Handbook of Cell Signaling, Three-Volume Set (Cell Biology)

02003·76.84 MB·English

by  Ralph A. Bradshaw, Edward A. Dennis

Handbook of
Cell Signaling
Volume 1
This Page Intentionally Left Blank
Handbook of
Cell Signaling
Volume 1
Editors-in-Chief
Ralph A. Bradshaw
Department of Physiology and Biophysics
University of California Irvine
Irvine, California
Edward A. Dennis
Department of Chemistry and Biochemistry
University of California San Diego
La Jolla, California
Amsterdam Boston Heidelberg London New York Oxford
Paris San Diego San Francisco Singapore Sydney Tokyo
This book is printed on acid-free paper. (cid:2)∞
Copyright ©2003, Elsevier Science (USA).
All Rights Reserved.
No part of this publication may be reproduced or transmitted in any form or by any
means, electronic or mechanical, including photocopy, recording, or any information
storage and retrieval system, without permission in writing from the publisher.
Permissions may be sought directly from Elsevier’s Science & Technology Rights
Department in Oxford, UK: phone: [phone], fax: [phone],
e-mail: [email protected]. You may also complete your request on-line
via the Elsevier Science homepage (http://elsevier.com), by selecting “Customer
Support” and then “Obtaining Permissions.”
Academic Press
An imprint of Elsevier Science
525 B Street, Suite 1900, San Diego, California 92101-4495, USA
http://www.academicpress.com
Academic Press
84 Theobald’s Road, London WC1X 8RR, UK
http://www.academicpress.com
Library of Congress Catalog Card Number: 2003103352
International Standard Book Number: 0-12-124546-2 (Set)
International Standard Book Number: 0-12-124547-0 (Volume 1)
International Standard Book Number: 0-12-124548-9 (Volume 2)
International Standard Book Number: 0-12-124549-7 (Volume 3)
PRINTED IN THE UNITED STATES OF AMERICA
03 04 05 06 07 7 6 5 4 3 2 1
Contents
VOLUME 1 Prospects
References
Contributors xlv CHAPTER 3
Preface lxvii Computational Genomics: Prediction
of Protein Functional Linkages
CHAPTER 1
and Networks 15
Cell Signaling: Yesterday, Today, and
Todd O. Yeates and Michael J. Thompson
Tomorrow 1
Introduction
Ralph A. Bradshaw and Edward A. Dennis
Approaches to Analyzing Protein Functions on a
Origins of Cell Signaling Genome-Wide Scale
Enter Polypeptide Growth Factors Current Issues and Future Prospects for Computing
Cell Signaling at the Molecular Level Functional Interactions
Lipid Signaling References
Cell Signaling Tomorrow
References
CHAPTER 4
Molecular Sociology 21
P I
ART Irene M. A. Nooren and Janet M. Thornton
INITIATION: EXTRACELLULAR Transmembrane Signaling Paradigms
AND MEMBRANE EVENTS Structural Basis of Protein–Protein Recognition
Conclusion
James Wells, Editor
References
Section A: Molecular Recognition
CHAPTER 5
Ian Wilson, Editor
Free Energy Landscapes in
Protein–Protein Interactions 27
CHAPTER 2
Jacob Piehler and Gideon Schreiber
Structural and Energetic Basis of
Introduction
Molecular Recognition 11
Thermodynamics of Protein–Protein Interactions
Emil Alexov and Barry Honig
Interaction Kinetics
Introduction The Transition State
Principles of Binding Association of a Protein Complex
Nonspecific Association with Membrane Dissociation of a Protein Complex
Surfaces Summary
Protein–Protein Interactions References
v
vi Contents
CHAPTER 6 CHAPTER 11
Antibody–Antigen Recognition and T-Cell Receptor/pMHC Complexes 63
Conformational Changes 33 Markus G. Rudolph and Ian A. Wilson
Robyn L. Stanfield and Ian A. Wilson
TCR Generation and Architecture
Introduction Peptide Binding to MHC Class I and II
Antibody Architecture TCR/pMHC Interaction
Conformational Changes Conclusions and Future Perspectives
Conclusion References
References
CHAPTER 12
CHAPTER 7 Mechanistic Features of Cell-Surface
Binding Energetics in Antigen– Adhesion Receptors 74
Antibody Interfaces 39 Steven C. Almo, Anne R. Bresnick, and Xuewu Zhang
Roy A. Mariuzza Mechanosensory Mechanisms
Cell–Cell Adhesions/Adherens Junctions
Introduction
T-Cell Costimulation
Thermodynamic Mapping of Antigen–
Axon Guidance and Neural Development
Antibody Interfaces
Conclusions
Conclusions
References
References
CHAPTER 8 CHAPTER 13
The Immunological Synapse 79
Immunoglobulin–Fc Receptor
Michael L. Dustin
Interactions 45
Brian J. Sutton, Rebecca L. Beavil, and Introduction
Andrew J. Beavil Migration and the Immunological Synapse
The Cytoskeleton and the Immunological Synapse
Introduction
The Role of Self MHCp in T-Cell Sensitivity to
IgG–Receptor Interactions
Foreign MHCp
IgE–Receptor Interactions
Integration of Adaptive and Innate Responses
Summary
Summary
References
References
CHAPTER 9 CHAPTER 14
Plasticity of Fc Recognition 51
NK Receptors 83
Warren L. DeLano
Roland K. Strong
Introduction
Introduction
Structures of the Natural Fc Binding Domains
Immunoreceptors
The Consensus Binding Site on Fc
Natural Killer Cells
Evolution of an Fc Binding Peptide
Ig-Type NK Receptors: KIR
Factors Promoting Plasticity
C-Type Lectin-Like NK Receptors: Ly49A
Conserved and Functionally Important
C-Type Lectin-Like NK Receptors: NKG2D
Molecular Interactions
References
Conclusion
References CHAPTER 15
Carbohydrate Recognition and Signaling 87
CHAPTER 10
James M. Rini and Hakon Leffler
Ig-Superfold and Its Variable Uses in
Introduction
Molecular Recognition 57
Biological Roles of Carbohydrate Recognition
Nathan R. Zaccai and E. Yvonne Jones
Carbohydrate Structure and Diversity
Introduction Lectins and Carbohydrate Recognition
The Immunoglobulin Superfamily Carbohydrate-Mediated Signaling
Ig-Superfold-Mediated Recognition Conclusions
References References
Contents vii
CHAPTER 16 Concluding Remarks
References
Rhinovirus–Receptor Interactions 95
Elizabeth Hewat CHAPTER 22
References Structures of Heterotrimeric G Proteins
and Their Complexes 127
CHAPTER 17
Stephen R. Sprang
HIV-1 Receptor Interactions 99
Introduction
Peter D. Kwong
GαSubunits
Molecular Interactions Ga-Effector Interactions
Atomic Details GTP Hydrolysis by Gαand Its Regulation by
Recognition in the Context of a Humoral RGS Proteins
Immune Response GβγDimers
References GPR/GoLoco Motifs
Gα-GPCR Interactions
CHAPTER 18 References
Influenza Virus Neuraminidase
Inhibitors 105 Section B: Vertical Receptors
Garry L. Taylor
Henry Bourne, Editor
Introduction
Flu Virus: Role of NA CHAPTER 23
Structure of NA
Structure and Function of G-Protein-
Active Site
Coupled Receptors: Lessons from the
Inhibitor Development
Crystal Structure of Rhodopsin 139
Conclusion
References Thomas P. Sakmar
Introduction
CHAPTER 19
Introduction to Rhodopsin: a Prototypical
Signal Transduction and Integral G-Protein-Coupled Receptor
Membrane Proteins 115 Molecular Structure of Rhodopsin
Geoffrey Chang and Christopher B. Roth Molecular Mechanism of Receptor Activation
References
Introduction
Electrophysiology: Rapid Signal Transduction CHAPTER 24
Mechanosensation: How Do We Feel?
Human Olfactory Receptors 145
Active Transporters: Rapid Response and
Orna Man, Tsviya Olender, and Doran Lancet
Energy Management
Receptors: Gate Keepers for Cell Signaling References
References
CHAPTER 25
CHAPTER 20 Chemokines and Chemokine Receptors:
Structural Basis of Signaling Events Structure and Function 149
Involving Fibrinogen and Fibrin 119 Carol J. Raport and Patrick W. Gray
Russell F. Doolittle Introduction
References Chemokine Structure and Function
Chemokine Receptors
CHAPTER 21 References
Structural Basis of Integrin Signaling 123
CHAPTER 26
Robert C. Liddington
The Binding Pocket of G-Protein-
Introduction Coupled Receptors for Biogenic
Structure
Amines, Retinal, and Other Ligands 155
Quaternary Changes
Lei Shi and Jonathan A. Javitch
Tertiary Changes
Tail Interactions Introduction
viii Contents
The Binding Pocket of GPCRs CHAPTER 31
A Role of the Second Extracellular Loop in
Agonist-Induced Desensitization
Ligand Binding
and Endocytosis of G-Protein-
References
Coupled Receptors 181
CHAPTER 27 Mark von Zastrow
Glycoprotein Hormone Receptors: A
Introduction
Unique Paradigm for Ligand Binding General Processes of GPCR Regulation
and GPCR Activation 161 Mechanisms of GPCR Desensitization
Gilbert Vassart, Marco Bonomi, Sylvie Claeysen, Cedric and Endocytosis
Govaerts, Su-Chin Ho, Leonardo Pardo, Guillaume Smits, Functional Consequences of GPCR Endocytosis
Virginie Vlaeminck, and Sabine Costagliola References
Introduction CHAPTER 32
Molecular Pathophysiology
Functional Role(s) of Dimeric
Structure Function Relationships of the Glycoprotein
Complexes Formed from G-Protein-
Hormone Receptors
Conclusions and Perspectives Coupled Receptors 187
References Marta Margeta-Mitrovic and Lily Yuh Jan
CHAPTER 28 References
Protease-Activated Receptors 167 CHAPTER 33
Shaun R. Coughlin
The Role of Chemokine Receptors in
Introduction HIV Infection of Host Cells 191
Mechanisms of Activation
Jacqueline D. Reeves and Robert W. Doms
Protease-Activated Receptor Family
Roles of PARs In Vivo Introduction
References HIV Entry
Coreceptor Use In Vivo
CHAPTER 29 Env Domains Involved in Coreceptor Interactions
Constitutive and Regulated Signaling in Coreceptor Domains Involved in HIV Infection
Receptor Presentation and Processing
Virus-Encoded 7TM Receptors 173
Role of Signaling in HIV Infection
Thue Schwartz
Summary
Virus-Encoded Proteins Are Developed through References
Targeted Evolution In Vivo
The Redundant Chemokine System Is an Optimal CHAPTER 34
Target for Viral Exploitation Chemotaxis Receptor in Bacteria:
Multiple Virus-Encoded 7TM Receptors Transmembrane Signaling, Sensitivity,
Constitutive Signaling through Altered Pathways
Adaptation, and Receptor Clustering 197
Viral Receptors Recognize Multiple Ligands with
Weiru Wang and Sung-Hou Kim
Variable Function
Attempts to Identify the Function of Virus-Encoded Signaling at Periplasmic Ligand Binding Domain
ReceptorsIn Vivo Signaling at the Cytoplasmic Domain
References Adaptation
Clustering of the Chemoreceptor and Sensitivity
CHAPTER 30 Future Studies
Frizzleds as G-Protein-Coupled Receptors References
for Wnt Ligands 177
CHAPTER 35
Sarah H. Louie, Craig C. Malbon, Randall T. Moon
Overview: Function and Three-
Introduction
Dimensional Structures of Ion Channels 203
Wnt Signaling
Daniel L. Minor, Jr.
Evidence for Frizzleds as G-Protein- Coupled
Receptors Introduction
Perspective Studies of Full-Length Ion Channels
References General Pore Features Revealed by Bacterial Channels
Contents ix
Pore Helices: Electrostatic Aids to Permeation CHAPTER 41
Open Channels
Regulation of Ion Channels by Direct
Eukaryotic Ion Channels at High Resolution:
Binding of Cyclic Nucleotides 233
Divide and Conquer
Edgar C. Young and Steven A. Siegelbaum
Ion Channel Accessory Subunits: Soluble
and Transmembrane Introduction
The Future: Ion Channels as Electrosomes The Cyclic Nucleotide-Gated Channels
References Other Channels Directly Regulated by
Cyclic Nucleotides
CHAPTER 36
References
How Do Voltage-Gated Channels Sense
the Membrane Potential? 209
Section C: Horizontal Receptors
Chris S. Gandhi and Ehud Y. Isacoff
Robert Stroud, Editor
Introduction
The Voltage-Sensing Gating Particle
S4 Is the Primary Voltage Sensor CHAPTER 42
Physical Models of Activation: Turning a Screw Overview of Cytokine Receptors 239
through a Bolt
Robert M. Stroud
Coupling Gating to S4 Voltage-Sensing Motions
References
CHAPTER 43
CHAPTER 37 Growth Hormone and IL-4 Families
Ion Permeation: Mechanisms of Ion of Hormones and Receptors: The
Selectivity and Block 215 Structural Basis for Receptor Activation
Bertil Hille and Regulation 241
Aqueous Pore Anthony A. Kossiakoff
Ion Selectivity
Introduction
Block
The Growth Hormone Family of Hormones
References
and Receptors
Structural Basis for Receptor Homodimerization
CHAPTER 38
Hormone Specificity and Cross-Reactivity Determine
Agonist Binding Domains of Glutamate Physiological Roles
Receptors: Structure and Function 219 Hormone-Receptor Binding Sites
Mark L. Mayer Receptor–Receptor Interactions
Hormone–Receptor Binding Energetics
References
Biological Implications of Transient
CHAPTER 39 Receptor Dimerization
A High-Affinity Variant of hGH (hGH ) Reveals an
Nicotinic Acetylcholine Receptors 223 v
Altered Mode for Receptor Homodimerization
Arthur Karlin Site1 and Site2 Are Structurally and
Function Functionally Coupled
Structure IL-4 Hormone-Induced Receptor Activation
References IL-4–α-Chain Receptor Interface
Binding of the γ-Chain Receptor
CHAPTER 40 Comparisons of IL-4 with GH(PRL)
Small Conductance Ca2+-Activated K+ Concluding Remarks
References
Channels: Mechanism of Ca2+ Gating 227
John P. Adelman
CHAPTER 44
Introduction Erythropoietin Receptor as a Paradigm
Clones Encoding SK Channels
for Cytokine Signaling 251
Biophysical and Pharmacological Profiles
Deborah J. Stauber, Minmin Yu, and Ian A. Wilson
Mechanisms of Ca2+-gating
Pantophobiac After All Introduction
References Biochemical Studies Supporting Preformed Dimers