1
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Świderski G, Kalinowska M, Gołębiewska E, Świsłocka R, Lewandowski W, Kowalczyk N, Naumowicz M, Cudowski A, Pietryczuk A, Nalewajko-Sieliwoniuk E, Wysocka I, Arciszewska Ż, Godlewska-Żyłkiewicz B. Structures, Antioxidant Properties, and Antimicrobial Properties of Eu(III), Gd(III), and Dy(III) Caffeinates and p-Coumarates. Molecules 2023; 28:6506. [PMID: 37764282 PMCID: PMC10535667 DOI: 10.3390/molecules28186506] [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: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we investigated the structures of lanthanide (Eu(III), Dy(III), and Gd(III)) complexes with p-coumaric (p-CAH2) and caffeic (CFAH3) acids using the FTIRKBr, FTIRATR, and Raman spectroscopic methods. The compositions of the solid phase caffeinates and p-coumarates were obtained on the basis of the amounts of hydrogen and carbon determined using an elemental analysis. The degree of hydration and the thermal decomposition of each compound were examined via a thermal analysis of TG, DTG, and DSC. Antioxidant spectroscopic tests were performed using the DPPH (1,1-diphenyl-2-picrylhydrazyl radical), FRAP (ferric reducing antioxidant activity), and ABTS (2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (diammonium salt radical cation) methods. The antimicrobial activity of each compound against Escherichia coli, Bacillus subtilis, and Candida albicans was investigated. The electrical properties of the liposomes which mimicked the microbial surfaces formed in the electrolyte containing the tested compounds were also investigated. The above biological properties of the obtained complexes were compared with the activities of p-CAH2 and CFAH3. The obtained data suggest that lanthanide complexes are much more thermally stable and have higher antimicrobial and antioxidant properties than the ligands (with the exception of CFAH3 in the case of antioxidant activity tests). The Gd(III) complexes revealed the highest biological activity among the studied lanthanide complexes.
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Affiliation(s)
- Grzegorz Świderski
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Monika Kalinowska
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Ewelina Gołębiewska
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Renata Świsłocka
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Włodzimierz Lewandowski
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Natalia Kowalczyk
- Department of Chemistry Biology and Biotechnology, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland (E.G.); (N.K.)
| | - Monika Naumowicz
- Department of Physical Chemistry, Faculty of Chemistry, University of Bialystok, K. Ciołkowskiego 1K, 15-245 Białystok, Poland
| | - Adam Cudowski
- Department of Water Ecology, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Bialystok, Poland; (A.C.); (A.P.)
| | - Anna Pietryczuk
- Department of Water Ecology, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Bialystok, Poland; (A.C.); (A.P.)
| | - Edyta Nalewajko-Sieliwoniuk
- Department of Analytical Chemistry, Faculty of Chemistry, University of Bialystok, K. Ciołkowskiego 1K, 15-245 Białystok, Poland (Ż.A.); (B.G.-Ż.)
| | - Izabela Wysocka
- Department of Analytical Chemistry, Faculty of Chemistry, University of Bialystok, K. Ciołkowskiego 1K, 15-245 Białystok, Poland (Ż.A.); (B.G.-Ż.)
| | - Żaneta Arciszewska
- Department of Analytical Chemistry, Faculty of Chemistry, University of Bialystok, K. Ciołkowskiego 1K, 15-245 Białystok, Poland (Ż.A.); (B.G.-Ż.)
| | - Beata Godlewska-Żyłkiewicz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Bialystok, K. Ciołkowskiego 1K, 15-245 Białystok, Poland (Ż.A.); (B.G.-Ż.)
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2
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Sauve S, Williamson J, Polasa A, Moradi M. Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters. MEMBRANES 2023; 13:membranes13050462. [PMID: 37233523 DOI: 10.3390/membranes13050462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
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Affiliation(s)
- Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Williamson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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3
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Beckstein O, Naughton F. General principles of secondary active transporter function. BIOPHYSICS REVIEWS 2022; 3:011307. [PMID: 35434715 PMCID: PMC8984959 DOI: 10.1063/5.0047967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/23/2022] [Indexed: 04/13/2023]
Abstract
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.
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Affiliation(s)
- Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
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4
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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5
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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6
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Crul T, Maléth J. Endoplasmic Reticulum-Plasma Membrane Contact Sites as an Organizing Principle for Compartmentalized Calcium and cAMP Signaling. Int J Mol Sci 2021; 22:4703. [PMID: 33946838 PMCID: PMC8124356 DOI: 10.3390/ijms22094703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 01/14/2023] Open
Abstract
In eukaryotic cells, ultimate specificity in activation and action-for example, by means of second messengers-of the myriad of signaling cascades is primordial. In fact, versatile and ubiquitous second messengers, such as calcium (Ca2+) and cyclic adenosine monophosphate (cAMP), regulate multiple-sometimes opposite-cellular functions in a specific spatiotemporal manner. Cells achieve this through segregation of the initiators and modulators to specific plasma membrane (PM) subdomains, such as lipid rafts and caveolae, as well as by dynamic close contacts between the endoplasmic reticulum (ER) membrane and other intracellular organelles, including the PM. Especially, these membrane contact sites (MCSs) are currently receiving a lot of attention as their large influence on cell signaling regulation and cell physiology is increasingly appreciated. Depletion of ER Ca2+ stores activates ER membrane STIM proteins, which activate PM-residing Orai and TRPC Ca2+ channels at ER-PM contact sites. Within the MCS, Ca2+ fluxes relay to cAMP signaling through highly interconnected networks. However, the precise mechanisms of MCS formation and the influence of their dynamic lipid environment on their functional maintenance are not completely understood. The current review aims to provide an overview of our current understanding and to identify open questions of the field.
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Affiliation(s)
- Tim Crul
- First Department of Medicine, University of Szeged, H6720 Szeged, Hungary
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group, University of Szeged, H6720 Szeged, Hungary
- HCEMM-SZTE Molecular Gastroenterology Research Group, University of Szeged, H6720 Szeged, Hungary
| | - József Maléth
- First Department of Medicine, University of Szeged, H6720 Szeged, Hungary
- HAS-USZ Momentum Epithelial Cell Signaling and Secretion Research Group, University of Szeged, H6720 Szeged, Hungary
- HCEMM-SZTE Molecular Gastroenterology Research Group, University of Szeged, H6720 Szeged, Hungary
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7
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Zhou W, Fiorin G, Anselmi C, Karimi-Varzaneh HA, Poblete H, Forrest LR, Faraldo-Gómez JD. Large-scale state-dependent membrane remodeling by a transporter protein. eLife 2019; 8:50576. [PMID: 31855177 PMCID: PMC6957315 DOI: 10.7554/elife.50576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022] Open
Abstract
That channels and transporters can influence the membrane morphology is increasingly recognized. Less appreciated is that the extent and free-energy cost of these deformations likely varies among different functional states of a protein, and thus, that they might contribute significantly to defining its mechanism. We consider the trimeric Na+-aspartate symporter GltPh, a homolog of an important class of neurotransmitter transporters, whose mechanism entails one of the most drastic structural changes known. Molecular simulations indicate that when the protomers become inward-facing, they cause deep, long-ranged, and yet mutually-independent membrane deformations. Using a novel simulation methodology, we estimate that the free-energy cost of this membrane perturbation is in the order of 6–7 kcal/mol per protomer. Compensating free-energy contributions within the protein or its environment must thus stabilize this inward-facing conformation for the transporter to function. We discuss these striking results in the context of existing experimental observations for this and other transporters.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Giacomo Fiorin
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Claudio Anselmi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Hossein Ali Karimi-Varzaneh
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Horacio Poblete
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States.,Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
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8
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Conrard L, Tyteca D. Regulation of Membrane Calcium Transport Proteins by the Surrounding Lipid Environment. Biomolecules 2019; 9:E513. [PMID: 31547139 PMCID: PMC6843150 DOI: 10.3390/biom9100513] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Calcium ions (Ca2+) are major messengers in cell signaling, impacting nearly every aspect of cellular life. Those signals are generated within a wide spatial and temporal range through a large variety of Ca2+ channels, pumps, and exchangers. More and more evidences suggest that Ca2+ exchanges are regulated by their surrounding lipid environment. In this review, we point out the technical challenges that are currently being overcome and those that still need to be defeated to analyze the Ca2+ transport protein-lipid interactions. We then provide evidences for the modulation of Ca2+ transport proteins by lipids, including cholesterol, acidic phospholipids, sphingolipids, and their metabolites. We also integrate documented mechanisms involved in the regulation of Ca2+ transport proteins by the lipid environment. Those include: (i) Direct interaction inside the protein with non-annular lipids; (ii) close interaction with the first shell of annular lipids; (iii) regulation of membrane biophysical properties (e.g., membrane lipid packing, thickness, and curvature) directly around the protein through annular lipids; and (iv) gathering and downstream signaling of several proteins inside lipid domains. We finally discuss recent reports supporting the related alteration of Ca2+ and lipids in different pathophysiological events and the possibility to target lipids in Ca2+-related diseases.
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Affiliation(s)
- Louise Conrard
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute and Université catholique de Louvain, UCL B1.75.05, avenue Hippocrate, 75, B-1200 Brussels, Belgium.
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9
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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10
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Mirandela GD, Tamburrino G, Hoskisson PA, Zachariae U, Javelle A. The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB. FASEB J 2019; 33:1989-1999. [PMID: 30211659 PMCID: PMC6338640 DOI: 10.1096/fj.201800782r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022]
Abstract
The movement of ammonium across biologic membranes is a fundamental process in all living organisms and is mediated by the ubiquitous ammonium transporter/methylammonium permease/rhesus protein (Amt/Mep/Rh) family of transporters. Recent structural analysis and coupled mass spectrometry studies have shown that the Escherichia coli ammonium transporter AmtB specifically binds 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG). Upon POPG binding, several residues of AmtB undergo a small conformational change, which stabilizes the protein against unfolding. However, no studies have so far been conducted, to our knowledge, to explore whether POPG binding to AmtB has functional consequences. Here, we used an in vitro experimental assay with purified components, together with molecular dynamics simulations, to characterize the relation between POPG binding and AmtB activity. We show that the AmtB activity is electrogenic. Our results indicate that the activity, at the molecular level, of Amt in archaebacteria and eubacteria may differ. We also show that POPG is an important cofactor for AmtB activity and that, in the absence of POPG, AmtB cannot complete the full translocation cycle. Furthermore, our simulations reveal previously undiscovered POPG binding sites on the intracellular side of the lipid bilayer between the AmtB subunits. Possible molecular mechanisms explaining the functional role of POPG are discussed.-Mirandela, G. D., Tamburrino, G., Hoskisson, P. A., Zachariae, U., Javelle, A. The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB.
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Affiliation(s)
- Gaëtan Dias Mirandela
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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11
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Yu Y, Klauda JB. Modeling Pseudomonas aeruginosa inner plasma membrane in planktonic and biofilm modes. J Chem Phys 2018; 149:215102. [DOI: 10.1063/1.5052629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yalun Yu
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
| | - Jeffery B. Klauda
- Biophysics Graduate Program, University of Maryland, College Park, Maryland 20742, USA
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
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12
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Pace HP, Hannestad JK, Armonious A, Adamo M, Agnarsson B, Gunnarsson A, Micciulla S, Sjövall P, Gerelli Y, Höök F. Structure and Composition of Native Membrane Derived Polymer-Supported Lipid Bilayers. Anal Chem 2018; 90:13065-13072. [PMID: 30350611 DOI: 10.1021/acs.analchem.8b04110] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last two decades, supported lipid bilayers (SLBs) have been extensively used as model systems to study cell membrane structure and function. While SLBs have been traditionally produced from simple lipid mixtures, there has been a recent surge in compositional complexity to better mimic cellular membranes and thereby bridge the gap between classic biophysical approaches and cell experiments. To this end, native cellular membrane derived SLBs (nSLBs) have emerged as a new category of SLBs. As a new type of biomimetic material, an analytical workflow must be designed to characterize its molecular composition and structure. Herein, we demonstrate how a combination of fluorescence microscopy, neutron reflectometry, and secondary ion mass spectrometry offers new insights on structure, composition, and quality of nSLB systems formed using so-called hybrid vesicles, which are a mixture of native membrane material and synthetic lipids. With this approach, we demonstrate that the nSLB formed a continuous structure with complete mixing of the synthetic and native membrane components and a molecular stoichiometry that essentially mirrors that of the hybrid vesicles. Furthermore, structural investigation of the nSLB revealed that PEGylated lipids do not significantly thicken the hydration layer between the bilayer and substrate when on silicon substrates; however, nSLBs do have more topology than their simpler, purely synthetic counterparts. Beyond new insights regarding the structure and composition of nSLB systems, this work also serves to guide future researchers in producing and characterizing nSLBs from their cellular membrane of choice.
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Affiliation(s)
- Hudson P Pace
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Jonas K Hannestad
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden.,Biosciences and Materials , Research Institutes of Sweden , SE-501 15 Borås , Sweden
| | - Antonious Armonious
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Marco Adamo
- Institute Laue-Langevin , 38000 Grenoble , France.,Department of Chemical Engineering , Imperial College London , London SW7 2AZ , United Kingdom
| | - Bjorn Agnarsson
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Anders Gunnarsson
- Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg , Sweden
| | - Samantha Micciulla
- Institute Laue-Langevin , 38000 Grenoble , France.,Max Planck Institute of Colloids and Interfaces , 14476 Potsdam , Germany
| | - Peter Sjövall
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden.,Biosciences and Materials , Research Institutes of Sweden , SE-501 15 Borås , Sweden
| | - Yuri Gerelli
- Institute Laue-Langevin , 38000 Grenoble , France
| | - Fredrik Höök
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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13
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Saeloh D, Tipmanee V, Jim KK, Dekker MP, Bitter W, Voravuthikunchai SP, Wenzel M, Hamoen LW. The novel antibiotic rhodomyrtone traps membrane proteins in vesicles with increased fluidity. PLoS Pathog 2018; 14:e1006876. [PMID: 29451901 PMCID: PMC5833292 DOI: 10.1371/journal.ppat.1006876] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/01/2018] [Accepted: 01/12/2018] [Indexed: 12/11/2022] Open
Abstract
The acylphloroglucinol rhodomyrtone is a promising new antibiotic isolated from the rose myrtle Rhodomyrtus tomentosa, a plant used in Asian traditional medicine. While many studies have demonstrated its antibacterial potential in a variety of clinical applications, very little is known about the mechanism of action of rhodomyrtone. Preceding studies have been focused on intracellular targets, but no specific intracellular protein could be confirmed as main target. Using live cell, high-resolution, and electron microscopy we demonstrate that rhodomyrtone causes large membrane invaginations with a dramatic increase in fluidity, which attract a broad range of membrane proteins. Invaginations then form intracellular vesicles, thereby trapping these proteins. Aberrant protein localization impairs several cellular functions, including the respiratory chain and the ATP synthase complex. Being uncharged and devoid of a particular amphipathic structure, rhodomyrtone did not seem to be a typical membrane-inserting molecule. In fact, molecular dynamics simulations showed that instead of inserting into the bilayer, rhodomyrtone transiently binds to phospholipid head groups and causes distortion of lipid packing, providing explanations for membrane fluidization and induction of membrane curvature. Both its transient binding mode and its ability to form protein-trapping membrane vesicles are unique, making it an attractive new antibiotic candidate with a novel mechanism of action. Bacterial antibiotic resistance constitutes a major public healthcare issue and deaths caused by antimicrobial resistance are expected to soon exceed the number of cancer-related fatalities. In order to fight resistance, new antibiotics have to be developed that are not affected by existing microbial resistance strategies. Thus, antibiotics with novel or multiple targets are urgently needed. Rhodomyrtone displays excellent antibacterial activity, has been safely used in traditional Asian medicine for a long time, and resistance against this promising antibiotic candidate could not be detected in multiple passaging experiments. Here we demonstrate that rhodomyrtone possesses a completely novel mechanism of action, which is opposed to that of existing cell envelope-targeting drugs, minimizing the risk of cross-resistance, and in fact rhodomyrtone is highly active against e.g. vancomycin-resistant Staphylococcus aureus. Thus, rhodomyrtone is an extremely interesting compound for further antibacterial drug development.
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Affiliation(s)
- Dennapa Saeloh
- Excellence Research Laboratory on Natural Products, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Kin Ki Jim
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Marien P. Dekker
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), Neuroscience Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
- Department of Molecular Cell Biology, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Supayang P. Voravuthikunchai
- Excellence Research Laboratory on Natural Products, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Michaela Wenzel
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (MW); (LWH)
| | - Leendert W. Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (MW); (LWH)
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14
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Muallem S, Chung WY, Jha A, Ahuja M. Lipids at membrane contact sites: cell signaling and ion transport. EMBO Rep 2017; 18:1893-1904. [PMID: 29030479 DOI: 10.15252/embr.201744331] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/10/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Communication between organelles is essential to coordinate cellular functions and the cell's response to physiological and pathological stimuli. Organellar communication occurs at membrane contact sites (MCSs), where the endoplasmic reticulum (ER) membrane is tethered to cellular organelle membranes by specific tether proteins and where lipid transfer proteins and cell signaling proteins are located. MCSs have many cellular functions and are the sites of lipid and ion transfer between organelles and generation of second messengers. This review discusses several aspects of MCSs in the context of lipid transfer, formation of lipid domains, generation of Ca2+ and cAMP second messengers, and regulation of ion transporters by lipids.
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Affiliation(s)
- Shmuel Muallem
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Woo Young Chung
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Archana Jha
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Malini Ahuja
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
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15
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The Flip-Flop Diffusion Mechanism across Lipids in a Hybrid Bilayer Membrane. Biophys J 2017; 110:2451-2462. [PMID: 27276263 DOI: 10.1016/j.bpj.2016.04.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 04/03/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
In this study, we examine the mechanism of flip-flop diffusion of proton carriers across the lipid layer of a hybrid bilayer membrane (HBM). The HBM consists of a lipid monolayer appended on top of a self-assembled monolayer containing a Cu-based O2 reduction catalyst on a Au electrode. The flip-flop diffusion rates of the proton carriers dictate the kinetics of O2 reduction by the electrocatalyst. By varying both the tail lengths of the proton carriers and the lipids, we find the combinations of lengths that maximize the flip-flop diffusion rate. These experimental results combined with biophysical modeling studies allow us to propose a detailed mechanism for transmembrane flip-flop diffusion in HBM systems, which involves the bending of the alkyl tail of the proton carrier as the rate-determining step. Additional studies with an unbendable proton carrier further validate these mechanistic findings.
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16
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Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. Biophys J 2016; 110:1346-54. [PMID: 27028644 DOI: 10.1016/j.bpj.2016.01.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/15/2016] [Accepted: 01/21/2016] [Indexed: 11/21/2022] Open
Abstract
Bacterial pathogens or cancer cells can acquire multidrug resistance, which causes serious clinical problems. In cells with multidrug resistance, various drugs or antibiotics are extruded across the cell membrane by multidrug transporters. The multidrug and toxic compound extrusion (MATE) transporter is one of the five families of multidrug transporters. MATE from Pyrococcus furiosus uses H(+) to transport a substrate from the cytoplasm to the outside of a cell. Crystal structures of MATE from P. furiosus provide essential information on the relevant H(+)-binding sites (D41 and D184). Hybrid quantum mechanical/molecular mechanical simulations and continuum electrostatic calculations on the crystal structures predict that D41 is protonated in one structure (Straight) and, both D41 and D184 protonated in another (Bent). All-atom molecular dynamics simulations suggest a dynamic equilibrium between the protonation states of the two aspartic acids and that the protonation state affects hydration in the substrate binding cavity and lipid intrusion in the cleft between the N- and C-lobes. This hypothesis is examined in more detail by quantum mechanical/molecular mechanical calculations on snapshots taken from the molecular dynamics trajectories. We find the possibility of two proton transfer (PT) reactions in Straight: the 1st PT takes place between side-chains D41 and D184 through a transient formation of low-barrier hydrogen bonds and the 2nd through another H(+) from the headgroup of a lipid that intrudes into the cleft resulting in a doubly protonated (both D41 and D184) state. The 1st PT affects the local hydrogen bond network and hydration in the N-lobe cavity, which would impinge on the substrate-binding affinity. The 2nd PT would drive the conformational change from Straight to Bent. This model may be applicable to several prokaryotic H(+)-coupled MATE multidrug transporters with the relevant aspartic acids.
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17
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Ren Z, Zhang L, Shi Y, Leng X, Shao J. Effect and mechanism of a High Gradient Magnetic Separation (HGMS) and Ultraviolet (UV) composite process on the inactivation of microbes in ballast water. MARINE POLLUTION BULLETIN 2016; 108:180-185. [PMID: 27126180 DOI: 10.1016/j.marpolbul.2016.04.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 06/05/2023]
Abstract
The patented technology of a High Gradient Magnetic Separation (HGMS)-Ultraviolet (UV) composite process was used to treat ballast water. Staphylococcus aureus (S. aureus) was selected as the reference bacteria. After treatment by the HGMS-UV process, the concentration of S. aureus on the log 10 scale was lower than 2 at different flow rates, S. aureus suffered the most serious damage, and K(+) leakage of the bacteria was 1.73mg/L higher than separate 60min UV irradiation (1.17mg/L) and HGMS (0.12mg/L) processes. These results demonstrated that the HGMS-UV composite process was an effective approach to treat ballast water. Further, the HGMS process had synergistic action on the subsequent UV irradiation process and accelerated cell membrane damage. Meanwhile, the results of superoxide dismutase (SOD) activities of bacteria and DNA band analyses indicated that the inactivation mechanisms were different for HGMS and UV irradiation.
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Affiliation(s)
- Zhijun Ren
- College of Aerospace and Civil Engineering, Harbin Engineering University, Harbin 150001, China.
| | - Lin Zhang
- College of Aerospace and Civil Engineering, Harbin Engineering University, Harbin 150001, China
| | - Yue Shi
- College of Power and Energy Engineering, Harbin Engineering University, Harbin 150001, China
| | - Xiaodong Leng
- College of Aerospace and Civil Engineering, Harbin Engineering University, Harbin 150001, China
| | - Jingchao Shao
- College of Aerospace and Civil Engineering, Harbin Engineering University, Harbin 150001, China
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18
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Parkin J, Chavent M, Khalid S. Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes. Biophys J 2016; 109:461-8. [PMID: 26244728 DOI: 10.1016/j.bpj.2015.06.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 01/05/2023] Open
Abstract
In the following review we use recent examples from the literature to discuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selected bacterial membranes and proteins, with a particular focus on Gram-negative bacteria. As structural biology continues to provide increasingly high-resolution data on the proteins that reside within these membranes, simulations have an important role to play in linking these data with the dynamical behavior and function of these proteins. In particular, in the last few years there has been significant progress in addressing the issue of biochemical complexity of bacterial membranes such that the heterogeneity of the lipid and protein components of these membranes are now being incorporated into molecular-level models. Thus, in future we can look forward to complementary data from structural biology and molecular simulations combining to provide key details of structure-dynamics-function relationships in bacterial membranes.
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Affiliation(s)
- Jamie Parkin
- School of Chemistry, University of Southampton, Southampton, UK
| | | | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK.
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19
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Lee J, Jung SW, Cho AE. Molecular Insights into the Adsorption Mechanism of Human β-Defensin-3 on Bacterial Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1782-1790. [PMID: 26835546 DOI: 10.1021/acs.langmuir.5b04113] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Human β-defensin-3 (hBD3) is an endogenous antimicrobial peptide that exhibits broad-spectrum antibacterial activity without eukaryotic cytotoxicity. In this work, we carried out molecular dynamics (MD) simulations to explore its adsorption mechanism on, and the structural and thermodynamic contributions of individual residues to its antibacterial activity with both Gram-negative (GN) and Gram-positive (GP) bacterial membrane. Due to the strong electrostatic interaction of hBD3 with POPG lipids, which are more prevalent on the GP membrane, its adhesion to the GP membrane is stronger than to the GN membrane and stabilized more rapidly. On the surface of both bacterial membranes, the orientation of hBD3 is dominated by an electric dipole. We next analyzed the binding free energy decompositions of the hBD3-membrane complex using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The results of both the GN and the GP membrane simulations show that Arg17, Arg36, and Arg38 form both polar and nonpolar interactions and are potentially the key residues for hBD3 antibacterial activity. On the other hand, there was a significant difference in the energy contribution of Arg12 between the GP and GN membrane simulations, suggesting that Arg12 is a key factor in the toxicity of hBD3 to specifically GP bacteria. Our findings shed light on the antibacterial activity of hBD3 on bacterial membranes and yield insights useful for the design of potent antimicrobial peptides targeting multidrug resistant bacteria.
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Affiliation(s)
- Juho Lee
- Department of Bioinformatics, Korea University , Sejong 02841, Korea
| | - Sang Won Jung
- Department of Bioinformatics, Korea University , Sejong 02841, Korea
| | - Art E Cho
- Department of Bioinformatics, Korea University , Sejong 02841, Korea
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20
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Pace H, Simonsson Nyström L, Gunnarsson A, Eck E, Monson C, Geschwindner S, Snijder A, Höök F. Preserved transmembrane protein mobility in polymer-supported lipid bilayers derived from cell membranes. Anal Chem 2015; 87:9194-203. [PMID: 26268463 DOI: 10.1021/acs.analchem.5b01449] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supported lipid bilayers (SLBs) have contributed invaluable information about the physiochemical properties of cell membranes, but their compositional simplicity often limits the level of knowledge that can be gained about the structure and function of transmembrane proteins in their native environment. Herein, we demonstrate a generic protocol for producing polymer-supported lipid bilayers on glass surfaces that contain essentially all naturally occurring cell-membrane components of a cell line while still retaining transmembrane protein mobility and activity. This was achieved by merging vesicles made from synthetic lipids (PEGylated lipids and POPC lipids) with native cell-membrane vesicles to generate hybrid vesicles which readily rupture into a continuous polymer-supported lipid bilayer. To investigate the properties of these complex hybrid SLBs and particularly the behavior of their integral membrane-proteins, we used total internal reflection fluorescence imaging to study a transmembrane protease, β-secretase 1 (BACE1), whose ectoplasmic and cytoplasmic domains could both be specifically targeted with fluorescent reporters. By selectively probing the two different orientations of BACE1 in the resulting hybrid SLBs, the role of the PEG-cushion on transmembrane protein lateral mobility was investigated. The results reveal the necessity of having the PEGylated lipids present during vesicle adsorption to prevent immobilization of transmembrane proteins with protruding domains. The proteolytic activity of BACE1 was unadulterated by the sonication process used to merge the synthetic and native membrane vesicles; importantly it was also conserved in the SLB. The presented strategy could thus serve both fundamental studies of membrane biophysics and the production of surface-based bioanalytical sensor platforms.
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Affiliation(s)
- Hudson Pace
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Lisa Simonsson Nyström
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Elizabeth Eck
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
| | - Christopher Monson
- Department of Physical Science, Southern Utah University , Cedar City, Utah 84720 United States
| | | | - Arjan Snijder
- Discovery Sciences, AstraZeneca R&D Mölndal , SE-43183 Mölndal, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology , SE-41296 Gothenburg, Sweden
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21
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Multi-dimensional glycan microarrays with glyco-macroligands. Glycoconj J 2015; 32:483-95. [DOI: 10.1007/s10719-015-9580-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/06/2015] [Accepted: 03/10/2015] [Indexed: 01/16/2023]
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22
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Hilton JK, Rath P, Helsell CVM, Beckstein O, Van Horn WD. Understanding Thermosensitive Transient Receptor Potential Channels as Versatile Polymodal Cellular Sensors. Biochemistry 2015; 54:2401-13. [DOI: 10.1021/acs.biochem.5b00071] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jacob K. Hilton
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Parthasarathi Rath
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Cole V. M. Helsell
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
| | - Oliver Beckstein
- Center
for Biological Physics and Department of Physics, Arizona State University, 550 East Tyler Mall, Tempe, Arizona 85287, United States
| | - Wade D. Van Horn
- Center
for Personalized Diagnostics, Magnetic Resonance Research Center,
and Department of Chemistry and Biochemistry, Arizona State University, 551 East University Drive, PSG-106, Tempe, Arizona 85287, United States
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23
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Tse ECM, Barile CJ, Gewargis JP, Li Y, Zimmerman SC, Gewirth AA. Anion Transport through Lipids in a Hybrid Bilayer Membrane. Anal Chem 2015; 87:2403-9. [DOI: 10.1021/ac5043544] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edmund C. M. Tse
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Christopher J. Barile
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - John P. Gewargis
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ying Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Andrew A. Gewirth
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- International
Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka 812-8581, Japan
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24
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Hegedüs C, Telbisz Á, Hegedűs T, Sarkadi B, Özvegy-Laczka C. Lipid regulation of the ABCB1 and ABCG2 multidrug transporters. Adv Cancer Res 2015; 125:97-137. [PMID: 25640268 DOI: 10.1016/bs.acr.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This chapter deals with the interactions of two medically important multidrug ABC transporters (MDR-ABC), ABCB1 and ABCG2, with lipid molecules. Both ABCB1 and ABCG2 are capable of transporting a wide range of hydrophobic drugs and xenobiotics and are involved in cancer chemotherapy resistance. Therefore, the exploration of their mechanism of action has major therapeutic consequences. As discussed here in detail, both ABCB1 and ABCG2 are significantly affected by various lipid compounds especially those residing in their close proximity in the plasma membrane. ABCB1 is capable of transporting lipids and lipid derivatives, and thus may alter the general membrane composition by "flopping" membrane lipid constituents, while there is no such information regarding ABCG2. Still, both ABCB1 and ABCG2 show complex interactions with a variety of lipid molecules, and the transporters are significantly modulated by cholesterol and cholesterol derivatives at the posttranslational level. In this chapter, we explore the molecular details of the direct transporter-lipid interactions, the potential role of lipid-sensor domains within the proteins, as well as the application of experimental site-directed mutagenesis, detailed structural studies, and in silico modeling for examining these interactions. We also discuss the regulation of ABCB1 and ABCG2 expression at the transcriptional level, occurring through nuclear receptors involved in lipid sensing. The better understanding of lipid interactions with these medically important MDR-ABC transporters may significantly improve further drug development and clinical treatment options.
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Affiliation(s)
- Csilla Hegedüs
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Telbisz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Balázs Sarkadi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary; MTA-SE Molecular Biophysics Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Csilla Özvegy-Laczka
- MTA-SE Molecular Biophysics Research Group of the Hungarian Academy of Sciences, Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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25
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Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
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Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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26
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Kell DB, Oliver SG. How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 2014; 5:231. [PMID: 25400580 PMCID: PMC4215795 DOI: 10.3389/fphar.2014.00231] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022] Open
Abstract
One approach to experimental science involves creating hypotheses, then testing them by varying one or more independent variables, and assessing the effects of this variation on the processes of interest. We use this strategy to compare the intellectual status and available evidence for two models or views of mechanisms of transmembrane drug transport into intact biological cells. One (BDII) asserts that lipoidal phospholipid Bilayer Diffusion Is Important, while a second (PBIN) proposes that in normal intact cells Phospholipid Bilayer diffusion Is Negligible (i.e., may be neglected quantitatively), because evolution selected against it, and with transmembrane drug transport being effected by genetically encoded proteinaceous carriers or pores, whose “natural” biological roles, and substrates are based in intermediary metabolism. Despite a recent review elsewhere, we can find no evidence able to support BDII as we can find no experiments in intact cells in which phospholipid bilayer diffusion was either varied independently or measured directly (although there are many papers where it was inferred by seeing a covariation of other dependent variables). By contrast, we find an abundance of evidence showing cases in which changes in the activities of named and genetically identified transporters led to measurable changes in the rate or extent of drug uptake. PBIN also has considerable predictive power, and accounts readily for the large differences in drug uptake between tissues, cells and species, in accounting for the metabolite-likeness of marketed drugs, in pharmacogenomics, and in providing a straightforward explanation for the late-stage appearance of toxicity and of lack of efficacy during drug discovery programmes despite macroscopically adequate pharmacokinetics. Consequently, the view that Phospholipid Bilayer diffusion Is Negligible (PBIN) provides a starting hypothesis for assessing cellular drug uptake that is much better supported by the available evidence, and is both more productive and more predictive.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Cambridge Systems Biology Centre, University of Cambridge Cambridge, UK
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27
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Chavent M, Reddy T, Goose J, Dahl ACE, Stone JE, Jobard B, Sansom MSP. Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems. Faraday Discuss 2014; 169:455-75. [PMID: 25341001 PMCID: PMC4208077 DOI: 10.1039/c3fd00145h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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28
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Koshy C, Ziegler C. Structural insights into functional lipid-protein interactions in secondary transporters. Biochim Biophys Acta Gen Subj 2014; 1850:476-87. [PMID: 24859688 DOI: 10.1016/j.bbagen.2014.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Structural evidences with functional corroborations have revealed distinct features of lipid-protein interactions especially in channels and receptors. Many membrane embedded transporters are also known to require specific lipids for their functions and for some of them cellular and biochemical data suggest tight regulation by the lipid bilayer. However, molecular details on lipid-protein interactions in transporters are sparse since lipids are either depleted from the detergent solubilized transporters in three-dimensional crystals or not readily resolved in crystal structures. Nevertheless the steady increase in the progress of transporter structure determination contributed more examples of structures with resolved lipids. SCOPE OF REVIEW This review gives an overview on transporter structures in complex with lipids reported to date and discusses commonly encountered difficulties in the identification of functionally significant lipid-protein interactions based on those structures and functional in vitro data. Recent structures provided molecular details into regulation mechanism of transporters by specific lipids. The review highlights common findings and conserved patterns for distantly related transporter families to draw a more general picture on the regulatory role of lipid-protein interactions. MAJOR CONCLUSIONS Several common themes of the manner in which lipids directly influence membrane-mediated folding, oligomerization and structure stability can be found. Especially for LeuT-like fold transporters similarities in structurally resolved lipid-protein interactions suggest a common way in which transporter conformations are affected by lipids even in evolutionarily distinct transporters. Lipids appear to play an additional role as joints mechanically reinforcing the inverted repeat topology, which is a major determinant in the alternating access mechanism of secondary transporters. GENERAL SIGNIFICANCE This review brings together and adds to the repertoire of knowledge on lipid-protein interactions of functional significance presented in structures of membrane transporters. Knowledge of specific lipid-binding sites and modes of lipid influence on these proteins not only accomplishes the molecular description of transport cycle further, but also sheds light into localization dependent differences of transporter function. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Caroline Koshy
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Max-Planck Institute of Biophysics, Computational Structural Biology Group, Frankfurt am Main, Germany
| | - Christine Ziegler
- Max Planck Institute of Biophysics, Structural Biology Department, Frankfurt am Main, Germany; Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.
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29
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Joseph B, Korkhov VM, Yulikov M, Jeschke G, Bordignon E. Conformational cycle of the vitamin B12 ABC importer in liposomes detected by double electron-electron resonance (DEER). J Biol Chem 2013; 289:3176-85. [PMID: 24362024 DOI: 10.1074/jbc.m113.512178] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Double electron-electron resonance is used here to investigate intermediates of the transport cycle of the Escherichia coli vitamin B12 ATP-binding cassette importer BtuCD-F. Previously, we showed the ATP-induced opening of the cytoplasmic gate I in TM5 helices, later confirmed by the AMP-PNP-bound BtuCD-F crystal structure. Here, other key residues are analyzed in TM10 helices (positions 307 and 322) and in the cytoplasmic gate II, i.e. the loop between TM2 and TM3 (positions 82 and 85). Without BtuF, binding of ATP induces detectable changes at positions 307 and 85 in BtuCD in liposomes. Together with BtuF, ATP triggers the closure of the cytoplasmic gate II in liposomes (reported by both positions 82 and 85). This forms a sealed cavity in the translocation channel in agreement with the AMP-PNP·BtuCD-F x-ray structure. When vitamin B12 and AMP-PNP are simultaneously present, the extent of complex formation is reduced, but the short 82-82 interspin distance detected indicates that the substrate does not affect the closed conformation of this gate. The existence of the BtuCD-F complex under these conditions is verified with spectroscopically orthogonal nitroxide and Gd(III)-based labels. The cytoplasmic gate II remains closed also in the vanadate-trapped state, but it reopens in the ADP-bound state of the complex. Therefore, we suggest that the substrate likely trapped in ATP·BtuCD-F can be released after ATP hydrolysis but before the occluded ADP-bound conformation is reached.
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Affiliation(s)
- Benesh Joseph
- From the Laboratory of Physical Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10 and
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