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4. How Realistic is the Protein Model? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
5. The Putative Binding Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
6. Water in the Pore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
7. MD Simulations for Drug Screening? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
8. Other Viral Ion Channels and Blockers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
9. Speculation of Binding Sites in the Cytoplasmic Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
10. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
15. Virus Ion Channels Formed by Vpu of HIV-1, the 6K Protein
of Alphaviruses and NB of Influenza B Virus
Peter W. Gage, Gary Ewart, Julian Melton, and Anita Premkumar
1. Virus Ion Channels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
2. Vpu of HIV-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
2.1. Roles of Vpu in HIV-1 Replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
2.2. Evidence that Vpu Forms an Ion Channel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
2.2.1. Properties of the Vpu Channel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
2.3. The Link Between Budding Enhancement by Vpu and its Ion Channel Activity . . . . . . 213
2.3.1. Mutants Lacking Ion Channel Activity and Virus Budding . . . . . . . . . . . . . . . . 213
2.3.2. Channel-Blocking Drugs Inhibit Budding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
2.3.3. HMA Inhibits HIV-1 Replication in Monocytes and Macrophages . . . . . . . . . . . 215
3. Alphavirus 6K Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
3.1. Replication of Alphaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
3.1.2. Viral Budding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
3.2. The 6K Protein of Alphaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
3.3. The 6K Protein and Virus Budding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
3.4. Ion Channels Formed by BFV and RRV 6K Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
3.5. Antibody Inhibition of RRV 6K Channels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
4. NB of Influenza B Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
4.1. Structure of NB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
4.2. Similarities Between M2 and NB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
4.3. Channel Activity of the NB Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
4.4. Currents at pH 6.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
4.5. Currents at pH 2.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
4.6. Effect of C-Terminal Antibody . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
4.7. Effect of Amantadine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
4.8. Proton Permeability of NB Ion Channels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
16. The Alphavirus 6K Protein
M.A. Sanz, V. Madan, J.L. Nieva, and Luis Carrasco
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
2. Methods to Assess Whether 6K is a Membrane-Active Protein . . . . . . . . . . . . . . . . . . . . . . 234
2.1. Hydrophobicity Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
2.2. Inducible Synthesis of 6K in E. coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
2.3. Synthesis of 6K in Mammalian Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
3. Synthesis of 6K During Virus Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
4. Cell Membrane Permeabilization by 6K . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
x Contents
Contents xi
5. Function of 6K During the Alphavirus Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
6. A Model of 6K Function in Virion Budding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
Part IV. Membrane-Spanning/Membrane Associated
17. The Structure, Function, and Inhibition of Influenza
Virus Neuraminidase
Elspeth Garman and Graeme Laver
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
1.1. Structure of Influenza Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
2. Structure of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
2.1. Crystallization of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
2.2. Structure of the Conserved Catalytic Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
2.3. Structures of Other Influenza Virus Neuraminidases . . . . . . . . . . . . . . . . . . . . . . . . . . 253
2.4. Hemagglutinin Activity of Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
3. Function of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
3.1. Antigenic Properties of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . 256
3.2. Antigenic Drift in Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
4. Inhibition of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
4.1. Design and Synthesis of Novel Inhibitors of Influenza Virus Neuraminidase . . . . . . . . 259
4.1.1. Relenza . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
4.1.2. Tamiflu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
4.1.3. Other Inhibitors of Influenza Virus Neuraminidase . . . . . . . . . . . . . . . . . . . . . . 262
4.2. Drug Resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
5. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
18. Interaction of HIV-1 Nef with Human CD4 and Lck
Dieter Willbold
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
2. Interaction of Nef with Human CD4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
2.1. The CD4 Receptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
2.2. CD4 and HIV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
2.3. Three-Dimensional Structures of CD4 Cytoplasmic Domain and HIV-1 Nef . . . . . . . . 272
2.4. Nef Residues that are Important for CD4 Binding Map to the “Core Domain” . . . . . . . 272
2.5. Amino-Terminal Residues of Nef are also Important for CD4 Binding . . . . . . . . . . . . . 273
2.6. Leucines 413 and 414 of CD4 are Essential for Nef Binding . . . . . . . . . . . . . . . . . . . . 274
2.7. High Affinity Between CD4(403–433) and Full-Length Nef can be
Confirmed by NMR Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
2.8. The Presence of a Helix in Human CD4 Cytoplasmic Domain Promotes
Binding to HIV-1 Nef Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
2.9. Summary of the CD4–Nef Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
3. Interaction of Nef with Human Lck . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
3.1. Lymphocyte Specific Kinase Lck . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
xii Contents
3.2. X-ray Structures of Nef–SH3 Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
3.3. NMR Spectroscopy is a Suitable Tool to Map Nef–Lck Interaction Sites . . . . . . . . . . . 279
3.4. The Unique Domain of Lck is Not Involved in Nef Binding . . . . . . . . . . . . . . . . . . . . 280
3.5. Mapping of the Nef Interaction Site on Lck SH3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
3.6. Summary of the Lck–Nef Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
List of Contributors
Michael J. Adams, Plant Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts AL5
2JQ, UK.
John F. Antoniw, Plant Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts AL5
2JQ, UK.
Isaiah T. Arkin, The Alexander Silberman Institute of Life Science, Department of Biological
Chemistry, The Hebrew University, Givat-Ram, Jerusalem, 91904, Israel.
Burkhard Bechinger, Université Louis Pasteur, Faculté de chimie, ILB, 4 rue Blaise Pascal, 67070
Strasbourg, France.
S. Bour, Bioinformatics and Cyber Technology Center, Office of Technology and Information Systems,
National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Center Drive,
Bethesda, MD, USA.
Luis Carrasco, Centro de Biología Molecular Severo Ochoa, Facultad de Ciencias, Universidad
Autónoma, Cantoblanco, 28049 Madrid, Spain.
K. Cross, National Research for Medical Research, Mill Hill, London NW7 1AA, UK.
Gary Ewart, Division of Molecular Bioscience, John Curtin School of Medical Research, Australian
National University, Canberra, Australia.
D. Fischer, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks
Road, Oxford OX1 3QU, UK.
W.B. Fischer, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South
Parks Road, Oxford OX1 3QU, UK, and Bionanotechnology Interdisciplinary Research Consortium,
Clarendon Laboratory, Department of Physics, Oxford University, Parks Road, Oxford OX1 3SU, UK.
F. Fraternali, National Research for Medical Research, Mill Hill, London NW7 1AA, UK.
Peter W. Gage, Division of Molecular Bioscience, John Curtin School of Medical Research, Australian
National University, Canberra, Australia.
Thomas M. Gallagher, Department of Microbiology and Immunology, Loyola University Medical
Center, Maywood, IL, USA.
Elspeth Garman, Laboratory of Molecular Biophysics, Department of Biochemistry, University of
Oxford, South Parks Road, Oxford OX1 3QU, UK.
María Eugenia González, Unidad de Expresión Viral, Centro Nacional de Microbiologia, Instituto de
Salud Carlos III, Carretera de Majadahonda-Pozuelo, Km 2, Majadahonda 28220, Madrid, Spain.
Peter Henklein, Humboldt Universität, Institut für Biochemie, Hessische Str 3-4, 10115 Berlin,
Germany.
D. Jones, Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
Itamar Kass, The Alexander Silberman Institute of Life Science, Department of Biological Chemistry,
The Hebrew University, Givat-Ram, Jerusalem 91904, Israel.
C.G. Kim, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks
Road, Oxford OX1 3QU, UK.
Jared Knopman, Department of Neurobiology and Physiology, Northwestern University, Evanston, IL,
USA.
Y.H. Lam, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks
Road, Oxford OX1 3QU, UK.
xiii
Robert A. Lamb, Department of Biochemistry, Molecular Biology and Cell Biology, and Howard
Hughes Medical Institute, Northwestern University, Evanston, IL, USA.
Graeme Laver, Barton Highway, Murrumbateman, NSW 2582, Australia.
S. Lee, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman
Drive, La Jolla, CA, USA.
V. Lemaitre, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South
Parks Road, Oxford OX1 3QU, UK, and Nestec S.A., BioAnalytical Science Department, Vers-
Chez-Les-Blanc, CH-1000 Lausanne 26, Switzerland.
Tse-I Lin, Tibotec BVDV, Gen. De. Wittelaan 11B-3, B-2800 Mechelen, Belgium.
V. Madan, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Facultad de Ciencias,
Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
F.M. Marassi, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA, USA.
Julian Melton, Division of Molecular Bioscience, John Curtin School of Medical Research, Australian
National University, Canberra, Australia.
M. Mesleh, Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
M. Montal, Section of Neurobiology Division of Biology, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
Anna Moroni, Dipartimento di Biologia and CNR—IBF, Unità di Milano; Istituto Nazionale di Fisica
della Materia, Unità di Milano-Università, Milano, Italy.
A. Mrse, Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
A. Nevzorov, Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
J.L. Nieva, Unidad de Biofísica (CSIC-UPV/EHU), Departamento de Bioquímica, Universidad del País
Vasco, Aptdo. 644, 48080 Bilbao, Spain.
M. Oblatt-Montal, Section of Neurobiology Division of Biology, University of California, San Diego,
9500 Gilman Drive, La Jolla, CA, USA.
S.J. Opella, Department of Chemistry and Biochemistry, University of California, San Diego, 9500
Gilman Drive, La Jolla, CA, USA.
S. Park, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman
Drive, La Jolla, CA, USA.
Sergio G. Peisajovich, Department of Biological Chemistry, Weizmann Institute of Science, Rehovot
76100, Israel.
Lawrence H. Pinto, Department of Neurobiology and Physiology, Northwestern University, Evanston,
IL, USA.
Anita Premkumar, Division of Molecular Bioscience, John Curtin School of Medical Research,
Australian National University, Canberra, Australia.
M.A. Sanz, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Facultad de Ciencias,
Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
Cornelia Schroeder, Abteilung Virologie, Institut für Mikrobiologie und Hygiene, Universitätskliniken
Homburg/Saar, Germany.
Ulrich Schubert, Institute for Clinical and Molecular Virology, University of Erlangen-Nürnberg,
Schlossgarten 4, D-91054 Erlangen, Germany.
Yechiel Shai, Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100,
Israel.
J.J. Skehel, National Research for Medical Research, Mill Hill, London NW7 1AA, UK.
K. Strebel, Bioinformatics Core Facility, Laboratory of Molecular Microbiology, National Institute of
Allergy and Infectious Diseases, National Institutes of Health, 4 Center Drive, Bethesda, MD, USA.
Yajun Tang, Department of Neurobiology and Physiology, Northwestern University, Evanston,
IL, USA.
xiv List of Contributors
Gerhard Thiel, Institute for Botany, University of Technology, Darmstadt, Germany.
Edward B. Thorp, Department of Microbiology and Immunology, Loyola University Medical Center,
Maywood, IL, USA.
L. Vaccaro, National Research for Medical Research, Mill Hill, London NW7 1AA, UK.
James Van Etten, Department of Plant Pathology, Nebraska Center for Virology, University of
Nebraska, Lincoln, NE, USA.
Padmavati Venkataraman, Department of Neurobiology and Physiology, Northwestern University,
Evanston, IL, USA.
Gregory A. Voth, Department of Chemistry and Henry Eyring Center for Theoretical Chemistry,
University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, UT, USA.
A. Watts, Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks
Road, Oxford OX1 3QU, UK.
S.A. Wharton, National Research for Medical Research, Mill Hill, London NW7 1AA, UK.
Dieter Willbold, Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf,
Germany und Forschungszentrum Jülich, IBI-2, 52425 Jülich, Germany.
Victor Wray, Department of Structural Biology, German Research Centre for Biotechnology,
Mascheroder Weg 1, D-38124 Braunschweig, Germany.
Yujie Wu, Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of
Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, UT, USA.
List of Contributors xv
Preface
Viruses enter cells and modulate the biosynthetic machinery of the host for the synthesis of
their own building blocks. These building blocks assemble in an organized fashion and large
numbers of viral copies finally leave the host, ready to enter the next host cell. This life style
would be of little concern if it were not that many viruses have a fatal side effect to the host,
leading to the death of the host cell and sometimes to the death of the whole organism. Under
these circumstances, the first two sentences could be rewritten and the words “enter” and
“leave” replaced by more drastic words such as “attack,” “invade,” or “kill.” However, not all
the attacks lead to an immediate cell death or to a phenotypic manifestation in the organism.
Viruses are under constant survival pressure and have evolved mechanisms to resist
environmental pressure by having for example a high mutation rate. This may lead finally also
to an increased spreading to novel hosts, which can have a devastating effect on the invaded
organism, including humans, especially if the species barrier is crossed in an unpredicted way.
In the modern world, the large density of populations and travel habits can lead to a rapid spread
of the virus, with a possible major impact on our social behavior and the economy. The recent
appearance of the SARS virus or avian influenza viruses in humans represents such an imme-
diate threat. Once within a host, some viruses, such as HIV-1, replicate but rather than produce
faithful copies of the parent virus, constantly mutate making it almost impossible to produce a
vaccine and limiting the success of drug therapy. We are also directly or indirectly affected by
animal or plant viruses. The last foot and mouth outbreak within the United Kingdom and other
European countries resulted in the slaughter of large numbers of farm animals to prevent the
rapid spread of the disease. As an indirect effect, the country side, dependent to a very large
extent on tourism, had to be closed down to avoid any further spread of the disease. Plant viruses
threatening our annual harvest and can through price rises add to inflation. However, not all
viruses cause harm to us, some of the plant viruses may even cheer us up such as the tulip
mosaic virus that causes the striping pattern of tulip petals.
In this book, we aim to summarize the current knowledge on a special class of viral
molecules, the membrane proteins, from the full range of viruses, including plant viruses.
Research on these membrane proteins has been limited by a number of technical difficulties,
and rate of progress compared with globular proteins has been slow. Membrane proteins are
involved at the stage of viral entry into the host cell, in modulating subcellular electrochem-
ical gradients and/or shuffling proteins across cell membranes.
The first section is dedicated to viral membrane proteins from plant viruses with the
most recent computational research on the viral genome revealing the first experimental evi-
dence of a K
channel encoded by a plant virus. The second section in the book is dedicated
to the proteins involved in the early event of the life cycle of the viruses in the host cell, the
fusion proteins. The third section summarizes, in several chapters, the current state of the
research on ion channels and viroporins, which are known to modulate the electrochemical
balance in the virus itself and subcellular compartments in the host cell. The fourth section
xvii
describes membrane-bound and membrane-associated viral proteins. All chapters include
functional and structural data and address, where possible, the development of antiviral drugs.
A large number of techniques are described by the authors, revealing the way in which a wide
range of approaches are required to shed light on the molecular life of viruses.
I wish to thank the editorial team at Kluwer Academic Publishers for their enthusiasm
and physical support during the generation of this synthesis of our recent advances in viral
membrane protein research. Thanks go also to all the authors for their willingness and
patience while working on the book. My acknowledgment includes also Judy Armitage
(Oxford) and my colleagues in the lab for stimulating and helpful discussions.
xviii Preface
Part I
Membrane Proteins from Plant Viruses
1
Membrane Proteins in Plant Viruses
Michael J. Adams and John F. Antoniw
1. Introduction
The plant cell wall is a substantial barrier preventing direct entry of viruses and
therefore, unlike many animal viruses, plant viruses cannot initiate infection by any inde-
pendent ability to cross membranes. A few plant viruses enter through microscopic wounds
but most are introduced into their hosts by a vector, most frequently a leaf-feeding insect.
Small pores between adjacent cells (plasmodesmata) provide cytoplasmic continuity and
thus a channel for transport of nutrients and some larger molecules, and viruses exploit this
route for cell-to-cell transport. While some viruses remain restricted to a small area around
the initial site of infection and may be limited to certain cell types, many exhibit long distance
movement via the plant vascular system.
Among the plant viruses, cell-to-cell movement depends on one or more virus-encoded
movement proteins (MPs) and many of these are integral membrane proteins that interact with
the endoplasmic reticulum (ER). Many RNA viruses multiply within the cell cytoplasm and
there is recent evidence that replication proteins of such viruses are also targeted to membranes.
In addition, membrane proteins may play a role in plant virus transmission for those viruses
that enter the cells of their vectors. In this chapter, we survey the occurrence of membrane pro-
teins among all plant viruses and review the literature on their biological role. We also present
and discuss the limited structural information on plant virus integral membrane proteins.
2. Survey of Transmembrane Proteins in Plant Viruses
In preparation for this chapter, we have used a plant virus sequence database that we
developed to make a comprehensive survey of all published complete gene sequences of all
plant viruses.
2.1. The Database
The database used was developed from files originally prepared for the electronic
version of the Association of Applied Biologists (AAB) Descriptions of Plant Viruses
Michael J. Adams and John F. Antoniw • Plant Pathogen Interactions Division, Rothamsted Research,
Harpenden, United Kingdom.
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Viral Membrane Proteins: Structure, Function, and Drug Design, edited by Wolfgang Fischer.
Kluwer Academic / Plenum Publishers, New York, 2005.