of K+ channels, and how atomic-level structures, along with experimental techniques and molecular simulations, have helped guide our understanding of the importance of phospholipid interactions.
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Affiliation(s)
- Tanadet Pipatpolkai
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Physiology Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PT, UK
| | - Daniel Quetschlich
- Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK; Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Phillip J Stansfeld
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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22
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Borisov VB. Effect of Membrane Environment on the Ligand-Binding Properties of the Terminal Oxidase Cytochrome bd-I from Escherichia coli. BIOCHEMISTRY (MOSCOW) 2021; 85:1603-1612. [PMID: 33705298 DOI: 10.1134/s0006297920120123] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytochrome bd-I is a terminal oxidase of the Escherichia coli respiratory chain. This integral membrane protein contains three redox-active prosthetic groups (hemes b558, b595, and d) and couples the electron transfer from quinol to molecular oxygen to the generation of proton motive force, as one of its important physiological functions. The study was aimed at examining the effect of the membrane environment on the ligand-binding properties of cytochrome bd-I by absorption spectroscopy. The membrane environment was found to modulate the ligand-binding characteristics of the hemoprotein in both oxidized and reduced states. Absorption changes upon the addition of exogenous ligands, such as cyanide or carbon monoxide (CO), to the detergent-solubilized enzyme were much more significant and heterogeneous than those observed with the membrane-bound enzyme. In the native membranes, both cyanide and CO interacted mainly with heme d. An additional ligand-binding site (heme b558) appeared in the isolated enzyme, as was evidenced by more pronounced changes in the absorption in the Soret band. This additional reactivity could also be detected after treatment of E. coli membranes with a detergent. The observed effect did not result from the enzyme denaturation, since reconstitution of the isolated enzyme into azolectin liposomes restored the ligand-binding pattern close to that observed for the intact membranes.
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Affiliation(s)
- V B Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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23
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O'Brien KM, Joyce W, Crockett EL, Axelsson M, Egginton S, Farrell AP. Resilience of cardiac performance in Antarctic notothenioid fishes in a warming climate. J Exp Biol 2021; 224:268390. [PMID: 34042975 DOI: 10.1242/jeb.220129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Warming in the region of the Western Antarctic Peninsula is occurring at an unprecedented rate, which may threaten the survival of Antarctic notothenioid fishes. Herein, we review studies characterizing thermal tolerance and cardiac performance in notothenioids - a group that includes both red-blooded species and the white-blooded, haemoglobinless icefishes - as well as the relevant biochemistry associated with cardiac failure during an acute temperature ramp. Because icefishes do not feed in captivity, making long-term acclimation studies unfeasible, we focus only on the responses of red-blooded notothenioids to warm acclimation. With acute warming, hearts of the white-blooded icefish Chaenocephalus aceratus display persistent arrhythmia at a lower temperature (8°C) compared with those of the red-blooded Notothenia coriiceps (14°C). When compared with the icefish, the enhanced cardiac performance of N. coriiceps during warming is associated with greater aerobic capacity, higher ATP levels, less oxidative damage and enhanced membrane integrity. Cardiac performance can be improved in N. coriiceps with warm acclimation to 5°C for 6-9 weeks, accompanied by an increase in the temperature at which cardiac failure occurs. Also, both cardiac mitochondrial and microsomal membranes are remodelled in response to warm acclimation in N. coriiceps, displaying homeoviscous adaptation. Overall, cardiac performance in N. coriiceps is malleable and resilient to warming, yet thermal tolerance and plasticity vary among different species of notothenioid fishes; disruptions to the Antarctic ecosystem driven by climate warming and other anthropogenic activities endanger the survival of notothenioids, warranting greater protection afforded by an expansion of marine protected areas.
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Affiliation(s)
- Kristin M O'Brien
- Institute of Arctic Biology , University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
| | - William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Michael Axelsson
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Stuart Egginton
- School of Biomedical Sciences , University of Leeds, Leeds LS2 9JT, UK
| | - Anthony P Farrell
- Department of Zoology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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24
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Yuan X, Zhang D, Mao S, Wang Q. Filling the Gap in Understanding the Mechanism of GABA AR and Propofol Using Computational Approaches. J Chem Inf Model 2021; 61:1889-1901. [PMID: 33823589 DOI: 10.1021/acs.jcim.0c01290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
γ-Aminobutyric acid type-A receptors (GABAARs) play a critical role in neural transmission by mediating the inhibitory neural firing and are the target of many psychiatric drugs. Among them, propofol is one of the most widely used and important general anesthetics in clinics. Recent advances in structural biology revealed the structure of a human GABAAR in both open and closed states. Yet, the detailed mechanism of the receptor and propofol remains to be fully understood. Therefore, in this study, based on the previous successes in structural biology, a variety of computational techniques were applied to fill the gap between previous experimental studies. This study investigated the ion-conducting mechanism of GABAAR, predicted the possible binding mechanism of propofol, and revealed a new motion mechanism of transmembrane domain (TMD) helices. We hope that this study may contribute to future studies on ion-channel receptors, general anesthetics, and drug development.
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Affiliation(s)
- Xinghang Yuan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Di Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shengjun Mao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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25
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Miranda WE, Guo J, Mesa-Galloso H, Corradi V, Lees-Miller JP, Tieleman DP, Duff HJ, Noskov SY. Lipid regulation of hERG1 channel function. Nat Commun 2021; 12:1409. [PMID: 33658490 PMCID: PMC7930123 DOI: 10.1038/s41467-021-21681-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
The lipid regulation of mammalian ion channel function has emerged as a fundamental mechanism in the control of electrical signalling and transport specificity in various cell types. In this work, we combine molecular dynamics simulations, mutagenesis, and electrophysiology to provide mechanistic insights into how lipophilic molecules (ceramide-sphingolipid probe) alter gating kinetics and K+ currents of hERG1. We show that the sphingolipid probe induced a significant left shift of activation voltage, faster deactivation rates, and current blockade comparable to traditional hERG1 blockers. Microseconds-long MD simulations followed by experimental mutagenesis elucidated ceramide specific binding locations at the interface between the pore and voltage sensing domains. This region constitutes a unique crevice present in mammalian channels with a non-swapped topology. The combined experimental and simulation data provide evidence for ceramide-induced allosteric modulation of the channel by a conformational selection mechanism.
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Affiliation(s)
- Williams E Miranda
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada
| | - James P Lees-Miller
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada.
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, 3280 Hospital Dr., University of Calgary, Calgary, AB, Canada.
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences, 507 Campus Drive, University of Calgary, Calgary, AB, Canada.
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26
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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27
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Evans ER, Farnoud AM, O'Brien KM, Crockett EL. Thermal profiles reveal stark contrasts in properties of biological membranes from heart among Antarctic notothenioid fishes which vary in expression of hemoglobin and myoglobin. Comp Biochem Physiol B Biochem Mol Biol 2020; 252:110539. [PMID: 33242660 DOI: 10.1016/j.cbpb.2020.110539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 01/24/2023]
Abstract
Antarctic notothenioids are noted for extreme stenothermy, yet underpinnings of their thermal limits are not fully understood. We hypothesized that properties of ventricular membranes could explain previously observed differences among notothenioids in temperature onset of cardiac arrhythmias and persistent asystole. Microsomes were prepared using ventricles from six species of notothenioids, including four species from the hemoglobin-less (Hb-) family Channichthyidae (icefishes), which also differentially express cardiac myoglobin (Mb), and two species from the (Hb+) Nototheniidae. We determined membrane fluidity and structural integrity by quantifying fluorescence depolarization of 1,6-diphenyl-1,3,5-hexatriene (DPH) and leakage of 5(6)-carboxyfluorescein, respectively, over a temperature range from ambient (0 °C) to 20 °C. Compositions of membrane phospholipids and cholesterol contents were also quantified. Membranes from all four species of icefishes exhibited greater fluidity than membranes from the red-blooded species N. coriiceps. Thermal sensitivity of fluidity did not vary among species. The greatest thermal sensitivity to leakage occurred between 0 and 5 °C for all species, while membranes from the icefish, Chaenocephalus aceratus (Hb-/Mb-) displayed leakage that was nearly 1.5-fold greater than leakage in N. coriiceps (Hb+/Mb+). Contents of phosphatidylethanolamine (PE) were approximately 1.5-fold greater in icefishes than in red-blooded fishes, and phospholipids had a higher degree of unsaturation in icefishes than in Hb + notothenioids. Cholesterol contents were lowest in Champsocephalus gunnari (Hb-/Mb-) and highest in the two Hb+/Mb + species, G. gibberifrons and N. coriiceps. Our results reveal marked differences in membrane properties and indicate a breach in membrane fluidity and structural integrity at a lower temperature in icefishes than in red-blooded notothenioids.
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Affiliation(s)
- Elizabeth R Evans
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Amir M Farnoud
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, OH 45701, USA
| | - Kristin M O'Brien
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775, USA
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Selectivity filter ion binding affinity determines inactivation in a potassium channel. Proc Natl Acad Sci U S A 2020; 117:29968-29978. [PMID: 33154158 DOI: 10.1073/pnas.2009624117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Potassium channels can become nonconducting via inactivation at a gate inside the highly conserved selectivity filter (SF) region near the extracellular side of the membrane. In certain ligand-gated channels, such as BK channels and MthK, a Ca2+-activated K+ channel from Methanobacterium thermoautotrophicum, the SF has been proposed to play a role in opening and closing rather than inactivation, although the underlying conformational changes are unknown. Using X-ray crystallography, identical conductive MthK structures were obtained in wide-ranging K+ concentrations (6 to 150 mM), unlike KcsA, whose SF collapses at low permeant ion concentrations. Surprisingly, three of the SF's four binding sites remained almost fully occupied throughout this range, indicating high affinities (likely submillimolar), while only the central S2 site titrated, losing its ion at 6 mM, indicating low K+ affinity (∼50 mM). Molecular simulations showed that the MthK SF can also collapse in the absence of K+, similar to KcsA, but that even a single K+ binding at any of the SF sites, except S4, can rescue the conductive state. The uneven titration across binding sites differs from KcsA, where SF sites display a uniform decrease in occupancy with K+ concentration, in the low millimolar range, leading to SF collapse. We found that ions were disfavored in MthK's S2 site due to weaker coordination by carbonyl groups, arising from different interactions with the pore helix and water behind the SF. We conclude that these differences in interactions endow the seemingly identical SFs of KcsA and MthK with strikingly different inactivating phenotypes.
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