Encyclopedia of Biological Chemistry by William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland



Bibliographic Information:
Title: Encyclopedia of Biological Chemistry by William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland
Editor: William J. Lennarz, M. Daniel Lane, Paul Modrich, Jack Dixon, Ernesto Carafoli, John Exton, Don Cleveland
Edition: 1st ed
Publisher: Elsevier
Length: 503 pages
Size: 10.97 MB
Language: English
Format: .pdf

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Table of Contents:
Cover Page......Page 503
Editors-in-Chief......Page 437
Associate Editors......Page 439
Preface......Page 442
Notes on the Subject Index......Page 443
Volume 1......Page 444
Volume 2......Page 452
Volume 3......Page 460
Volume 4......Page 468
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 473
Metabolism, Vitamins and Hormones......Page 475
Cell Architecture and Function......Page 477
Protein/Enzyme Structure Function and Degradation......Page 480
Bioenergetics......Page 483
Molecular Biology......Page 489
Signaling......Page 495
Techniques and Methodology......Page 502
Volume 3 (N-R)......Page 0
Repetitive Secondary Structure: The -Helix......Page 1
Repetitive Secondary Structure: The 310-Helix......Page 2
Repetitive Secondary Structure: The Polyproline II Helix (PII)......Page 3
Programs to Identify Structure from Coordinates......Page 4
Neural Networks......Page 5
Further Reading......Page 6
Beta-Secretase......Page 7
Gama-Secretase......Page 9
Further Reading......Page 10
Soluble and Integral Membrane Proteins......Page 11
Chaperones and the ER Quality Control System......Page 12
Vesicular Transport between the ER and Golgi......Page 13
Protein Localization in the ER......Page 14
Protein Exit from the Golgi......Page 15
Further Reading......Page 16
Selenocysteine Biosynthesis......Page 17
Formation of the SelBx GTPxSelenocysteyl-tRNAx SECIS Complex......Page 18
Archaeal and Eukaryal Selenoprotein Synthesis......Page 20
Further Reading......Page 21
Septins Bind Guanine Nucleotide and Form Complexes and Filaments......Page 22
Septin Filaments Can Form Higher-Order Assemblies......Page 23
Septins Interact with Inositol Phospholipids......Page 24
Metazoa......Page 25
Further Reading......Page 26
Three-Dimensional Structures......Page 27
Interaction of PP1 with Diverse Regulatory Subunits......Page 28
PP5......Page 29
PPP Family......Page 30
See Also The Following Articles......Page 31
Further Reading......Page 32
Serotonin Receptors that Inhibit Adenylyl Cyclase......Page 33
Serotonin Receptors Linked to Activation of Adenylate Cyclase......Page 34
RNA Editing Produces Multiple Functional 5-HT2C Receptor Isoforms......Page 35
Summary: Potential Role of Receptor Diversity......Page 36
Further Reading......Page 37
Cell-Type Specific Expression......Page 38
Known and Putative Functions of the Siglecs......Page 39
Further Reading......Page 40
Bacterial RNA Polymerase and the Transcription Cycle......Page 41
Biochemical Properties......Page 42
Phylogenetic Distribution......Page 43
Further Reading......Page 44
Clamp Structure and Function......Page 45
Clamp Loader Structure......Page 46
Further Reading......Page 47
The Small GTPase Cycle and Its Regulation......Page 48
Small GTPase Structure......Page 51
Ras Proteins as Signaling Nodes and Regulators of Cell Proliferation......Page 52
Further Reading......Page 54
Somatostatin Receptor Subtypes......Page 55
Somatostatin Receptor Structure......Page 56
Pharmacology of Somatostatin Receptor Subtypes......Page 57
Somatostatin Receptor Signaling......Page 58
Further Reading......Page 59
SPG7/Paraplegin......Page 61
SPG10/KIF5A......Page 63
SPG20/Spartin......Page 64
Myelin-Associated Genes......Page 65
Further Reading......Page 66
Dual-Wavelength Technology......Page 67
Photochemical Action Spectra......Page 68
Control Of Respiration......Page 69
The Ruby Laser and Electron Tunneling......Page 70
NADH as an Oximeter......Page 71
NIR Imaging......Page 72
Brain Functional Activation......Page 73
Glossary......Page 74
Further Reading......Page 75
More Complex Phospho- and Glyco-Sphingolipids......Page 76
Serine Palmitoyltransferase......Page 77
Dihydroceramide Desaturase......Page 78
Glycosphingolipids......Page 79
Glossary......Page 80
Further Reading......Page 81
Neutral Sphingomyelinase (nSMase)......Page 82
Neutral Ceramidase......Page 83
Glycosphingolipid Catabolism......Page 84
Arylsulfatase A......Page 85
Beta-Glucocerebrosidase......Page 86
Further Reading......Page 87
Splicing Takes Place via Consecutive Transesterification Reactions......Page 88
Spliceosome Assembly and the Splicing Cycle......Page 89
Why is the Spliceosome so Complex......Page 90
Glossary......Page 91
Further Reading......Page 92
History of Src......Page 93
Other Vertebrate Src Family Kinases: Redundant and Specific Functions......Page 94
Regulation of Src Kinase Activity......Page 95
Summary: Integration of Many Inputs and Regulation of Many Outputs......Page 97
Further Reading......Page 98
Background......Page 99
Obesity and Starvation, and Clinical Features of Starvation......Page 100
Weight Loss, Body Composition, and Energy Requirements......Page 101
The Nature and Quantity of Fuels Oxidized during Starvation......Page 102
Changes in the Concentration of Substrates and Hormones in the Blood......Page 103
Hormonal Changes......Page 104
Control of Fatty Acid Release During Starvation......Page 105
Proteolysis and Amino Acid Metabolism......Page 106
Ketogenesis......Page 107
Urinary Nitrogen Excretion......Page 108
Fuel Consumption during Starvation......Page 109
Further Reading......Page 110
Overview of Nuclear Receptor Ligands and Mechanism of Action......Page 111
Receptor Structure......Page 112
Receptor Binding to DNA......Page 113
Steroid Receptor Coregulators......Page 114
Functional Interactions between Nuclear Receptors and Signal-Regulated Transcription Factors......Page 115
Further Reading......Page 116
Characteristics of SOCE......Page 117
Molecular Candidates for SOCC......Page 118
Conformational Coupling......Page 119
Ca2+ Signaling Microdomains......Page 120
Further Reading......Page 122
Catalysis......Page 123
Free-Energy Profiles......Page 124
Rate-Limiting Steps for V......Page 125
Further Reading......Page 126
Structure of Golgi Nucleotide Sugar Transporters......Page 127
Topography of Nucleotide Sugar Transporters in the Golgi Membrane......Page 128
Further Reading......Page 129
Conjugation......Page 130
Deconjugation......Page 132
See Also the Following Articles......Page 133
Further Reading......Page 134
The Cu, Zn SODs......Page 135
E. coli......Page 136
See Also the Following Articles......Page 137
Further Reading......Page 138
Interaction of ZAP-70 with the TCR ITAM......Page 139
Tyrosine Phosphorylation of ZAP-70......Page 141
Tyrosine Phosphorylation of Syk......Page 142
T Lymphocyte Development......Page 143
ZAP-70 and Syk in Integrin-Mediated Functions......Page 144
Further Reading......Page 145
Similarities to Other Polymerases......Page 146
Promoter Release and Elongation......Page 148
Regulation......Page 149
Further Reading......Page 150
SP......Page 151
Full-Length SPR......Page 152
Role of the Carboxyl-Tail in SPR Function......Page 154
SPR in Emesis......Page 155
Further Reading......Page 156
T1R Receptors......Page 157
Transduction Cascades......Page 159
Further Reading......Page 160
T Cell Antigen Receptor......Page 161
Invariant Chains: CD3, CD247, and Pre-TAlpha......Page 164
Cell Biology......Page 165
Further Reading......Page 166
PH Domain......Page 168
Tec Family Kinase Functions......Page 169
Tec Family Kinases in Signal Transduction......Page 170
Further Reading......Page 171
Telomeric DNA......Page 173
Telomerase......Page 174
Telomere Proteins......Page 175
A Negative Regulatory Loop Stabilizes Telomere Length......Page 176
See Also the Following Articles......Page 177
Further Reading......Page 178
The Luteinizing Hormone Receptor......Page 179
Extracellular Domains......Page 180
Naturally Occurring Mutations of the Glycoprotein Hormone Receptors......Page 183
Further Reading......Page 184
Peripheral Membrane Proteins......Page 186
Glossary......Page 187
Further Reading......Page 188
MyD88-Dependent Signaling Pathway......Page 189
Structural and Functional Homologues of TLRs......Page 191
Further Reading......Page 193
Intrinsic Termination......Page 194
Rho-Mediated Termination......Page 195
Regulated Termination and Antitermination......Page 196
Further Reading......Page 197
Budding Yeast, S. cerevisiae......Page 199
Metazoans......Page 201
Further Reading......Page 202
E. coli......Page 203
Alkylation Damage......Page 205
Oxidative Damage......Page 206
Further Reading......Page 207
Receptor-Ligand Interactions......Page 208
Accessory Receptors......Page 209
Receptor Activation......Page 210
See Also The Following Articles......Page 211
Further Reading......Page 212
The Three Basic Reactions of Elongation......Page 213
The Hybrid Site Model......Page 214
Selection of the Ternary Complex: Decoding and A Site Occupation......Page 216
An Additional Role of EF-Tu......Page 217
Peptide-Bond Formation......Page 218
Translocation......Page 221
Further Reading......Page 222
The Traditional Elongation Cycle: The A and P Sites......Page 223
Molecular Mimicry......Page 225
Influence of Other Sites......Page 226
Glossary......Page 227
Further Reading......Page 228
The Translation Initiation Region of Prokaryotic mRNAs......Page 229
Initiation Complex Formation......Page 230
IF1......Page 231
IF2......Page 232
IF3......Page 233
Further Reading......Page 235
Recruitment of Initiator tRNA to the 40S Ribosomal Subunit......Page 236
Attachment of 43S Preinitiation Complexes to mRNA......Page 237
Regulation of Translation Initiation......Page 239
Further Reading......Page 240
Prokaryotic Polypeptide Chain Release Factors......Page 241
Eukaryotic Chain Release Factors......Page 242
Bypassing Stop Codons: The Causes and Consequences......Page 244
Further Reading......Page 245
Structural Features......Page 246
Lesion Bypass Specificity......Page 247
Cellular Role(s)......Page 248
Further Reading......Page 249
Occurrence of Trehalose in the Biological World......Page 250
As a Stabilizer and Protectant of Proteins and Membranes Against Various Stresses......Page 251
Glossary......Page 253
Further Reading......Page 254
History of the Discovery of the TCA Cycle......Page 255
Into the Wilderness and Back Again......Page 257
The TCA Cycle Today......Page 258
Glossary......Page 260
Further Reading......Page 261
tRNAs......Page 262
tRNA Dependent Amidation......Page 263
Novel Functions of tRNA Synthetases......Page 264
Further Reading......Page 265
Attenuation Control of the E. coli trp Operon......Page 266
The B. subtilis trp Leader......Page 268
The Role of Pausing in TRAP Mediated Attenuation......Page 269
Further Reading......Page 270
Physical Properties......Page 271
Tubulin Polymerization......Page 272
Gamma-Tubulin and Microtubule Nucleation......Page 273
Further Reading......Page 274
Expression......Page 276
TRAF Signaling......Page 277
Death Receptor Signaling......Page 279
Costimulation......Page 280
Further Reading......Page 281
2D PAGE in the Future......Page 283
Second Dimension: SDS-PAGE......Page 284
Applications of 2D PAGE......Page 285
Differential Analysis......Page 286
Further Reading......Page 287
The Yeast Two-Hybrid System......Page 289
Advanced Applications......Page 290
Role in Proteomics......Page 291
Further Reading......Page 292
The Tyrosine Sulfation Reaction......Page 293
Properties of TPST......Page 294
TPST-1- and TPST-2-Deficient Mice......Page 295
Further Reading......Page 296
Degradation......Page 297
Substrate Recognition......Page 298
Diseases......Page 299
Drug Development......Page 300
Further Reading......Page 301
Proteins Modified by Sentrin......Page 302
Rub1/NEDD8 Modification of CDC53/Cullins......Page 304
Further Reading......Page 305
The Discovery of Pol V......Page 306
The Fidelity of Pol V......Page 307
In vivo Function of Pol V......Page 308
Eukaryotic Homologues of Pol V......Page 309
Further Reading......Page 310
Brown Adipose Tissue and UCP1: History of a True Respiration Uncoupling......Page 311
Respiration Uncoupling is the Thermogenic Mechanism in Brown Adipocytes......Page 312
The Novel UCPs......Page 313
Role and Function of UCPs other than UCP1: A Role in Controlling the Level of Reactive Oxygen Species......Page 314
UCP1, UCP2, and UCP3, Conclusions and Perspectives......Page 315
Further Reading......Page 316
Physiological and Pathological ER Stress......Page 317
Unconventional Splicing of HAC1 mRNA......Page 318
Conservation of the IRE1 Pathway......Page 319
PERK Couples ER Stress to eIF2 Phosphorylation and Translational Repression......Page 320
Gene Expression, eIF2 Phosphorylation and Integration of Signals in the UPR, and Other Stress Pathways......Page 321
See Also the Following Articles......Page 322
Further Reading......Page 323
Urea Cycle Defects......Page 324
Other Hyperammonemia States due to Amino Acid Transporter Defects......Page 325
Long-Term Management......Page 327
Further Reading......Page 328
Vacuole Function in Yeast......Page 329
Vacuole Biogenesis and Transport Pathways to the Vacuole in Yeast......Page 330
Cytoplasm to Vacuole Transport and Macro-Autophagy......Page 331
Glossary......Page 333
Further Reading......Page 334
VEGFR-2......Page 335
VEGF Structure and Receptor Binding......Page 336
Coreceptors......Page 337
Signal Transduction Cascades......Page 338
Nonmitogenic Functions......Page 339
Further Reading......Page 340
The Functions of Vasopressin and Oxytocin......Page 341
Vasopressin and Oxytocin Receptors......Page 345
Further Reading......Page 346
Function of Plasma Membrane V-ATPases......Page 347
V-ATPase Structure......Page 348
Glossary......Page 350
Further Reading......Page 351
The Chemistry of atROH Generation, Storage, and Metabolic Activation......Page 352
Retinoid Binding-Proteins and their Contributions to Retinoid Homeostasis......Page 353
Control of Vitamin A Homeostasis......Page 356
Further Reading......Page 357
B12-Derivatives in Electron Transfer Reactions......Page 358
Organometallic Reactions of B12-Derivatives......Page 359
Coenzyme B12-Dependent Enzymes......Page 361
Further Reading......Page 363
Chemistry......Page 365
Nutritional and Biochemical Importance......Page 366
Defining Ascorbic Acid Status......Page 367
Glossary......Page 368
Further Reading......Page 369
The N-Terminal DNA-Binding Domain (DBD)......Page 370
Ligand-Binding Domain (LBD)......Page 371
VDR Interaction with Vitamin D Responsive Elements......Page 372
Communication between VDR and the Transcriptional Machinery......Page 373
Further Reading......Page 374
Conversion of Vitamin D to its Hormonal Form......Page 376
The Vitamin D Endocrine System......Page 377
Molecular Mechanism......Page 378
New and Nonclassical Roles of the Vitamin D Hormone......Page 379
Glossary......Page 380
Further Reading......Page 381
Dietary Sources and Recommended Intake of Vitamin E......Page 382
Uptake, Distribution, and Metabolism of Vitamin E......Page 383
Effects of Vitamin E on Cell Signaling and Gene Expression......Page 384
Recognition of Vitamin E Deficiency Diseases and the Beneficial Effects of Vitamin E Supplements in Human Health.........Page 385
Further Reading......Page 386
Biochemical Role of Vitamin K......Page 387
The Vitamin K-Dependent Carboxylase......Page 388
Metabolic Interconversion of Vitamin K......Page 389
Nutritional Aspects of Vitamin K......Page 390
Further Reading......Page 391
Blood Coagulation......Page 392
Nutrition......Page 395
Further Reading......Page 396
Voltage-Dependent K+ Channel Structure and Diversity......Page 397
Ether-a-go-go K+ Channels......Page 398
Calcium-Activated K+ Channel......Page 399
Further Reading......Page 401
Calmodulin Binding......Page 403
Physiology......Page 404
Further Reading......Page 406
The Alpha-Subunits of Sodium Channels......Page 407
The Outer Pore and Selectivity Filter......Page 408
Modulation of Channel Activity......Page 409
Genetic Defects Affecting Voltage-Gated Sodium Channels......Page 410
Toxins and Channel Modifiers......Page 411
Glossary......Page 412
Further Reading......Page 413
Structure of the VHL Ubiquitin Ligase......Page 414
Regulation of HIF Ubiquitylation by the VHL Ubiquitin Ligase......Page 415
Further Reading......Page 416
Catalytic Activity......Page 417
Localization......Page 418
Further Reading......Page 419
Diffraction Measurements......Page 420
Fitting Electron Density Maps......Page 421
Studies of Molecular Complexes and Conformational Changes......Page 422
The Importance of Resolution......Page 423
Structures at Very High Resolution......Page 424
Further Reading......Page 426
The Gene-Specific Regulatory Factors......Page 427
Chromosomal Organization......Page 428
How Gal4p Activates Transcription......Page 429
Glossary......Page 430
Further Reading......Page 431
Classical Zinc Fingers......Page 432
Interactions with DNA and RNA......Page 434
Non-Nucleic Acid Interactions......Page 435
Further Reading......Page 436




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