DOCSLIB.ORG

Moving Fe from Ferritin Ion Channels to Catalytic OH Centers

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Moving Fe from Ferritin Ion Channels to Catalytic OH Centers + Moving Fe2 from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates Rabindra K. Beheraa,1 and Elizabeth C. Theila,b,2 aChildren’s Hospital Oakland Research Institute, Oakland, CA 94609; and bDepartment of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622 Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved April 15, 2014 (received for review September 30, 2013) Ferritin biominerals are protein-caged metabolic iron concentrates Ferritin protein ion channels are 15 Å long, analogous to short used for iron–protein cofactors and oxidant protection (Fe2+ and ion channels in biological membranes (3). Positioned around the 2+ O2 sequestration). Fe passage through ion channels in the pro- threefold symmetry axes of the cage (Fig. 1), ferritin protein ion tein cages, like membrane ion channels, required for ferritin biomin- channels form during cage self-assembly from three proximal + eral synthesis, is followed by Fe2 substrate movement to ferritin subunits; ion channel amino acids are highly conserved (Table 1) 2+ enzyme (Fox)sites.Fe and O2 substrates are coupled via a diferric (14). Both external and internal ferritin ion channel pores are 3+ peroxo (DFP) intermediate, λmax 650 nm, which decays to [Fe –O– 4–5 Å in diameter with a midchannel constriction, 2.3 Å in di- + Fe3 ] precursors of caged ferritin biominerals. Structural studies show ameter, created by the carboxylate side chains from the three multiple conformations for conserved, carboxylate residues E136 and glutamate residues at position 130. In protein crystals, ferritin B E57, which are between ferritin ion channel exits and enzymatic sites, ion channels bind a variety of divalent metal ions (Fig. S2 and suggesting functional connections. Here we show that E136 and E57 Table S1). Because hydrated ions have diameters of 6.4–6.9 Å, are required for ferritin enzyme activity and thus are functional links partial dehydration must occur for ion passage through the E130 between ferritin ion channels and enzymatic sites. DFP formation (Kcat constriction (2.3-Å diameter). Only single metal atoms are ob- and kcat/Km), DFP decay, and protein-caged hydrated ferric oxide ac- served in protein–metal crystal structures at the ring of three cumulation decreased in ferritin E57A and E136A; saturation required E130 residues, contrasting with the multiple metal atoms accu- + higher Fe2 concentrations. Divalent cations (both ion channel and mulated near the channel exits around the ring of three D127 intracage binding) selectively inhibit ferritin enzyme activity (block residues with shorter carboxylate side chains (Fig. 1 B and C); Fe2+ access), Mn2+ << Co2+ < Cu2+ < Zn2+, reflecting metal ion– + multiple ordered water molecules also accumulate near D127. protein binding stabilities. Fe2 –Cys126 binding in ferritin ion chan- Here we report functional studies that trace the movement of 2+ + nels, observed as Cu –S–Cys126 charge-transfer bands in ferritin Fe2 from ferritin ion channel exits to ferritin enzyme sites (Fig. 1). 2+ E130D UV-vis spectra and resistance to Cu inhibition in ferritin The strategy is to compare enzymatic reactions among variant 2+ CHEMISTRY C126S, was unpredicted. Identifying E57 and E136 links in Fe move- ferritins E57A, E136A, and E57A/E136A to WT and to an ion ment from ferritin ion channels to ferritin enzyme sites completes channel variant, E130D, which has detectable enzymatic activity; 2+ a bucket brigade that moves external Fe into ferritin enzymatic sites. in protein crystal structures, ferritin cage residues E57 and E136 2+ The results clarify Fe transport within ferritin and model molecular have multiple conformations and bind metal ions. Enzymatically + links between membrane ion channels and cytoplasmic destinations. active ferritin subunits (type H) in eukaryotic ferritin couple Fe2 iron traffic | oxidoreductase enzyme activity | antioxidant | ferrihydrite | Significance BioIron BIOCHEMISTRY How ions move between ion channel exits and final desti- iological and synthetic ion channels transport metal ions nations is poorly understood. Fe2+ substrate enters ferritin Bthrough barriers, including those in ferritin protein cages protein nanocages through cage-penetrating ion channels – + (1 8). How ions reach specific destinations, after exiting ion chan- analogous to membrane ion channels. Fe2 then moves to nels, remains unknown. Ion channels embedded in soluble fer- ferritin cage enzyme (Fox) sites, reacting with oxygen substrate ritin protein cages are more accessible to study than membrane + to produce diferric oxy complexes, the precursors of ferritin ion channels embedded in lipid-rich membranes. Fe2 substrate minerals (Fe2O3·H2O). Ferritin iron is used in heme and iron– is transported into ferritin protein cages through multiple ion sulfur cofactors. Monitoring rapid (ms) diferric peroxo forma- A–D channels that penetrate the cages (Fig. 1 ) and is delivered tion in WT ferritin and E57 and E136 variants showed that to multiple ferritin enzyme (Fox) sites. Each ferritin enzyme site 2+ these conserved residues are required for enzyme activity. binds 2 Fe substrate ions which, in eukaroytic ferritins, react Combining the results with older structural studies identifies + with O2 substrate; the intermediate of enzyme activity is diferric ferritin E57 and E136 links in the Fe2 bucket brigade con- peroxo (DFP) that decays to diferric oxy, the precursors of necting ferritin ion channels and destinations. By analogy, key · protein-caged ferritin biominerals (Fe2O3 H2O). Ferritin bio- carboxylates in ion transporters link ion channels to cytoplas- minerals vary in size, depending on iron availability, up to 4,500 mic destinations. Fe/cage. Rapid (ms) formation of blue color DFP (λmax: 650 nm) 2+ (9, 10) requires cooperative binding of 2 Fe /active site (Hill Author contributions: R.K.B. and E.C.T. designed research; R.K.B. performed research; R.K.B. 2+ coefficient = 3) (11) and indicates correct Fe delivery to the and E.C.T. analyzed data; and R.K.B. and E.C.T. wrote the paper. multiple ferritin enzymatic centers. Ferritin protein-caged iron The authors declare no conflict of interest. biominerals, slow to dissolve in solution (Fig. S1), are metabolic This article is a PNAS Direct Submission. iron concentrates for cofactor biosynthesis such as heme or iron- 1Present address: Department of Chemistry, National Institute of Technology, Rourkela 2+ sulfur clusters. The conversion of Fe and O2 into protein- 769008, Odisha, India. coated solids inside ferritin cages is an antioxidant activity, and 2To whom correspondence should be addressed. E-mail: [email protected]. ferritin genes are regulated with other antioxidant response This article contains supporting information at www.pnas.org/lookup/suppl/doi:10.1073/ proteins (4, 12, 13). pnas.1318417111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1318417111 PNAS | June 3, 2014 | vol. 111 | no. 22 | 7925–7930 Downloaded by guest on September 23, 2021 2+ Fig. 1. Ion channels in soluble ferritin protein nanocages transport Fe to multiple catalytic centers (Fox or oxidoreductase sites). (A) The 24-subunit ferritin + + protein cage. Red helices, Fe2 channels. (B) A ferritin Fe2 ion channel (side view). Green spheres, metal ions. Conserved residues E57 and E136 are putative 2+ carboxylate links in Fe transit between ferritin ion channel carboxylate (E130 and D127) and ferritin enzyme (Fox) sites based on phylogenetic structural location and conformational flexibility in protein crystals (16, 18). (C) A single ferritin protein cage subunit (side view). Tan, channel helix segments. (D)Ion channel (viewed from inside the protein cage). Green spheres, metal ions. Prepared from PDB 3KA3 using PyMol. and O2 substrates in an oxidoreductase reaction that may be Results written as Conserved Carboxylates E57 and E136 Are Required for Rapid Reactions + Â Ã ÂÀ ÁÃ of Fe2 at Ferritin Enzyme Centers. Ferritin variants E57A and 2+• + → • 3+‐ ‐ ‐ 3+• 2 Fe H2O O2 H2O Fe O O Fe H2O E136A (Fig. 1C) (16, 17) were constructed for the following rea- + i ii → Fe2O3 • H2O + 4H : sons: ( ) E57 and E136 are highly conserved, ( ) E57 and E136 lie between internal exits and diiron catalytic centers (Table S1) A blue diferric peroxo intermediate forms in ms and decays quickly (<1 s) (4, 12, 13). Diferric oxy enzymatic reaction prod- 2+ ucts in ferritin are released inside the protein cage and coalesce Table 1. Conservation of ferritin amino acids in Fe cage into ferric-oxo multimers within nucleation channels between the transfer residues and ion channel walls enzyme sites and the central mineral growth cavity (Fig. 1); stoi- + Transfer carboxylates: E136 chiometric amounts of hydrogen peroxide and Fe3 are detected at + Organism and E57 Ion channel: helix 4 subsaturating amounts of Fe2 (<36 Fe/cage). Sets of four prox- imal nucleation channel exits surround the inner surface of the Eukaryotes fourfold cage axes, which can facilitate ordered interactions Frog M HSHEEREHAE–EEQVKDIK DPHLCDFLESEYL among the emerging biomineral precursors (8). Engineered ferritin Frog H QSHEEREHAE–EEQVKSIK DPHLCDFLETEYL variants E57A and E136A lack the conserved carboxylate residues Human H QSHEEREHAE–NEQVKAIK DPHLCDFIETHYL that lie between the ion channel exits and the diiron enzymatic sites. Human L LAEEKREGYE–DEEVKLIK DPHLCDFLETHFL Ferritin E130D ion channels were designed to compare an enzy- Human Mt-H QSREETEHAE–NEQVKSIK DPHLCDFLETYYL
Load more

Recommended publications
  • S41467-019-13834-7.Pdf
    ARTICLE https://doi.org/10.1038/s41467-019-13834-7 OPEN Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes Manish Debnath1, Sandipan Chakraborty1, Y. Pavan Kumar1, Ritapa Chaudhuri1, Biman Jana1 & Jyotirmayee Dash1* 1234567890():,; The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabi- lizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, elec- trophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications. 1 School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 West Bengal, India. *email: [email protected] NATURE COMMUNICATIONS | (2020) 11:469 | https://doi.org/10.1038/s41467-019-13834-7 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-13834-7 he transport of ions across the semi-permeable cell mem- Binding studies of MG with h-TELO G-quadruplex.
    [Show full text]
  • Maintext Frac Final-Accepted
    Delft University of Technology Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate Zhao, Shidi; Restrepo-Pérez, Laura; Soskine, Misha; Maglia, Giovanni; Joo, Chirlmin; Dekker, Cees; Aksimentiev, Aleksei DOI 10.1021/acsnano.8b09266 Publication date 2019 Document Version Accepted author manuscript Published in ACS Nano Citation (APA) Zhao, S., Restrepo-Pérez, L., Soskine, M., Maglia, G., Joo, C., Dekker, C., & Aksimentiev, A. (2019). Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate. ACS Nano, 13(2), 2398-2409. https://doi.org/10.1021/acsnano.8b09266 Important note To cite this publication, please use the final published version (if applicable). Please check the document version above. Copyright Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons. Takedown policy Please contact us and provide details if you believe this document breaches copyrights. We will remove access to the work immediately and investigate your claim. This work is downloaded from Delft University of Technology. For technical reasons the number of authors shown on this cover page is limited to a maximum of 10. Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate Shidi Zhao‡a, Laura Restrepo-Pérez‡b, Misha Soskine c, Giovanni Maglia c, Chirlmin Joo b, Cees Dekker b and Aleksei Aksimentiev a a Center for Biophysics and Quantitative Biology, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
    [Show full text]
  • 10Th ISMSC-2015 Strasbourg, France (June 28Th - July 2Nd, 2015)
    10th ISMSC-2015 Strasbourg, France (June 28th - July 2nd, 2015) Code Presenting Author Title Authors Perspectives in Chemistry: From Supramolecular Chemistry towards PL-1 Jean-Marie Lehn Jean-Marie Lehn Adaptive Chemistry PL-2 E.W. (Bert) Meijer Folding of Macromolecules; Functional single-chain polymer nanoparticles E.W. (Bert) Meijer PL-3 Samuel Stupp Bio-Inspired Supramolecular Materials Samuel Stupp Functional Materials Constructed by Combining Traditional Polymers and PL-4 Feihe Huang Feihe Huang, Xiaofan Ji, Mingming Zhang, Xiaodong Chi Host-Guest Molecular Recognition Motifs Supramolecular Liquid-Crystalline Materials for Energy, Water, and PL-5 Takashi Kato Takashi Kato Environment PL-6 Tanja Weil Programmed Self-Assembly of Bioactive Architectures Tanja Weil, David Y. W. Ng PL-7 Paul D. Beer Interlocked Host Molecules for Anion Recognition and Sensing Paul D. Beer PL-8 Takuzo Aida Rational Strategy for Chain-Growth Supramolecular Polymerization Takuzo Aida IL-1 Pablo Ballester Mechanically Interlocked Molecules Containing Calix[4]pyrrole Scaffolds Pablo Ballester IL-2 Davide Bonifazi Supramolecular Colorlands Davide Bonifazi IL-3 Kentaro Tanaka Columnar Liquid Crystalline Macrocycles Kentaro Tanaka IL-4 Ian Manners Recent Advances in “Living” Crystallization-Driven Self-Assembly Ian Manners Light-driven catenation and intermolecular communication in solution and Nathan D. McClenaghan, A. Tron, R. Bofinger, J. IL-5 Nathan McClenaghan nanocapsules Thevenot, S. Lecommandoux, J.H.R. Tucker Supramolecular Chemistry and Photophysics of Light-Harvesting IL-6 Harry Anderson Harry Anderson Nanorings Jeroen J. L. M. IL-7 Supramolecular Protein Assemblies, from Cages to Tubes Jeroen J. L. M. Cornelissen Cornelissen Light-driven liquids, particles, and interfaces: from microfluidics to coffee IL-8 Damien Baigl Damien Baigl rings B.C.
    [Show full text]
  • Novel Principles
    Part I Self-Assembly and Nanoparticles: Novel Principles Nanobiotechnology II. Edited by Chad A. Mirkin and Christof M. Niemeyer Copyright 8 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-31673-1 3 1 Self-Assembled Artificial Transmembrane Ion Channels Mary S. Gin, Emily G. Schmidt, and Pinaki Talukdar 1.1 Overview Natural ion channels are large, complex proteins that span lipid membranes and allow ions to pass in and out of cells. These multimeric channel assemblies are capable of performing the complex tasks of opening and closing in response to specific signals (gating) and allowing only certain ions to pass through (selectiv- ity). This controlled transport of ions is essential for the regulation of both intra- cellular ion concentration and the transmembrane potential. Ion channels play an important role in many biological processes, including sensory transduction, cell proliferation, and blood-pressure regulation; abnormally functioning channels have been implicated in causing a number of diseases [1]. In addition to large ion channel proteins, peptides (e.g., gramicidin A) and natural small-molecule antibiotics (e.g., amphotericin B and nystatin) form ion channels in lipid mem- branes. Due to the complexity of channel proteins, numerous research groups have during recent years been striving to develop artificial analogues [2–7]. Initially, the synthetic approach to ion channels was aimed at elucidating the minimal structural requirements for ion flow across a membrane. However, more recently the focus has shifted to the development of synthetic channels that are gated, pro- viding a means of controlling whether the channels are open or closed.
    [Show full text]
  • Iii Explorations in Synthetic Ion Channel Research
    iii Explorations in synthetic ion channel research: metal-ligand self-assembly and dissipative assembly by Andrew Krisjanis Dambenieks Master of Science, The University of Western Ontario, 2006 Bachelor of Science, The University of Western Ontario, 2004 A Doctoral Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY in the Department of Chemistry Andrew Krisjanis Dambenieks, 2013 University of Victoria All rights reserved. This dissertation may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. ii Supervisory Committee Explorations in synthetic ion channel research: metal-ligand self-assembly and dissipative assembly by Andrew Krisjanis Dambenieks Master of Science, The University of Western Ontario, 2006 Bachelor of Science, The University of Toronto, 2004 Supervisory Committee Dr. Thomas Fyles, Department of Chemistry Supervisor Dr. Natia L. Frank, Department of Chemistry Departmental Member Dr. Fraser Hof, Department of Chemistry Departmental Member Dr. Francis E. Nano, Department of Biochemistry Outside Member iii Abstract Supervisory Committee Dr. Thomas Fyles, Department of Chemistry Supervisor Dr. Natia L. Frank, Department of Chemistry Departmental Member Dr. Fraser Hof, Department of Chemistry Departmental Member Dr. Francis E. Nano, Department of Biochemistry Outside Member This thesis explores fundamental design strategies in the field of synthetic ion channel research from two different perspectives. In the first part the synthesis of complex, shape persistent and thermodynamically stable structures based on metal- ligand self-assembly is explored. The second part examines transport systems with dynamic transport behavior in response to chemical inputs which more closely mimic the dissipative assembly of Natural ion channels.
    [Show full text]
  • Synthetic Ion Channels and DNA Logic Gates As Components of Molecular Robots Ryuji Kawano*[A]
    DOI:10.1002/cphc.201700982 Minireviews Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots Ryuji Kawano*[a] Amolecular robot is anext-generation biochemical machine sensorsare useful components for molecular robots with that imitates the actions of microorganisms. It is made of bio- bodies consisting of alipid bilayer because they enablethe in- materials such as DNA, proteins,and lipids. Three prerequisites terface between the inside and outside of the molecular robot have been proposedfor the construction of such arobot:sen- to functionasgates. After the signal molecules arrive inside sors, intelligence, and actuators. This Minireviewfocuseson the molecular robot, they can operate DNA logic gates, which recent research on synthetic ion channels and DNA computing perform computations. These functions will be integrated into technologies, which are viewed as potential candidate compo- the intelligence and sensor sections of molecularrobots. Soon, nents of molecularrobots. Synthetic ion channels, which are these molecular machines will be able to be assembled to op- embedded in artificial cell membranes (lipid bilayers), sense erate as amass microrobot and play an active role in environ- ambient ions or chemicals and import them. These artificial mental monitoring and in vivo diagnosis or therapy. 1. Molecular Robots and the Lipid Bilayer Platform Molecular robots have recently emerged based on biomole- source by chemotaxis. These accomplished functions are inte- cules andbiochemical processes. Approximately30years ago, grated in amicron-sized body surrounded with abilayer lipid aself-constructing machine, aso-called “assembler,” was origi- membrane (BLM). Sato et al. reported the development of a nally proposed by Drexler.[1] Based on the idea of an assembler, sophisticated molecularrobot prototype in 2017.[9] Their devel- molecular machinesthat operate autonomously have been de- oped amoeba-type robot has light-induced DNA clutches for velopedusing DNA or RNA.
    [Show full text]
  • Design, Synthesis and Characterization of Synthetic Ion Receptors As Biologically Functional Ion Carriers and Channels Carl Yamnitz Washington University in St
    Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) January 2010 Design, Synthesis and Characterization of Synthetic Ion Receptors as Biologically Functional Ion Carriers and Channels Carl Yamnitz Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Yamnitz, Carl, "Design, Synthesis and Characterization of Synthetic Ion Receptors as Biologically Functional Ion Carriers and Channels" (2010). All Theses and Dissertations (ETDs). 390. https://openscholarship.wustl.edu/etd/390 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Department of Chemistry Dissertation Examination Committee: George W. Gokel, Co-Chairperson Joshua A. Maurer, Co-Chairperson Jianmin Cui Peter P. Gaspar Kevin D. Moeller John-Stephen A. Taylor Design, Synthesis and Characterization of Synthetic Ion Receptors as Biologically Functional Ion Carriers and Channels By Carl Robert Yamnitz A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2010 St. Louis, Missouri ABSTRACT OF THE DISSERTATION Design, Synthesis and Characterization of Synthetic Ion Receptors as Biologically Functional Ion Carriers and Channels by Carl Yamnitz Doctor of Philosophy in Chemistry Washington University, 2010 Dr. George W. Gokel, Thesis Advisor The study of proteins and natural molecules that transport cations and anions across biological membranes has been a major focus of biochemistry and cellular biology for more than a century.
    [Show full text]
  • Book Chapter
    Book Chapter The Characterization of Synthetic Ion Channels and Pores MATILE, Stefan, SAKAI, Naomi Abstract This chapter contains sections titled: Methods : Planar Bilayer Conductance, Fluorescence Spectroscopy with Labeled Vesicles. Characteristics : pH Gating, Concentration Dependence, Size Selectivity, Voltage Gating, Ion Selectivity, Blockage and Ligand Gating. Structural Studies : Binding to the Bilayer, Location in the Bilayer, Self-Assembly, Molecular Recognition. Reference MATILE, Stefan, SAKAI, Naomi. The Characterization of Synthetic Ion Channels and Pores. In: Schalley Christoph. Analytical Methods in Supramolecular Chemistry. Weinheim : Wiley, 2012. p. 711-742 DOI : 10.1002/9783527610273.ch11 Available at: http://archive-ouverte.unige.ch/unige:8374 Disclaimer: layout of this document may differ from the published version. 1 / 1 The Characterization of Synthetic Ion Channels and Pores Stefan Matile and Naomi Sakai Department of Organic Chemistry, University of Geneva, Geneva, Switzerland Table of Contents 1. Introduction 01 2. Methods 03 2.1. Planar Bilayer Conductance 04 2.2. Fluorescence Spectroscopy with Labeled Vesicles 07 2.3. Miscellaneous 09 3. Characteristics 10 3.1. pH Gating 10 3.2. Concentration Dependence 12 3.3. Size Selectivity 14 3.4. Voltage Gating 15 3.5. Ion Selectivity 17 3.6. Blockage and Ligand Gating 21 3.7. Miscellaneous 25 4. Structural Studies 26 4.1. Binding to the Bilayer 28 4.2. Location in the Bilayer 29 4.3. Self-Assembly 30 4.4. Molecular Recognition 31 5. Concluding Remarks 31 6. References 32 1. Introduction “Membrane transport is the quintessential supramolecular function.” The objective of this chapter is not to defend this statement by one of the pioneers of the field[1] but to provide a supramolecular chemist newly entering the field with an introductory guideline how to measure this function.
    [Show full text]
  • 1 Molecular Engineering of Membrane Nanopores Stefan Howorka
    Molecular Engineering of Membrane Nanopores Stefan Howorka University College London, Institute of Structural and Molecular Biology, Department of Chemistry, London, UK Membrane nanopores – hollow nanoscale barrels that puncture biological or synthetic membranes – have become powerful tools in chemical- and bio-sensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic-organic compounds, and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and explore what the next-generation of nanopore structures could be and where further practical applications might emerge. Membrane nanopores are the most important border crossings in the molecular world. They form water-filled openings across membrane barriers composed of lipids or semifluid polymers in order to transport ionic or molecular cargo (Box 1). Given their small dimensions, nanopores function as size-selective filters that can limit transport to individual molecules. Nanopores can also select molecules based on charge and other physicochemical properties, and act as stimulus-responsive molecular valves that open or close and thereby regulate transport across membranes. Reflecting these functions, membrane nanopores have been exploited for many applications. Pores can help sequence individual DNA strands1-4, sense a wide range of analytes of biomedical and environmental relevance5-11, and study single-molecule chemistry and biophysics.
    [Show full text]
  • Topics in Current Chemistry
    277 Topics in Current Chemistry Editorial Board: V.Balzani · A. de Meijere · K. N. Houk · H. Kessler · J.-M. Lehn S. V.Ley · S. L. Schreiber · J. Thiem · B. M. Trost · F. Vögtle H. Yamamoto Topics in Current Chemistry Recently Published and Forthcoming Volumes Creative Chemical Sensor Systems Atomistic Approaches in Modern Biology Volume Editor: Schrader, T. From Quantum Chemistry Vol. 277, 2007 to Molecular Simulations Volume Editor: Reiher, M. In situ NMR Methods in Catalysis Vol. 268, 2006 Volume Editors: Bargon, J., Kuhn, L. T. Vol. 276, 2007 Glycopeptides and Glycoproteins Synthesis, Structure, and Application Sulfur-Mediated Rearrangements II Volume Editor: Wittmann, V. Volume Editor: Schaumann, E. Vol. 267, 2006 Vol. 275, 2007 Microwave Methods in Organic Synthesis Sulfur-Mediated Rearrangements I Volume Editors: Larhed, M., Olofsson, K. Volume Editor: Schaumann, E. Vol. 266, 2006 Vol. 274, 2007 Supramolecular Chirality Bioactive Conformation II Volume Editors: Crego-Calama, M., Volume Editor: Peters, T. Reinhoudt, D. N. Vol. 273, 2007 Vol. 265, 2006 Bioactive Conformation I Radicals in Synthesis II Volume Editor: Peters, T. Complex Molecules Vol. 272, 2007 Volume Editor: Gansäuer, A. Vol. 264, 2006 Biomineralization II Mineralization Using Synthetic Polymers and Radicals in Synthesis I Templates Methods and Mechanisms Volume Editor: Naka, K. Volume Editor: Gansäuer, A. Vol. 271, 2007 Vol. 263, 2006 Biomineralization I Molecular Machines Crystallization and Self-Organization Process Volume Editor: Kelly, T. R. Volume Editor: Naka, K. Vol. 262, 2006 Vol. 270, 2007 Immobilisation of DNA on Chips II Novel Optical Resolution Technologies Volume Editor: Wittmann, C. Volume Editors: Vol. 261, 2005 Sakai, K., Hirayama, N., Tamura, R.
    [Show full text]
  • Electrokinetic Flow in Micro- and Nano-Fluidic Components
    ELECTROKINETIC FLOW IN MICRO- AND NANO-FLUIDIC COMPONENTS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Zhi Zheng, M.S. ***** The Ohio State University 2003 Dissertation Committee: Approved by Professor A. Terry Conlisk, Adviser Professor Derek J. Hansford __________________________ Adviser Professor L, James Lee Biomedical Engineering Center ABSTRACT In this work, electrokinetic flow through nano- and micro-channels is investigated. The governing equations for the flow in three dimensional channels are derived from Poisson-Nernst-Planck theory. The boundary conditions for the governing equations are obtained from the electrochemical equilibrium requirements. The results are compared with three sets of experimental data, provided by iMEDD inc., Oak Ridge National Laboratory, and Georgia Institute of Technology. The results of comparison are extremely good. A finite difference method is used to solve the governing equations numerically. For asymptotic cases, the governing equations are solved analytically using singular perturbation method. The results show that multivalent counterions decrease the electroosmotic flow extraordinarily. Scaling laws for the governing equations are introduced which clarify that several dimensionless parameters determine the potential and velocity profiles and the distribution patterns of ion species. The relationship between the channel surface charge density and the ζ potential is explored. The diffusive fluxes, electric migrational fluxes and convective fluxes of different ion species in the electrokinetic flow are obtained from the governing equations. Results are also obtained for electroosmosis in 2D nanochannels. At the end of this work, the governing equations for unsteady flow are derived, the transport of macromolecules through micro- and nano- channels is discussed and the future work in these areas is suggested.
    [Show full text]
  • Synthetic Ion Channel Activity Documented by Electrophysiological Methods in Living Cells W
    Published on Web 11/10/2004 Synthetic Ion Channel Activity Documented by Electrophysiological Methods in Living Cells W. Matthew Leevy,‡ James E. Huettner,§ Robert Pajewski,‡ Paul H. Schlesinger,§ and George W. Gokel*,†,‡ Contribution from the Departments of Chemistry, Molecular Biology and Pharmacology, and Cell Biology and Physiology, Washington UniVersity School of Medicine, 660 South Euclid AVenue, Campus Box 8103, St. Louis, Missouri 63110 Received June 8, 2004; E-mail: [email protected] Abstract: Hydraphiles are synthetic ion channels that use crown ethers as entry portals and that span phospholipid bilayer membranes. Proton and sodium cation transport by these compounds has been demonstrated in liposomes and planar bilayers. In the present work, whole cell patch clamp experiments show that hydraphiles integrate into the membranes of human embryonic kidney (HEK 293) cells and significantly increase membrane conductance. The altered membrane permeability is reversible, and the cells under study remain vital during the experiment. Control compounds that are too short (C8-benzyl channel) to span the bilayer or are inactive owing to a deficiency in the central relay do not induce similar conductance increases. Control experiments confirm that the inactive channel analogues do not show nonspecific effects such as activation of native channels. These studies show that the combination of structural features that have been designed into the hydraphiles afford true, albeit simple, channel function in live cells. Introduction channel compounds has demonstrated the classic, stochastic Phospholipid bilayer membranes circumscribe nearly all cells. open/closed channel behavior in planar bilayer conductance 3,7,8 While the membrane establishes the fundamental barrier be- experiments and has shown significant activity in synthetic 9,10 tween the interior and exterior of the cell, it must be selectively liposomes.
    [Show full text]