Viral Membrane Proteins: Structure, Function, and Drug Design by Wolfgang B. FischerViral Membrane Proteins: Structure, Function, and Drug Design by Wolfgang B. Fischer

Viral Membrane Proteins: Structure, Function, and Drug Design

EditorWolfgang B. Fischer

Paperback | December 15, 2010

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In Viral Membrane Proteins: Structure, Function, and Drug Design, Wolfgang Fischer summarizes the current structural and functional knowledge of membrane proteins encoded by viruses. In addition, contributors to the book address questions about proteins as potential drug targets. The range of information covered includes signal proteins, ion channels, and fusion proteins.This book has a place in the libraries of researchers and scientists in a wide array of fields, including protein chemistry, molecular biophysics, pharmaceutical science and research, bioanotechnology, molecular biology, and biochemistry.
Title:Viral Membrane Proteins: Structure, Function, and Drug DesignFormat:PaperbackDimensions:304 pages, 9.25 × 6.1 × 0.01 inPublished:December 15, 2010Publisher:Springer USLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1441934537

ISBN - 13:9781441934536

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Table of Contents

Part I. Membrane Proteins from Plant Viruses1. Membrane Proteins in Plant VirusesMichael J. Adams and John F. Antoniw1. Introduction2. Survey of Transmembrane Proteins in Plant Viruses2.1. The Database2.2. Software3. Cell-To-Cell Movement Proteins3.1. The "30k" Superfamily3.2. Triple Gene Block3.3. Carmovirus-Like3.4. Other Movement Proteins3.5. General Comments4. Replication Proteins5. Proteins Involved in Transmission by Vectors5.1. Insect Transmission5.2. Fungus Transmission6. Other Membrane Proteins7. ConclusionsAcknowledgmentsReferences2. Structure and Function of a Viral Encoded K ChannelAnna Moroni, James Van Etten, and Gerhard Thiel1. Introduction2. K Channels are Highly Conserved Proteins with Important Physiological Functions3. Structural Aspects of Viral K Channel Proteins as Compared to thosefrom Other Sources4. The Short N-Terminus is Important for Kcv Function5. Functional Properties of Kcv Conductance in Heterologous Expression Systems6. Kcv is a K Selective Channel7. Kcv has some Voltage Dependency8. Kcv has Distinct Sensitivity to K Channel Blockers9. Ion Channel Function in Viral ReplicationvVimp-FM.qxd 17/07/2004 03:07 PM Page v10. Kcv is Important for Viral Replication11. Evolutionary Aspects of the Kcv GeneAcknowledgmentsReferencesPart II. Fusion Proteins3. HIV gp41: A Viral Membrane Fusion MachineSergio G. Peisajovich and Yechiel Shai1. Introduction2. HIV Envelope Native Conformation3. Receptor-Induced Conformational Changes3.1. CD4 Interaction3.2. Co-Receptor Interaction4. The Actual Membrane Fusion Step4.1. The Role of the N-Terminal Fusion Domain4.2. The Role of the C-Terminal Fusion Domain5. HIV Entry Inhibitors5.1. CD4-Binding Inhibitors5.2. Co-Receptor Binding Inhibitors5.3. Improving the Activity of Inhibitors that Block Conformational Changes6. Final RemarksAcknowledgmentReferences4. Diversity of Coronavirus Spikes: Relationship toPathogen Entry and DisseminationEdward B. Thorp and Thomas M. Gallagher1. Introduction2. S Functions during Coronavirus Entry3. S Functions during Dissemination of Coronavirus Infections4. S Polymorphisms Affect Coronavirus Pathogenesis5. Applications to the SARS Coronavirus6. Relevance to Antiviral Drug DevelopmentsReferences5. Aspects of the Fusogenic Activity of Influenza HemagglutininPeptides by Molecular Dynamics SimulationsL. Vaccaro, K. Cross, S.A. Wharton, J.J. Skehel, and F. Fraternali1. Introduction2. Methods3. Results3.1. Comparison with Experimental Structures3.2. Membrane Anchoringvi ContentsVimp-FM.qxd 17/07/2004 03:07 PM Page viContents vii4. ConclusionsAcknowledgmentReferencesPart III. Viral Ion Channels/Viroporins6. Viral Proteins that Enhance Membrane PermeabilityMaría Eugenia González and Luis Carrasco1. Introduction2. Measuring Alterations in Membrane Permeability2.1. The Hygromycin B Test2.2. Entry of Macromolecules into Virus-Infected Cells2.3. Other Assays to Test the Entry or Exit of Macromolecules fromVirus-Infected Cells2.3.1. Entry or Exit of Radioactive Molecules2.3.2. Entry of ONPG and Dyes2.3.3. Entry of Propidium Iodide2.3.4. Release of Cellular Enzymes to Culture Medium3. Viral Proteins that Modify Permeability3.1. Viroporins3.2. Viral Glycoproteins that Modify Membrane Permeability3.2.1. Rotavirus Glycoprotein3.2.2. The HIV-1 gp413.2.3. Other Viral Glycoproteins4. Membrane Permeabilization and Drug Design4.1. Antibiotics and Toxins that Selectively Enter Virus-Infected Cells4.2. Viroporin Inhibitors4.3. Antiviral Agents that Interfere with Viral GlycoproteinsAcknowledgmentsReferences7. FTIR Studies of Viral Ion ChannelsItamar Kass and Isaiah T. Arkin1. Introduction1.1. Principles of Infrared Spectroscopy1.1.1. Amide Group Vibrations1.1.2. Secondary Structure2. SSID FTIR2.1. Dichroic Ratio2.2. Sample Disorder2.3. Orientational Parameters Derivation2.4. Data Utilization3. Examples3.1. M2 H Channel from Influenza A Virus3.2. vpu Channel from HIV3.3. CM2 from Influenza C VirusVimp-FM.qxd 17/07/2004 03:07 PM Page vii4. Future DirectionsAcknowledgmentReferences8. The M2 Proteins of Influenza A and B Virusesare Single-Pass Proton ChannelsYajun Tang, Padma Venkataraman, Jared Knopman,Robert A. Lamb, and Lawrence H. Pinto1. Introduction2. Intrinsic Activity of the A/M2 Protein of Influenza Virus3. Mechanisms for Ion Selectivity and Activation of the A/M2 Ion Channel4. The BM2 Ion Channel of Influenza B Virus5. ConclusionAcknowledgmentsReferences9. Influenza A Virus M2 Protein: Proton Selectivity of the Ion Channel,Cytotoxicity, and a Hypothesis on Peripheral Raft Associationand Virus BuddingCornelia Schroeder and Tse-I Lin1. Determination of Ion Selectivity and Unitary Conductance`1.1. Background1.2. Method1.2.1. Expression, Isolation, and Quantification of the M2 Protein1.2.2. Reconstitution of M2 into Liposomes1.2.3. Proton Translocation Assay1.3. Proton Selectivity1.4. Average Single-Channel Parameters and Virion Acidification during Uncoating2. Cytotoxicity of Heterologous M2 Expression3. The M2 Protein Associates with Cholesterol4. M2 as a Peripheral Raft Protein and a Model of its Role in Virus Budding4.1. Interfacial Hydrophobicity and Potential Cholesterol and Raft-BindingMotifs of the M2 Post-TM Region4.2. M2 as a Peripheral Raft Protein4.3. M2 as a Factor in the Morphogenesis and Pinching-Off of Virus ParticlesAcknowledgmentReferences10. Computer Simulations of Proton Transport Throughthe M2 Channel of the Influenza A VirusYujie Wu and Gregory A. Voth1. Introduction2. Overview of Experimental Studies for the M2 Channel2.1. The Roles of the M2 Channel in the Viral Life Cycle2.2. The Architecture of the M2 Channel2.3. Ion Conductance Mechanisms3. Molecular Dynamics Simulations of Proton Transport in the M2 Channelviii ContentsVimp-FM.qxd 17/07/2004 03:07 PM Page viii3.1. Explicit Proton Transport Simulations and Properties ofthe Excess Proton in the M2 Channel3.2. Implications for the Proton Conductance Mechanism4. Possible Closed and Open Conformations4.1. A Possible Conformation for the Closed M2 Channel4.2. A Possible Conformation for the Open M2 Channel4.3. Further MD Simulations with the Closed Structure5. A Revised Gating Mechanism and Future WorkAcknowledgmentsReferences11. Structure and Function of Vpu from HIV-1S.J. Opella, S. Park, S. Lee, D. Jones, A. Nevzorov, M. Mesleh, A. Mrse,F.M. Marassi, M. Oblatt-Montal, M. Montal, S. Bour, and K. Strebel1. Introduction2. Structure Determination of Vpu3. Correlation of Structure and Function of Vpu4. Vpu-Mediated Enhancement of Viral Particle Release5. Vpu-Mediated Degradation of the Cd4 Receptor6. SummaryAcknowledgmentsReferences12. Structure, Phosphorylation, and Biological Function of theHIV-1 Specific Virus Protein U (Vpu)Victor Wray and Ulrich Schubert1. Introduction2. Structure and Biochemistry of Vpu3. Biochemical Analysis of Vpu PhosphorylationReferences13. Solid-State NMR Investigations of Vpu Structural Domains inOriented Phospholipid Bilayers: Interactions and AlignmentBurkhard Bechinger and Peter Henklein1. Introduction2. Peptide Synthesis3. Results and DiscussionAcknowledgmentsReferences14. Defining Drug Interactions with the Vpu Ion Channel from HIV-1V. Lemaitre, C.G. Kim, D. Fischer, Y.H. Lam, A. Watts, and W.B. Fischer1. Introduction1.1. Short Viral Membrane Proteins1.2. The Vpu Protein2. The MethodsContents ixVimp-FM.qxd 17/07/2004 03:07 PM Page ix2.1. Docking Approach2.2. Molecular Dynamics (MD) Simulations3. Analysis of Drug-Protein Interactions of Vpu with a Potential Blocker3.1. Using the Docking Approach3.2. Applying MD Simulations4. How Realistic is the Protein Model?5. The Putative Binding Site6. Water in the Pore7. MD Simulations for Drug Screening?8. Other Viral Ion Channels and Blockers9. Speculation of Binding Sites in the Cytoplasmic Site10. ConclusionsAcknowledgmentsReferences15. Virus Ion Channels Formed by Vpu of HIV-1, the 6K Proteinof Alphaviruses and NB of Influenza B VirusPeter W. Gage, Gary Ewart, Julian Melton, and Anita Premkumar1. Virus Ion Channels2. Vpu of HIV-12.1. Roles of Vpu in HIV-1 Replication2.2. Evidence that Vpu Forms an Ion Channel2.2.1. Properties of the Vpu Channel2.3. The Link Between Budding Enhancement by Vpu and its Ion Channel Activity2.3.1. Mutants Lacking Ion Channel Activity and Virus Budding2.3.2. Channel Blocking Drugs Inhibit Budding2.3.3. HMA Inhibits HIV-1 Replication in Monocytes and Macrophages3. Alphavirus 6K Proteins3.1. Replication of Alphaviruses3.2. The 6K Protein of Alphaviruses3.3. The 6K Protein and Virus Budding3.4. Ion Channels Formed by BFV and RRV 6K Protein3.5. Antibody Inhibition of RRV 6K Channels4. NB of Influenza B Virus4.1. Structure of NB4.2. Similarities Between M2 and NB4.3. Channel Activity of the NB Protein4.4. Currents at pH 6.04.5. Currents at pH 2.54.6. Effect of C-Terminal Antibody4.7. Effect of Amantadine4.8. Proton Permeability of NB Ion ChannelsReferences16. The Alphavirus 6K ProteinM.A. Sanz, V. Madan, J.L. Nieva, and L. Carrasco1. Introduction2. Methods to Assess Whether 6K is a Membrane-Active Proteinx ContentsVimp-FM.qxd 17/07/2004 03:07 PM Page xContents xi2.1. Hydrophobicity Tests2.2. Inducible Synthesis of 6K in E. Coli2.3. Synthesis of 6K in Mammalian Cells3. Synthesis of 6K During Virus Infection4. Cell Membrane Permeabilization by 6K5. Function of 6K During the Alphavirus Life Cycle6. A Model of 6K Function in Virion BuddingAcknowledgmentsReferencesPart IV. Membrane-Associated/Membrane Spanning17. The Structure, Function, and Inhibition ofInfluenza Virus NeuraminidaseElspeth Garman and Graeme Laver1. Introduction1.1. Structure of Influenza Virus2. Structure of Influenza Virus Neuraminidase2.1. Crystallization of Influenza Virus Neuraminidase2.2. Structure of the Conserved Catalytic Site2.3. Structures of Other Influenza Virus Neuraminidases2.4. Hemagglutinin Activity of Neuraminidase3. Function of Influenza Virus Neuraminidase3.1. Antigenic Properties of Influenza Virus Neuraminidase3.2. Antigenic Drift in Influenza Virus Neuraminidase4. Inhibition of Influenza Virus Neuraminidase4.1. Design and Synthesis of Novel Inhibitors of Influenza Virus Neuraminidase4.1.1. Relenza4.1.2. Tamiflu4.1.3. Other Inhibitors of Influenza Virus Neuraminidase4.2. Drug Resistance5. ConclusionsAcknowledgmentsReferences18. Interaction of HIV-1 Nef with Human CD4 and LckDieter Willbold1. Introduction2. Interaction of Nef with Human CD42.1. The CD4 Receptor2.2. CD4 and HIV2.3. Three-Dimensional Structures of CD4 Cytoplasmic Domain and HIV-1 Nef2.4. Nef Residues that are Important for CD4 Binding Map to the "Core Domain"2.5. Amino Terminal Residues of Nef are also Important for CD4 Binding2.6. Leucines 413 and 414 of CD4 are Essential for Nef Binding2.7. High Affinity Between CD4(403-433) and Full-Length Nef can beConfirmed by NMR SpectroscopyVimp-FM.qxd 17/07/2004 03:07 PM Page xi2.8. The Presence of a Helix in Human CD4 Cytoplasmic Domain PromotesBinding to HIV-1 Nef Protein2.9. Summary of the CD4-Nef Interaction3. Interaction of Nef with Human Lck3.1. Lymphocyte Specific Kinase Lck3.2. X-Ray Structures of Nef-SH3 Complexes3.3. NMR Spectroscopy is a Suitable Tool to Map Nef-Lck Interaction Sites3.4. The Unique Domain of Lck is Not Involved in Nef Binding3.5. Mapping of the Nef Interaction Site on Lck SH33.6. Summary of the Lck-Nef InteractionReferences