handbook of cell signaling - dandelon.com
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Handbook of Cell SignalingSecond Edition
Volume 2
Editors-in-Chief
Ralph A. BradshawDepartment of Pharmaceutical Chemistry,
University of California, San Francisco,San Francisco, California
Edward A. DennisDepartment of Chemistry and Biochemistry,
University of California, San Diego,La Jolla, California
->*-*-"NCi ' -S i -
AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD • PARISSAN DIEGO • SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO
ELSEVIER Academic Press is an imprint of Elscvier
Contents
VOLUME 2
Contributors xxiPreface to the Second Edition xliiiPreface to the First Edition xlv
Part IITransmission: Effectors andCytosolic Events 385Tony Hunter
Section A - Protein Phosphorylation 391Tony Pawson
56. Eukaryotic Kinomes: Genomics andEvolution of Protein Kinases 393Gerard Manning and Tony Hunter
57. Modular Protein Interaction Domains inCellular Communication 399Tony Pawson and Piers Nash
58. Structures of Serine/Threonine andTyrosine Kinases 413Stevan R. Hubbard
59. Protein Tyrosine Kinase ReceptorSignaling Overview 419Carl-Henrik Heldin
60. Signaling by the Platelet-DerivedGrowth Factor Receptor Family 427Lars Ronnstrand
61. The Epidermal Growth Factor ReceptorFamily 435Wolfgang J. Kostler and Yosef Yarden
62. Mechanisms and Functions of EphReceptor Signaling 443Martin Lackmann
63. Cytokine Receptor Signaling 451Mojib Javadi Javed, Terri D. Richmond andDwayne L Barber
64. The Negative Regulation of JAK/STATsignaling 467James M. Murphy, Gillian M. Tannahill,Douglas J. Hilton and Christopher J. Greenhalgh
65. Protein Kinase InhibitorsAlexander Levitzki
481
66. Integrin Signaling: Cell Migration,Proliferation, and Survival 491J. Thomas Parsons, Jill K. Slack-Davis, Robert W.Tilghman, Marcin Iwanicki and Karen H. Martin
67. Downstream Signaling Pathways:Modular Interactions 501Bruce J. Mayer
68. Non-Receptor Tyrosine Kinases in T CellAntigen Receptor Function 507Susan E. Levin and Arthur Weiss
69. Receptor Tyrosine Kinase Signaling andUbiquitination 517Daniela Hoeller and Ivan Dikic
70. TGFp Signal Transduction 521Cristoforo Silvestri, Rohit Bose, Liliana Attisano andJeffrey L. Wrana
71. Mitogen-Activated Protein KinasesEric Ho and Jim Woodgett
533
72. Recognition of Phospho-Serine/Threonine Phosphorylated Proteins byPhospho-Serine/Threonine-BindingDomains 539Stephen J. Smerdon and Michael B. Yaffe
73. AMP-Activated Protein Kinase 551D. Grahame Hardie
74. Principles of Kinase Regulation 559Bostjan Kobe and Bruce E. Kemp
Contents
75. Calcium/Calmodulin-DependentProtein Kinase II 565Mary B. Kennedy
76. Glycogen Synthase Kinase 3 569Philip Cohen and Sheelagh Frame
77. The PIKK Family of ProteinKinases 575Graeme C. M. Smith and Stephen P. Jackson
78. Histidine Kinases in Two-ComponentSignaling Pathways 581Alia O. Kaserer and Ann H. West
79. The EF2K/MHCK/TRPM7 Family ofAtypical Protein Kinases 587Shari L. Wiseman, Fan-Yan Wei, andAngus C. Nairn
80. The Leucine-Rich Repeat ReceptorProtein Kinases of Arabidopsisthaliana - a Paradigm for Plant LRRReceptors 601John C. Walker and Kevin A. Lease
81. Engineering Protein Kinases withSpecificity for Unnatural Nucleotidesand Inhibitors 609Chao Zhang and Kevan M. Shokat
82. Clinical Applications of KinaseInhibitors in Solid Tumors 615William Pao and Nicolas Girard
83. Ubiquitin-mediated Regulationof Protein Kinases in NFK,B
Signaling 633Ming Xu and Zhijian J. Chen
84. Global Analysis of PhosphoregulatoryNetworks 645Janine Mok and Michael Snyder
Section B - Protein Dephosphorylation 657Nick Tonks
85. Phosphatase FamiliesDephosphorylating Serine andThreonine Residues in ProteinsPatricia T.W. Cohen
659
86. The Structure and Topology of ProteinSerine/Threonine Phosphatases 677David Barford
87. Naturally Occurring Inhibitors of ProteinSerine/Threonine Phosphatases 683Carol MacKintosh and Julie Diplexcito
88. Protein Phosphatase 1 BindingProteins 689Anna A. DePaoli-Roach
89. Protein Serine/Threonine PhosphataseInhibitors and Human Disease 699Shirish Shenolikar and Matthew H. Brush
90. Calcineurin 705Claude B. Klee and Seun-Ah Yang
91. Protein Serine/Threonine-Phosphatase2C (PP2C) 711His'ashi Tatebe and Kazuhiro Shiozaki
92. Approaches to the Identificationof Protein Tyrosine PhosphataseSubstrates 717Anton M. Bennett and Tony Tiganis
93. Inhibitors of Protein TyrosinePhosphatases 727Zhong-Yin Zhang
94. Regulating Receptor PTP Activity 737Aurnab Ghose and David Van Vactor
95. CD45 743Michelle L. Hermiston, Vikas Gupta andArthur Weiss
96. Cell-Cycle Functions and Regulation ofCdc14 Phosphatases 749Harry Charbonneau
97. MAP Kinase Phosphatases 755Stephen M. Keyse
98. SH2 Domain-Containing Protein-Tyrosine Phosphatases 771Benjamin G. Neel, Gordon Chan, andSalim Dhanji
Contents
99. Insulin Receptor PTP: PTP1B 811Sofi G. Julien and Michel L. Tremblay
100. STYX/Dead Phosphatases 817Matthew J. Wishart
101. Zebrafish and PhosphataseFunction 827Jeroen den Hertog and Mark van Eekelen
102. Eyes Absent Protein TyrosinePhosphatases: A New EukaryoticBranch of the Haloacid DehalogenaseSuperfamily 835Carolyn N. Wrobel and llaria Rebay
103. PHLPP: PH Domain Leucine-RichRepeat Protein Phosphatase 843Alexandra C. Newton
104. PTEN 849Lloyd C. Trotman
105. PTP Oxidation 855Ming-Fo Hsu, Yi-Wei Lou, Yi-Yun Chen andTzu-Ching Meng
106. Chronophin and Slingshot CofilinPhosphatases in CytoskeletalRegulation 863Celine DerMardirossian, Timothy Y. Huang andGary M. Bokoch
107. Large Scale Structural Analysis ofProtein Tyrosine Phosphatases 871AlastairJ. Barr and Stefan Knapp
108. Protein Phosphatases and CircadianClocks 877Yanshan Fang and Amita Sehgal
Section C - Calcium Signal Transduction 883Martin D. Bootman
109. Calcium Signalling; Messengers,Transport Pathways, Sensors, andPhysiological Outcomes 885Martin D. Bootman andH. Llewelyn Roderick
110. Phospholipase C 887Hong-Jun Liao and Graham Carpenter
111. Cyclic ADP-ribose and NAADP 893Antony Galione and Grant C. Churchill
112. Voltage-Gated Calcium Channels 897William A. Catterall
113. Store-Operated Calcium Channels 911James W. Putney
114. Arachidonic Acid-Regulated Ca2+
Channel 915Trevor J. Shuttleworth
115. IP3 Receptors 921Colin W. Taylor and Zhao Ding
116. Ryanodine Receptors 927David H. MacLennan and S. R. Wayne Chen
117. Intracellular Calcium Signaling 937Dagmar Harzheim, H. Llewelyn Roderick andMartin D. Bootman
118. Calcium Pumps 943Ernesto Carafoli, Laura Fedrizzi,Teuta Domi, Francesca Di Leva andMarisa Brini
119. Sodium/Calcium Exchange 949Mordecai P. Blaustein
120. Ca2+ Buffers 955Beat Schwaller
121. Mitochondria as Organizers of theCellular Ca2+ Signaling Network 963Gydrgy Szabadkai and Michael R. Duchen
122. EF-Hand Proteins and CalciumSensing: The Neuronal CalciumSensor Proteins 973tee P. Haynes and Robert D. Burgoyne
123. Calmodulin-Mediated Signaling 979Anthony R. Means
124. The Family of S100 Cell SignalingProteins 983Claus W. Heizmann and Gunter Fritz
Contents
125. Annexins and Calcium Signaling 995Stephen E. Moss
126. Calpain 999Alan Wells and Ludovic Leloup
127. Calcium Signaling in SmoothMuscle 1009Susan Wray
128. Calcium Signaling in CardiacMuscle 1027K.M. Dibb, A.W. Traffordand D.A. Eisner
Section D - Lipid-Derived SecondMessengers 1031Lewis Cantley
129. Historical Overview: ProteinKinase C, Phorbol Ester and LipidMediators 1033Yasutomi Nishizuka and Ushio Kikkawa
130. Type I Phosphatidylinositol4-Phosphate 5-Kinases (PHP5-kinases) 1037K.A. Hinchliffe and R.F. Irvine
131. Type II PIP4-kinases 1043Lucia Rameh
132. Phosphoinositide 3-Kinases 1049David A. Fruman
133. PTEN/MTM PhosphatidylinositolPhosphatases 1061Knut Martin Torgersen, Soo-A Kim andJack E. Dixon
134. The Src Homology 2 ContainingInositol 5' Phosphatases 1065Frann Antignano, Jens Ruschmann,Melisa Hamilton, Victor Ho, Vivian Lam,Etsushi Kuroda, Laura M. Sly and Gerald Krystal
135. Structural Principles of Lipid SecondMessenger Recognition 1085Roger L. Williams
136. Pleckstrin Homology (PH)Domains 1093Mark A. Lemmon
137. PX Domains 1103Christian D. Ellson and Michael B. Yaffe
138. FYVE Domains in Membrane Traffickingand Cell Signaling 1111Christopher Stefan, Anjon Audhya andScott D. Emr
139. Protein Kinase C: Relaying Signalsfrom Lipid Hydrolysis to ProteinPhosphorylation 1123Alexandra C. Newton
140. Modulation of Monomeric G Proteinsby Phosphoinositides 1131Sonja Vermeren, Len Stephens andPhillip T. Hawkins
141. Phosphoinositides and ActinCytoskeletal Rearrangement 1141Paul A. Janmey, Robert Bucki and Helen L. Yin
142. Phosphatidylinositol TransferProteins 1151Shamshad Cockcroft
143. Inositol Pentakisphosphate: A SignalTransduction Hub 1159Stephen B. Shears
144. Phospholipase D 1167Wenjuan Su and Michael A. Frohman
145. Diacylglycerol Kinases 1177Matthew K. Topham and Steve M. Prescott
146. Sphingosine-1-Phosphate Receptors:An Update 1183Michael Maceyka and Sarah Spiegel
147. Lysophosphatidic Acid andSphingosine-1 -Phosphate Activation ofG-Protein-Coupled Receptors 1191Tetsuji Mutoh and Jerold Chun
148. The Role of Ceramide in CellRegulation 1201Leah J. Siskind, Thomas D. Mullen andLina M. Obeid
Contents IX
149. Role of Phospholipase A2 Forms inArachidonicAcid Mobilization andEicosanoid Generation 1213Jesus Balsinde and Edward A. Dennis
150. Prostaglandin Mediators 1219Emer M. Smyth and Garret A. FitzGerald
151. Leukotriene Mediators 1229JesperZ. Haeggstrom and Anders Wetterholm
152. Lipoxins and Aspirin-Triggered15-epi-Lipoxins: Pro-ResolvingMediators in Anti-Inflammationand Resolution 1235Charles N. Serhan
Section E - Protein ProximityInteractions 1243John D. Scott
153. Protein Proximity InteractionsMatthew G. Gold and John D. Scott
1245
154. Rapid Characterization of in vivoPhosphorylation Sites and the ProteinKinases and Phosphatases that Regulatethem by Affinity Capture 1247TimothyA.J. Haystead
155. FRET Analysis of Signaling Events inCells 1253Peter J. Verveer and Philippe I.H. Bastiaens
156. The Focal Adhesion: A Network ofMolecular Interactions 1259Jianxin A. Yu, Nicholas O. Deakin andChristopher E. Turner
157. WASP and WAVE Family ProteinComplexes 1265Frank M. Mason and Scott H. Soderling
158. Synaptic NMDA-Receptor SignalingComplex 1271Mary B. Kennedy
159. Toll Family Receptors 12 77Yann Hyvert and Jean-Luc Imler
160. Signaling and the ImmunologicalSynapse 1283Emanuele Giurisato and Andrey S. Shaw
161. The Ubiquitin-ProteasomeSystem 1293Mark Hochstrasser
162. Caspases: Cell Signaling byProteolysis 1297Guy S. Salvesen
163. MAP Kinase in Yeast 1303Rupam Sahoo, Amjad Husain, and Elaine A. Elion
164. Mammalian MAP Kinases 1315Norman J. Kennedy and Roger J. Davis
165. Subcellular Targeting of PKA throughAKAPs: Conserved Anchoring andUnique Targeting Domains 1329
• Mathew D. Pink and Mark L. Dell'Acqua
166. AKAP Transduction Units: Contextdependent Assembly of SignalingComplexes 1337John D. Scott and Lorene K. Langeberg
167. Dendritic Protein PhosphataseComplexes 1343Anthony J. Baucum II and Roger J. Colbran
168. Protein Phosphatase 2A 1353Adam M. Silverstein, Anthony J. Davis,Vincent A. Bielinski, Edward D. Esplin,Nadir A. Mahmood and Marc C. Mumby
169. 14-3-3 Proteins 1367Hubert Hondermarck
170. Protein Interaction DataResources 1375Ian M. Donaldson
Section F - Cyclic Nucleotides 1387Jackie D. Corbin
171. Adenylyl Cyclases 13 89Adam J. Kuszak and Roger K. Sunahara
Contents
172. Guanylyl CyclasesLincoln R. Potter
1399
173. Phosphodiesterase FamiliesJames Surapisitchat andJoseph A. Beavo
1409
174. The cAMP-SpecificPhosphodiesterases: A Class ofDiverse Enzymes that Define theProperties and Localization ofcAMP Signals 1415James L. Weeks II and Marco Conti
175. cAMP/cGMP Dual-SpecificityPhosphodiesterases 1425Lena Stenson, Eva Degerman andVincent C. Manganiello
176. Phosphodiesterase-5 1439Sharron H. Francis and Jackie D. Corbin
X77. Function and Regulation ofPhotoreceptor Phosphodiesterase(PDE6) in the Visual SignalingPathway 1445Rick H. Cote and Karyn B. Cahill
178. Regulation of Cyclic Nucleotide Levelsby Sequestration 1453Jackie D. Corbin, Jun Kotera,Venkatesh K. Gopal, Gary Z. Morris,Rick H. Cote and Sharron H. Francis
179. cAMP-Dependent Protein Kinase 1461Susan S. Taylor and Elzbieta Radzio-Andzelm
180. Cyclic GMP-Dependent ProteinKinase: Targeting and Control ofExpression 1471Thomas M. Lincoln, Hassan Sellak,Nupur Dey, Chung-Sik Choi, andFelricia Brown
181. Inhibitors of Cyclic AMP- and CyclicGMP-Dependent Protein Kinases 1479Wolfgang R. Dostmann and Christian K. Nickl
182. Substrates of Cyclic Nucleotide-Dependent Protein Kinases 1489Ne/7 F. W. Saunders, Ross I. Brinkworth,Bruce E. Kemp and Bostjan Kobe
183. Physiological Substrates of PKA andPKG 1497Anja Ruppelt, Nikolaus G. Oberprieler,George Magklaras and Kjetil Tasken
184. Effects of cGMP-Dependent ProteinKinase Knockouts 1515Franz Hofmann and Thomas Kleppisch
185. Cyclic Nucleotide-Regulated CationChannels 1519Martin Biel
186. Epac, cAMP-Regulated GuanineNucleotide Exchange Factors for Rap1and Rap2 1525Holger Rehmann, Johan de Rooij andJohannes L. Bos
187. Cyclic Nucleotide-Binding GAFDomains in Phosphodiesterases andAdenylyl Cyclases 1 531Sergio E. Martinez, Clemens C. Heikaus andJoseph A. Beavo
188. Use of Chimeric Adenylyl Cyclasesto Study Cyclic NucleotideSignaling 1537Jiirgen LJ. Linder and Joachim E. Schultz
189. Cyclic Nucleotide Signaling in theKinetoplastids 1543Stefan Kunz, Mihaela Minca,Edith Luginbiihl, Patrick Bregy andThomas Seebeck
190. Cyclic Nucleotide Specificity andCross-Activation of Cyclic NucleotideReceptors 1549John B. Shabb
191. Cyclic Nucleotide Analogs as Toolsto Investigate Cyclic NucleotideSignaling 1555Anne Elisabeth Christensen, Kristin Viste andStein Ove Doskeland
Contents XI
192. cGMP and PKG Signaling inPlatelets 1563Stepan Gambaryan and Ulrich Walter
193. Use of siRNA and AntisenseKnockdown to Study the RegulationofPKAbyPKI 1569Edward M. Greenfield and Xin Chen
194. Cyclic Nucleotide Signaling in theCentral Nervous System 1573Diego A. Golombek and Patricia V. Agostino
195. Compartmentation of cAMP incardiomyocytes 1581Gregoire Vandecasteele and RodolpheFischmeister
196. Phosphodiesterase-9A: cGMP-SpecificEnzyme 1589Jun Kotera, Takashi, Sasaki, and Kenji Omori
Section G - G Proteins 1595Heidi E. Hamm
197. Signal Transduction by G Proteins: BasicPrinciples, Molecular Diversity, andStructural Basis of Their Actions 1597Lutz Birnbaumer
198. Heterotrimeric G-Protein Signaling atAtomic Resolution 1615David G. Lambright
199. In Vivo Functions of HeterotrimericG Proteins 1621Stefan Offermanns
200. Regulation of G Proteins by CovalentModification 1629Benjamin C. Jennings and Maurine E. Linder
201. G-Protein-coupled Receptors, SignalFidelity, and Cell Transformation 1635Todd R. Palmby, Hans Rosenfeldt, andJ. Silvio Gutkind
202. Signaling through Gz 1 649Michelle E. Kimple, Rainbo C. Hultman andPatrick J. Casey
203. Effectors of C a o 1655Yana Zorina, Ravi lyengar, andKenneth D. Bromberg
204. Mono-ADP-ribosylation ofHeterotrimeric G Proteins 1665Maria Di Girolamo and Daniela Corda
205. Specificity of G Protein (3^ DimerSignaling 1673Carl A. Hansen, William F. Schwindinger andJanet D. Robishaw
206. The Superfamily of "Regulator ofG-protein Signaling" (RGS)Proteins 1683Melinda D. Willard, Francis S. Willard andDavid P. Siderovski
207. G-Protein Signaling inChemotaxis 1705Jonathan Franca-Koh, Stacey Sedore Willard andPeter N. Devreotes
208. Reversible Palmitoylation in G ProteinSignaling 1713Philip B. Wedegaertner
209. G Proteins in GustatoryTransduction 1721Bedrich Mosinger, Sami Damak andRobert F. Margolskee
210. Regulation of Synaptic Fusion byHeterotrimeric G Proteins 1727Simon Alford, Edaeni Hamid, Trillium Blackmer, andTatyana Gerachshenko
211. G-protein Regulation of ChannelsOfer Wiser and Lily Yeh Jan
1735
212. Ras and CancerFrank McCormick
1741
213. The Influence of Intracellular Locationon Function of Ras Proteins 1 745Jodi McKay and Janice E. Buss
214. Role of R-Ras in Cell Growth 1 753Gretchen A. Repasky, Adrienne D. Cox, Ariella B.Hanker, Natalia Mitin and ChanningJ. Der
Contents
215. The Ran GTPase: Cellular Roles andRegulation 1763Mary Dasso
216. Regulation of NADPH Oxidases by RacGTPase 1773Gary M. Bokoch, Davide Gianni, Jun-Sub Kim andYu-Ya Kao
217. The Role of Rac and Rho in Cell CycleProgression 1781Laura J. Taylor and Dafna Bar-Sagi
218. Cdc42 and its Cellular Functions 1785Qiyu Feng and Richard A. Cerione
219. Tissue Transglutaminase: A UniqueGTP-binding/GTPase 1795Marc Antonyak and Richard A. Cerione
220. Roles for ADP-Ribosylation Factors inMembrane Traffic 1803Amanda Caster and Richard A. Kahn
221. Yeast Small G Protein Function:Molecular Basis of Cell Polarity inYeast 1813Keith C. Kozminski and Hay-Oak Park
222. Farnesyltransferase Inhibitors 1819James J. Fiordalisi and Adrienne D. Cox
223. Structure of Rho Family Targets 1827Helen R. Mott and Darerca Owen
224. Structural Features of RhoGEFs 1843Jason T. Snyder, Kent L. Rossman, David K.Worthylake, and John Sondek
225. Structural Considerations of SmallGTP-Binding Proteins 1849Alfred Wittinghofer
226. Mx Proteins: High MolecularWeight GTPases with AntiviralActivity 1855Georg Kochs and Otto Haller
Section H - Developmental Signaling 1865Geraldine Weinmaster
227. Interactions between Wnt/|3-catenin/Fgf and Chemokine Signaling inLateral Line Morphogenesis 1867Tatjana Piotrowski
228. Wnt Signaling in Development 1873Stefan Rudloff,Daniel Messerschmidt andRolfKemler
229. Hedgehog Signaling in Developmentand Disease 1879Frederic de Sauvage
230. Regulation of VertebrateLeft-Right Axis Developmentby Calcium 1885Adam D. Langenbacher andJa'u-Nian Chen
231. LIN-12/Notch Signaling:Induction, Lateral Specificationand Interaction with the EGF/RasPathway 1891Sophie Jarriault
232. Proteolytic Activation ofNotch Signaling: Roles forLigand Endocytosis andMechanotransduction 1897James T. Nichols andGerry Weinmaster
233. BMPs in Development 1905Kelsey N. Retting and Karen M. Lyons
234. Neurotrophin Signaling inDevelopment 1913Katrin Deinhardt andMoses V. Chao
235. Mechanisms UnderlyingContext-Dependent VEGFSignaling for Distinct BiologicalResponses 1919M. Luisa Iruela-Arispe andSunyoungLee
Contents XIII
236. Vascular Endothelial Growth Factorsand Receptors: Signaling in VascularDevelopment 1927Anna Dimberg, Charlotte Rolny,Laurens A. van Meeteren, andLena Claesson-Welsh
237. Signaling from Fibroblast GrowthFactor Receptors in Development andDisease 1939Kristine A. Drafahl,Christopher W. McAndrew, andDaniel J. Donoghue
238. The Role of Receptor ProteinTyrosine Phosphatases in AxonalPathfinding 1949Andrew W. Stoker
239. Attractive and Repulsive Signaling inNerve Growth Cone Navigation 1955Guo-li Ming, and Mu-ming Poo
240. Semaphorins and their Receptors inVertebrates and Invertebrates 1961Eric F. Schmidt, Hideaki Togashi, andStephen M. Strittmatter
241. Signaling Pathways that RegulateCell Fate in the EmbryonicSpinal Cord 1967Matthew T. Pankratz and Samuel L. Pfaff
242. Cadherin Regulation of AdhesiveInteractions 1975Barbara Ranscht
243. Integration of BMP, RTK andWnt Signaling through SmadiPhosphorylations 1989Luis C. Fuentealba, Edward Eivers,Hojoon X. Lee and E. M. De Robertis
VOLUME 1
Contributors xxiPreface to the Second Edition xliiiPreface to the First Edition xlv
1. Cell Signaling: Yesterday, Today, andTomorrow 1Ralph A. Bradshaw and Edward A. Dennis
PartiInitiation: Extracellular andMembrane Events 5James A. Wells
Section A - Molecular Recognition 9Ian Wilson
2. Structural and Energetic Basis ofMolecular Recognition 11Emil Alexov and Barry Honig
3. Free Energy Landscapes in Protein-Protein Interactions 15Jacob Piehler and Gideon Schreiber
4. Molecular Sociology 23Irene M. A. Nooren and Janet M. Thornton
5. Antibody-Antigen Recognition andConformational Changes 29Robyn L. Stanfield, and Ian A. Wilson
6. Binding Energetics in Antigen-AntibodyInterfaces 37Roy A. Mariuzza
7. Immunoglobulin-Fc ReceptorInteractions 41Jenny M. Woof
8. Ig-Superfold and its Variable Uses inMolecular Recognition 49Nathan R. Zaccai and E. Yvonne Jones
9. T Cell Receptor/pMHC Complexes 55Markus G. Rudolph, Robyn L. Stanfield, andIan A. Wilson
10. Mechanistic Features of Cell-SurfaceAdhesion Receptors 63Steven C. Almo, Anne R. Bresnick, andXuewu Zhang
11. The Immunological Synapse 71Michael L. Dustin
12. NK Receptors 77Roland K. Strong
13. Carbohydrate Recognition andSignaling 85James M. Rini and Hakon Leffler
Contents
14. Rhinovirus-Receptor Interactions 93Elizabeth A. Hewat
15. HIV-1-Receptor Interactions 97Peter D. Kwong
16. Influenza Virus NeuraminidaseInhibitors 103Garry Taylor and Rupert Russell
17. Structural Basis of Signaling EventsInvolving Fibrinogen and Fibrin 111Russell F. Doolittle
18. Structural Basis of IntegrinSignaling 115Robert C. Liddington
19. Structures of Heterotrimeric G Proteinsand their Complexes 119Stephen R. Sprang
20. G Protein-Coupled ReceptorStructures 129Veli-Pekka Jaakola and Raymond C. Stevens
21. Toll-Like Receptors-Structure andSignaling 139Istvan Botos and David R. Davies
22. Variable Lymphocyte Receptors 145Brantley R. Herrin and Max D. Cooper
Section B - Multi-pass Receptors 149James A. Wells
23. Structure and Function of G-Protein-Coupled Receptors: Lessons fromRecent Crystal Structures 151Thomas P. Sakmar
24. Chemokines and Chemokine Receptors:Structure and Function 157Carol J. Raport and Patrick W. Gray
25. The (32 Adrenergic Receptor as a Modelfor G-Protein-Coupled ReceptorStructure and Activation by DiffusibleHormones 163Daniel M. Rosenbaum, S0ren G. F. Rasmussen andBrian K. Kobilka
26. Protease-Activated ReceptorsShaun R. Coughlin
171
27. Agonist-Induced Desensitization andEndocytosis of G-Protein-CoupledReceptors 177Michael Tanowitz and Mark von Zastrow
28. Functional Role(s) of DimericComplexes Formed from G-ProteinCoupled-Receptors 185Raphael Rozenfeld and Lakshmi A Devi
29. Chemotaxis Receptors in Bacteria:Transmembrane Signaling, Sensitivity,Adaptation and Receptor Clustering 195Weiru Wang and Sung-Hou Kim
30. An Overview of Ion ChannelStructure 201Daniel L. Minor
31. Molecular Mechanism of Store-Operated Ca2+ Signaling and CRACChannel Activation Mediated bySTIM & Orai 209Aubin Penna, Shenyuan L. Zhang,Andy V. Yeromin, and Michael D. Cahalan
32. Ion Permeation: Mechanisms of IonSelectivity and Block 217Bertil Hille
33. Nicotinic Acetylcholine Receptors 221Arthur Karlin
34. Ion Channels Regulated by DirectBinding of Cyclic Nucleotides 225Edgar C. Young
Section C - Horizontal Receptors 233Robert M. Stroud
35. Overview of Cytokine ReceptorsRobert M. Stroud
235
36. Growth Hormone and ProlactinFamily of Hormones and Receptors:The Structural Basis for ReceptorActivation and Regulation 237Anthony A. Kossiakoff and Charles V. Clevenger
Contents xv
37. Erythropoietin Receptor as a Paradigmfor Cytokine Signaling 245Deborah J. Stauber, Minmin Yu, and Ian A. Wilson
38. The Fibroblast Growth Factor (FGF)Signaling Complex 253Wallace L. McKeehan, Fen Wang and Yongde Luo
39. Structure of IFIShf and itsReceptors 261Mark R. Walter
40. Structure and Function of TumorNecrosis Factor (TNF) at the CellSurface 265Hao Wu and Sarah G. Hymowitz
41. The Mechanism of NGF SignalingSuggested by the p75 and TrkAReceptor Complexes 277J. Fernando Bazan and Christian Wiesmann
42. The Mechanism of VEGFR ActivationbyVEGF 287Christian Wiesmann
43. Receptor-Ligand Recognition in theTGF(3 Superfamily as Suggested byCrystal Structures of their EctodomainComplexes 293Matthias K. Dreyer
44. Insulin Receptor Complex and Signalingby Insulin 301Lindsay G. Sparrow and S. Lance Macaulay
45. Structure and Mechanism of the InsulinReceptor Tyrosine Kinase 307Stevan R. Hubbard
46. IL-21 Increased Potency Design 315Kent Bondensgaard, Lishan Kang, and SivA. Hjorth
47. Signaling of IL-4R, a Typical Class ICytokine Receptor: What Defines theQuiescent State? 323Thomas Weidemann, Siegfried Hofinger, andManfred Auer
48. Epidermal Growth Factor Kinases andtheir Activation in Receptor MediatedSignaling 329Andrew H.A. Clayton
Section D - Membrane Proximal Events 337James A. Wells
49. Tumor Necrosis Factor Receptor-Associated Factors in Immune ReceptorSignal Transduction 339Qian Yin, Su-Chang Lin, Yu-Chih Lo,Steven M. Damo and Hao Wu
50. Assembly of Signaling Complexes forTNF Receptor Family Molecules 347Gail A. Bishop and Bruce S. Hostager
51. Mechanisms of CD40 Signaling theImmune System 353Randolph Noelle, Victor C. de Vries and Raul Elgueta
52. Role of Lipid Domains in EGF ReceptorSignaling 359Linda J. Pike
53. Lipid-Mediated Localization of SignalingProteins 365Maurine E. Linder
54. Organization of Photoreceptor SignalingComplexes 373Susan Tsunoda
55. Transmembrane ReceptorOligomerization 379Darren R. Tyson and Ralph A. Bradshaw
VOLUME 3
Contributors xxiPreface to the Second Edition xliiiPreface to the First Edition xlv
Part IIITranscription and Translation:Nuclear and Cytoplasmic Events 1995Michael Karin
Section A - Nuclear Receptors 1997Michael G. Rosenfeld
244. Nuclear Receptor Coactivators 1999Joshua D. Stender and Christopher K. Glass
XVI Contents
245. Corepressors in Mediating Repressionby Nuclear Receptors 2005Gratien G. Prefontaine, Peter J. Cook andMichael G. Rosenfeld
246. Steroid Hormone ReceptorSignaling 2015Vincent Giguere
247. Role of COUP-TFII in CongenitalDiaphragmatic Hernia 2021Sumiyasu Ishii, Sophia Y. Tsai andMing-Jer Tsai
248. Nuclear Receptors in DrosophilaMelanogaster 2027Vincent C. Henrich and Joshua M. Beatty
Section B -Transcription Factors 2039Marc Montminy
249. JAK-STAT Signaling 2041Li Song and Christian Schindler
250. FOXO Transcription Factors: KeyTargets of the PI3K-Akt Pathway ThatRegulate Cell Proliferation, Survival,and Organismal Aging 2049Anne Brunet, Hien Tran, andMichael E. Greenberg
251. The Multi-gene Family of TranscriptionFactor AP-1 2059Peter Angel and Jochen Hess
252. NFK,B: a Key Integrator of CellSignaling 2069John K. Westwick, Klaus Schwamborn, andFrank Mercurio
253. Transcriptional Regulation via the cAMPResponsive Activator CREB 2077Paul K. Brindle
254. The NFAT Family: Structure, Regulationand Biological Functions 2083Fernando Macian, Fernando Cruz-Guilloty,Sonia Sharma and Anjana Rao
255. Ubiquitination / Proteasome 2093Daniel Kornitzer and Aaron Ciechanover
256. The Smads 2099Malcolm Whitman
Section C - Damage/Stress Responses 2105Albert J. Fornace, Jr.
257. Complexity of Stress Signaling 2107Daniel R. Hyduke, Sally A. Amundson, andAlbert J. Fornace, Jr.
258. Signal Transduction in the Escherichiacoli SOS Response 2127James J. Foti, Lyle A. Simmons, Penny J. Beuningand Graham C. Walker
259. Oxidative Stress and Free RadicalSignal Transduction 2137Bruce Demple
260. Screening Approaches to IdentifyGenes Required for DNA Double-Strand Break Damage Signaling in theYeast Saccharomyces Cerevisiae 2145Craig B. Bennett
261. Radiation Responses inDrosophila 2159Wan-Jin Lu, Naoko Sogame and John M. Abrams
262. Double-strand Break Recognitionand its Repair by Non-homologousEnd-Joining 2165Xiaopoing Cui and Michael R. Lieber
263. ATM Mediated Signaling Defends theIntegrity of the Genome 2171Martin F. Lavin, Magtouf Gatei, Philip Chen,Amanda Kijas and Sergei Kozlov
264. Signaling to the p53 Tumor Suppressorthrough Pathways Activated byGenotoxic and Non-GenotoxicStresses 2185Carl W. Anderson and Ettore Appella
265. The p53 Master Regulator andRules of Engagement with TargetSequences 2205Alberto Inga, Jennifer J. Jordan, Daniel Menendez,Veronica De Sanctis and Michael A. Resnick
Contents
266. Nuclear and Cytoplasmic Functions ofAbl Tyrosine Kinase 221 7Jean Y.J.Wang
267. Radiation Induced CytoplasmicSignaling 2225Frank-D. Bohmer, Carsten Weiss andPeter Herrlich
268. The Heat Shock Response and theStress of Misfolded Proteins 2231Richard I. Morimoto and Sandy D. Westerheide
269. Hypoxia Mediated SignalingPathways 2241Denise A. Chan, Albert C. Koong, andAmatoJ. Giaccia
270. Regulation of mRNA Turnover byCellular Stress 2247Subramanya Srikantan and Myriam Gorospe
271. Oncogenic Stress Responses 2257Dmitry V. Bulavin
272. Ubiquitin and FANC StressResponses 2265Stacy A. Williams and Gary M. Kupfer
273. Stress and 1-H2AX 2273Jennifer S. Dickey, Christophe E. Redon,Asako J. Nakamura, Brandon J. Baird,Olga A. Sedelnikova, and William M. Bonner
Section D - Post-transcriptionalControl 2283NahumSonenberg
274. Translational Control by Amino Acidsand Energy 2285Kathrin Thedieck and Michael N. Hall
275. Translation Control and InsulinSignaling 2295Anand Selvaraj and George Thomas
276. ERand oxidative stress: Implications indisease 2301Jyoti D. Malhotra and Randal J. Kaufman
277. Regulation of mRNA Turnover 2311Ann-Bin Shyu and Chyi-Ying A. Chen
278. Signaling to CytoplasmicPolyadenylation and TranslationJong Heon Kim and Joel D. Richter
2317
279. Translational Control in InvertebrateDevelopment 2323Jocelyn Moore and Paul Lasko
280. The Role of Alternative Splicing Duringthe Cell Cycle and Programmed CellDeath 2329Xialu Li and James L. Manley
281. Signaling Pathways that MediateTranslational Control of RibosomeRecruitment to mRNA 2335Ryan J. O. Dowling and Nahum Sonenberg
Section E - Chromatin and itsModification 2343Jerry L. Workman
282. The SWI/SNF and RSC NucleosomeRemodeling Complexes 2345Nilanjana Chatterjee, Payel Sen, andBlaine Bartholomew
283. ISWI Chromatin RemodelingComplexes 2357Toshio Tsukiyama, Naomi Bogenschutz, TraceyKwong, Jairo Rodriguez, Ashwin Unnikrishnan,and Adam Yadon
284. The INO80 Chromatin RemodelingComplex 2363Mingming Chen and Xuetong Shen
285. Histone Acetylation ComplexesTara L. Burke and Patrick A. Grant
2369
286. Regulation of Histone DeacetylaseActivities and Functionsby Phosphorylation andDephosphorylation 2379Edward Seto and Xiang-Jiao Yang
287. Histone Methylation: ChemicallyInert But Chromatin Dynamic 2389Johnathan R. Whetstine
Contents
288. Histone Phosphorylation:Chromatin Modifications that LinkCell Signaling Pathways to NuclearFunction Regulation 2399Priscilla Nga leng Lau and Peter Cheung
289. Histone Variants: Signaling orStructural Modules? 2409Toyotaka Ishibashi, Andra Li and Juan Ausio
290. Silent Chromatin Formation andRegulation in the YeastSaccharomyces cerevisiae 2427Melissa R. Koch and Lorraine Pillus
291. Gene Silencing and ChromatinModification by PolycombComplexes in Flies andHumans 2437Jeffrey A. Simon
292. Histone Ubiquitination 2449Vikki M. Weake and Jerry L. Workman
293. Chromatin Mediated Control of GeneExpression in Innate Immunity andInflammation 2461Gioacchino Natoli
Part IVSignaling from IntracellularCompartments 2467Marilyn C. Farquhar and SureshSubramani
294. Protein Quality Control in theEndoplasmic Reticulum 2471Yuki Okuda-Shimizu, Ying Shen, andLinda Hendershot
295. Quality Control and Quality Assurancein the Mitochondrion 2477Carolyn K. Suzuki
296. Protein Quality Control in Peroxisomes:Ubiquitination of the PeroxisomalTargeting Signal Receptors 2489Chris Williams and Ben Distel
297. Mitochondrial Dynamics: Fusion andDivision 2499Yasushi Tamura, Miho lijima and Hiromi Sesaki
298. The SREBP Pathway: Gene Regulationthrough Sterol Sensing and GatedProtein Trafficking 2505Arun Radhakrishnan, Li-Ping Sun,Peter J. Espenshade, Joseph L. Goldstein andMichael S. Brown
299. Regulating Endoplasmic ReticulumFunction through the Unfolded ProteinResponse 2511Alicia A. Bicknell and Maho Niwa
300. Signaling Pathways from Mitochondriato the Cytoplasm and Nucleus 2527Immo E. Scheffler
301. Apoptosis Signaling: A Means toan End 2535Lisa}. Pagliari, Michael J. Pinkoski, andDouglas R. Green
302. Regulation of Cell CycleProgression 2545Jennifer Scorah, and Claire H. McGowan
303. Signaling During Organelle Divisionand Inheritance: Peroxisomes 2555Andrei D. Fagarasanu and Richard A. Rachubinski
304. Signaling at the Nuclear EnvelopeGeza Ambrus and Larry Gerace
2563
305. Bidirectional Crosstalk between ActinDynamics and Endocytosis 2571Giorgio Scita and Pier Paolo Di Fiore
306. Signaling in Autophagy RelatedPathways 2583Patrice Codogno and Alfred J. Meijer
PartVCell-Cell and Cell-MatrixInteraction 2589E. Brad Thompson
307. Overview of Cell-Cell and Cell-MatrixInteractions 2591E. Brad Thompson and Ralph A. Bradshaw
Contents
308. Interactive Signaling Pathways in theVasculature 2593Igor Prudovsky, Volkhard Lindner, Calvin Vary andRobert E. Friesel
309. Signaling Pathways Involved inCardiogenesis 2601Deepak Srivastava and Chulan Kwon
310. Regulatory Signaling in PancreaticOrganogenesis: Implications forAberrant Signaling in PancreaticCancer 2611Catherine Carriere and Murray Korc
311. Trophic Effects of Gut Hormones in theGastrointestinal Tract 2621Kanika A. Bowen and B. Mark Evers
312. The Neurotrophin Factors 2631J. ReginoPerez-Polo
313. Cell to Cell and Cell-MatrixInteractions in Bone 2647Lynda F. Bonewald
314. Cell-Cell Signaling in the Testis andOvary 2663Michael K. Skinner, Eric E. Nilsson andRamji K. Bhandari
315. Signal Transduction in TLymphocytes 2679RolfKonig
316. Signal Transduction via the B CellAntigen Receptor: A Crucial Regulatorof B Cell Biology 2689Louis B. Justement
317. Signaling Pathways in the Normal andNeoplastic Breast 2699Tushar B. Deb, Danica Ramljak,Robert B. Dickson2, Michael D. Johnson, andRobert Clarke
318. Kidney 2707William J. Arendshorst and ElsaBello-Reuss
319. Cytokines and Cytokine ReceptorsRegulating Cell Survival,Proliferation, and Differentiation inHematopoiesis 2733Fiona J. Pixley and E. Richard Stanley
320. Signaling Pathways Regulating Growthand Differentiation of Adult StemCells 2743Larry Denner, Margaret Howe andRandall J. Urban
321. In Vivo Imaging of Cellular NetworkSignaling 2753Werner Gobel, Bjorn M. Kampa andFritjof Helmchen
Part VIDisease Pathophysiology:Translational Implications 2759Murray Korc
322. The Roles of Ras Family Small GTPasesin Breast Cancer 2763Ariella B. Hanker and ChanningJ. Der
323. Translational Implications of Stromal-Epithelial Interactions in ProstateCancer and the Potential Role ofProstate Cancer Stem/ProgenitorCells 2773Sophia L. Maund and Scott D. Cramer
324. Aberrant Signaling Pathways inPancreatic Cancer: Opportunities forTargeted Therapeutics 2783Alixanna Norris and Murray Korc
325. The Evolution and Maintenanceof the Multiple Myeloma CellClone within the Liquid BoneMarrow Compartment: TherapeuticImplications 2799Klaus Podar and Kenneth C. Anderson
326. The Pathophysiologic Role of the BoneMarrow Environment and its Niches inMultiple Myeloma 2811Klaus Podar and Kenneth C. Anderson
Contents
327. Signaling Targets in MyeloidLeukemias 2821Muneyoshi Futami and Seth J. Corey
328. Signaling Targets in LymphoidLeukemias 2831Muneyoshi Futami and Seth J. Corey
329. Targeting Ras for Anticancer DrugDiscovery 2837Jen Jen Yeh, James P. Madigan, Paul M. Campbell,Patrick J. Roberts, Lanika DeGraffenreid andChanningJ. Der
330. Targeting EWS/FLI1 Driven SignalingPathways as Therapy for Tumors of theEwing's Sarcoma Family 2859Vicente Notario, Silvia Mateo-Lozano,Joaqufn Villar, and Oscar M. Tirado
331. IRS-Protein Scaffolds and Insulin/IGF Action in Central and PeripheralTissues 2873Morris F. White
332. Adipokine Signaling: Implications forObesity 2885Rexford S. Ahima and Gladys M. Varela
333. Angiogenesis Signaling Pathways asTargets in Cancer Therapy 2895Chery A. Whipple and Murray Korc
334. CXC Chemokine Signaling in InterstitialLung Diseases 2907Robert M. Strieter and Borna Mehrad
335. Systemic Sclerosis 2913Carol A. Feghali-Bostwick, and John Varga
336. Signal Transduction in RheumatoidArthritis and Systemic LupusErythematosus 2919Thomas Dorner, and Peter E. Lipsky
337. Translational Concepts inVasculitis 2933Daniel A. Albert and David B. Talmadge
338. Advances in Understanding thePathogenesis of Inflammatory BowelDisease 2945David S. Kotlyar, Wojciech C. Blonski, andGary R. Lichtenstein
339. Translational Implications ofProteomics 2959Sam Hanash
340. Translational Implications ofmicroRNAs in Clinical Diagnostics andTherapeutics 2965Lorenzo F. Sempere and Sakari Kauppinen
Index 2983