Encyclopedia Of Biological Chemistry

Phylogeny......Page 1
Cover Page......Page 895
Editors-in-Chief......Page 829
Associate Editors......Page 831
Preface......Page 834
Notes on the Subject Index......Page 835
Volume 1......Page 836
Volume 2......Page 844
Volume 3......Page 852
Volume 4......Page 860
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 865
Metabolism, Vitamins and Hormones......Page 867
Cell Architecture and Function......Page 869
Protein/Enzyme Structure Function and Degradation......Page 872
Bioenergetics......Page 875
Molecular Biology......Page 881
Signaling......Page 887
Techniques and Methodology......Page 894
Volume 3 (N-R)......Page 0
Function and Diseases......Page 2
Structure and Biochemical Mechanism......Page 3
The Substrate Specificity of the ABC Multidrug Exporters......Page 4
Further Reading......Page 5
ABA Biosynthesis......Page 6
Role of ABA in Seed Development and Maturation......Page 7
Stomatal Closure Meditated by ABA......Page 8
ABA-Induced Modulation of Gene Expression......Page 10
Further Reading......Page 11
General Concepts in Actin Assembly/Disassembly......Page 12
Capping Proteins......Page 14
Cellular Aspects of Actin Assembly/Disassembly......Page 15
Further Reading......Page 17
Actin......Page 19
Pointed-End Binding and Branching......Page 20
Evolutionary and Structural Relationships between Some Severing and Severing/Barbed-End-Capping Proteins......Page 21
The Six Segment Proteins: Gelsolin, Villin, and Adseverin/Scinderin......Page 22
The Single Domain ADF/Cofilin Family......Page 23
Barbed-End-Capping Proteins......Page 24
Further Reading......Page 25
Prokaryotic Arps......Page 27
Conventional Actin......Page 30
Arp2 and Arp3......Page 31
Chromatin-Associated Conventional Actin......Page 32
Further Reading......Page 33
Sequence Similarity......Page 34
A1 Receptors......Page 35
Signaling Downstream of Adenosine Receptors......Page 36
A2A Receptors......Page 37
Glossary......Page 38
Further Reading......Page 39
Members of the Family......Page 40
Regulation of Adenylyl Cyclase Activity by G Proteins and Calcium......Page 41
Physiological Roles of Adenylyl Cyclases......Page 42
See Also the Following Articles......Page 44
Further Reading......Page 45
Classification and Mechanism of Action of Adrenergic Receptors......Page 46
Pharmacological and Molecular Characteristics of Alpha-1 Adrenergic Receptors......Page 47
Pharmacological and Molecular Characteristics of Beta Adrenergic Receptors......Page 48
Adrenergic Receptor Polymorphisms......Page 49
Further Reading......Page 50
Why and Where AC Works......Page 51
Activation of and Coupling to Carriers......Page 52
Adsorption......Page 53
AC and DNA Recombinant Techniques......Page 54
Glossary......Page 55
Further Reading......Page 56
Linker Peptide Composition......Page 57
Protein-Ligand Interaction Affinity Tags......Page 58
Antibody-Epitope Interaction Affinity Tags......Page 59
Glossary......Page 62
Further Reading......Page 63
The PKA Anchoring Hypothesis......Page 64
Anchoring Protein Targeting Regions......Page 65
Alternatively Spliced Scaffolds......Page 66
Further Reading......Page 67
The Hill n, a Measure of Cooperativity......Page 68
Two-State Models to Explain Cooperativity in Allosteric Proteins......Page 69
Ribonucleotide Reductase (RR)......Page 71
Further Reading......Page 72
Alternative Splicing of FGF-R2 Transcripts......Page 74
Exonic Splicing Enhancers......Page 75
Layers of Regulation......Page 76
Further Reading......Page 77
Details of the Hierarchy......Page 78
TRA: A Simple Blockage Model......Page 79
Sxl Autoregulation......Page 81
Alternative Splicing and Sex Determination in Other Species......Page 82
Further Reading......Page 83
FAD-Containing Monoamine Oxidases......Page 85
Cu/TPQ Amine Oxidases......Page 86
Further Reading......Page 88
Intestinal Metabolism......Page 90
Liver Metabolism......Page 91
Inter-Organ Exchanges......Page 92
Ureagenesis......Page 93
Catabolic Hormones......Page 94
Further Reading......Page 95
N-Terminal Cotranslational Processing......Page 96
Properties of MetAPs......Page 97
Further Reading......Page 98
History......Page 99
Physiological Factors in Amyloid Formation......Page 100
Evolved Amyloid......Page 101
Amyloid Assembly......Page 102
Glossary......Page 103
Further Reading......Page 104
Entry at Malate and Oxaloacetate......Page 105
Exit of Intermediates: Balancing Anaplerosis......Page 106
Expression and Activity of Proteins Regulating Anaplerosis......Page 107
Renal Ammonia Formation during Starvation......Page 108
Summary and Perspective......Page 109
Further Reading......Page 110
Ang I Binding Protein......Page 111
Ang II Receptors......Page 112
Ang IV......Page 114
Further Reading......Page 115
Control of DNA Looping......Page 116
The Discovery and Demonstration of DNA Looping......Page 117
History and Historical Significance......Page 118
Further Reading......Page 119
ARF-Related Proteins......Page 120
Regulators of ARF Activity......Page 121
Further Reading......Page 122
Structure......Page 123
Overall Structure......Page 124
Cancer......Page 125
Naturally Occurring Inhibitors......Page 126
Further Reading......Page 127
Mitochondrial Electron Transport Chain in Plants......Page 128
Substrates for ATP Synthesis......Page 129
Inhibitors of ATP Synthesis......Page 130
Nonphosphorylating Respiration......Page 131
Further Reading......Page 132
Cyanide-Resistant Respiration......Page 133
AOX Structure......Page 134
Physiological Role(s) of AOX......Page 136
Further Reading......Page 137
Macroautophagy in Mammals......Page 138
Macroautophagy in Yeast......Page 139
Glossary......Page 142
Further Reading......Page 143
The Cobalamin Cofactor......Page 144
Radical-Mediated Rearrangement Reactions......Page 145
Cobalamin-Dependent Methionine Synthase......Page 148
Further Reading......Page 149
Structure of Bcl2 Family Proteins......Page 151
Role of the Mitochondria......Page 152
Further Reading......Page 153
B-Cell Antigen Receptor Diversity......Page 154
Early Signaling Events......Page 155
The B-Cell Antigen Receptor and the Immune Response......Page 156
Further Reading......Page 157
Bile Salt Synthesis and its Regulation......Page 158
Bile Salt Transport and its Regulation......Page 160
Further Reading......Page 161
Mitochondrial Antigens and the Cellular Immune System......Page 163
Pathology......Page 164
Clinical Findings......Page 165
Treatment of the Underlying Disease Process......Page 166
Further Reading......Page 167
Gibbs Free Energy......Page 169
Redox Potentials......Page 170
The Thermodynamics of Bioenergetic Interconversions......Page 171
Further Reading......Page 172
Biotin Enzymes......Page 173
Biotin Domains......Page 174
Biotin Domain Structure......Page 175
E. coli Biotin Ligase, BirA......Page 176
Further Reading......Page 177
Biosynthesis and Degradation of Natively Biotinylated Proteins......Page 178
Clinical Application of Biotinylated Antibodies......Page 179
Further Reading......Page 180
B1 Receptor......Page 181
Regulation of B1 Receptor Induction......Page 182
B2 Receptor Knockout Animals......Page 183
Further Reading......Page 184
Interorgan Relationships......Page 185
The Macromolecular Organization of the BCKD Complex......Page 187
Brain Neuropathology of BCKAs......Page 188
Further Reading......Page 189
Brassinosteroid Biosynthesis......Page 191
Campesterol to Brassinolide......Page 192
Receptor Kinases and BR Perception......Page 194
Downstream Components......Page 195
Further Reading......Page 196
Signaling Triggered by Cell-Cell Contact......Page 197
Mechanisms of Cadherin Signaling......Page 198
Rho Family GTPase Signaling......Page 199
Wnt/Beta-Catenin Signaling......Page 200
Phosphorylation and Dephosphorylation......Page 201
Further Reading......Page 202
Protocadherins......Page 203
Extracellular Domain Structure (cis- and trans-Dimers)......Page 204
Linkage to Beta-Catenin Family Members......Page 205
Roles of Cadherins in Cell and Tissue Morphogenesis......Page 206
See Also The Following Articles......Page 208
Further Reading......Page 209
CGRP Receptor-Selective Drugs and their Pharmacological Properties......Page 210
Cellular Signaling and RCP......Page 211
The Pathophysiology of CGRP and Adrenomedullin Receptors......Page 213
Further Reading......Page 214
Protein Structure......Page 215
Signaling......Page 216
CTR-Like Receptor (CTRLR)......Page 217
Further Reading......Page 218
Distribution and Localization......Page 219
Distribution and Localization......Page 220
Knockout Animals......Page 221
Further Reading......Page 222
Ca2+ Buffering in the ER Lumen......Page 224
Grp94 (Glucose-Regulated Protein)......Page 225
The Protein Disulfide Isomerase (PDI) Family of Proteins......Page 226
See Also the Following Articles......Page 227
Further Reading......Page 228
Mechanism of [Ca2+]c Oscillations......Page 229
Role and Functional Significance of [Ca2+]c Oscillations......Page 231
Further Reading......Page 232
Structure......Page 233
Intracellular Signaling Pathways Used by the CaR......Page 235
CaR in Hypercalcemia......Page 236
Further Reading......Page 237
Structure......Page 239
Substrate Specificity......Page 240
Regulation of Gene Expression......Page 241
Neuronal Functions......Page 242
Further Reading......Page 243
Cell-Cycle Regulators......Page 244
Oocyte Prophase and Metaphase Arrest......Page 245
Calcium and Meiosis......Page 246
Further Reading......Page 247
Tropomyosin Shift and Steric Blocking Model......Page 248
Molecular Organization of Troponin and its Ca2+-Induced Changes......Page 249
Ca2+-Induced Troponin Shift on the Thin Filaments......Page 251
Molecular Mechanism of Ca2+ Regulation......Page 252
Further Reading......Page 253
Calmodulin Interactions with Ca2+ and with NOS......Page 254
Ca2+/CaM Regulation of NOS......Page 255
Further Reading......Page 258
The Origins and the Fundamental Principles......Page 259
The Renaissance......Page 260
One (or Many) Roles......Page 261
Further Reading......Page 263
Mechanisms......Page 265
History, Roles, and Visualization......Page 266
Further Reading......Page 267
Soluble Complex Ions and Their Binding Strengths......Page 268
Concentrations and Selectivity of Binding in Organisms......Page 269
Overall Functional Fitness of Calcium Ions in Evolution......Page 270
Further Reading......Page 271
Neuronal CaMKII: Localization and Substrates......Page 272
Activation, Autoregulation, and Structure of CaMKII......Page 273
Ca2+/CaM-Dependent Autophosphorylation......Page 274
Autophosphorylation as an Index of Neuronal Activity......Page 275
CaMKII in LTP and Learning and Memory......Page 276
Glossary......Page 277
Further Reading......Page 278
Ca2+ Signaling......Page 279
Myosin Light Chain Kinase......Page 280
Ca2+/Calmodulin-Dependent Protein Kinase II......Page 281
Ca2+/Calmodulin-Dependent Protein Kinase IV......Page 282
Summary......Page 283
Further Reading......Page 284
Annexins......Page 285
Gelsolin......Page 286
C2-Domain Proteins......Page 288
Further Reading......Page 290
Temporal Buffering......Page 292
Structure of the EF-Hand......Page 293
Distribution of EF-Hand Domains......Page 294
Further Reading......Page 297
Structure and Function of Conventional Calpains......Page 298
Classifications......Page 301
Structure and Functions of Calpain Superfamily Members......Page 302
Further Reading......Page 303
Enzymatic Synthesis of Oligosaccharides......Page 305
Carbohydrate Chain Synthesis Utilizing Glycotransferases......Page 306
Chemical Synthesis of Oligosaccharides......Page 307
Solution Phase Chemical Oligosaccharide Synthesis......Page 308
See Also the Following Articles......Page 310
Further Reading......Page 311
Mitochondrial Beta-Oxidation......Page 312
Further Reading......Page 315
Structure and Active Site......Page 317
Mechanism of Action......Page 318
Sequence of Action......Page 319
Substrates during Apoptosis......Page 320
Inhibitors......Page 322
Pathological Implications......Page 323
Further Reading......Page 324
Regulators of G0 Exit and G1-S Progression......Page 326
Cell Growth Regulation......Page 328
Further Reading......Page 329
Initiation......Page 330
Cdc7 (DDK)......Page 331
Coupling Replication to the Cell-Cycle Engine......Page 332
CDK Inhibitors and Proteolysis......Page 333
Conclusions......Page 334
Further Reading......Page 335
G2/M Checkpoint......Page 336
Intra-S Checkpoint......Page 338
G1/S Checkpoint......Page 339
Protein Kinase of the PI3K Family......Page 340
Glossary......Page 341
Further Reading......Page 342
Molecular Components of the Mitotic Checkpoint......Page 343
Sequestration Model......Page 345
Direct Inhibitor Model......Page 346
Checkpoint Proteins Can Have Dual Functions......Page 347
Further Reading......Page 348
Executors of Ca2+ Death Signals......Page 350
Apoptosis, Necrosis, and Other Ca2+-Dependent Forms of Cell Death in Brain Ischemia......Page 351
See Also the Following Articles......Page 352
Further Reading......Page 353
The Actin Cytoskeleton......Page 354
Adhesion......Page 355
Microtubules and Cell Guidance......Page 357
Microtubules and Contractility......Page 358
Further Reading......Page 359
Adhesive Motifs......Page 360
Structure......Page 361
Conformational Changes......Page 362
Further Reading......Page 363
Heterochromatin Domain......Page 365
The Centromere as DNA......Page 366
The Centromere as Chromatin......Page 367
Further Reading......Page 369
Structure of the Centrosome......Page 370
GammaTuRC......Page 371
GammaTuRC-Mediated Microtubule Nucleation in Vivo......Page 372
Centrosome Abnormalities in Cancer......Page 373
Further Reading......Page 374
N-Terminal Region......Page 375
Myeloid Differentiation......Page 376
Small G Proteins......Page 377
PI3-K Pathway......Page 378
Further Reading......Page 379
Why the Need for Metal Trafficking?......Page 381
Delivering Copper to the Golgi: Pathways Involving the ATX1 Copper Chaperone......Page 382
Delivery of Copper to Mitochondrial Cytochrome Oxidase......Page 383
Further Reading......Page 384
Clp/Hsp100 Chaperones......Page 385
Structure of Clp ATPases and Their Associated Proteases......Page 386
Mechanism of Action of Clp Chaperones and Proteases......Page 387
Hsp90 Chaperones......Page 388
Further Reading......Page 389
Overall Mechanism......Page 391
Architecture......Page 393
Polypeptide Binding by Type I Chaperonins......Page 394
Substrate Proteins......Page 395
Further Reading......Page 396
Chemiluminescence: Fluorescence from a Chemical Reaction......Page 397
Bioluminescence: Chemiluminescence from a Biological Source......Page 400
Further Reading......Page 402
Protonmotive Force......Page 403
The Protonmotive Circuit......Page 404
Behavior of the Protonmotive Circuit......Page 405
Uncoupling Proteins......Page 406
Fourth Postulate - Ion Carriers and Channels......Page 407
The Sodium-Calcium Cycle......Page 408
Further Reading......Page 409
Structure......Page 411
Signal Transduction......Page 412
Internalization......Page 413
HIV Entry......Page 414
Tumor Growth and Metastasis......Page 415
Further Reading......Page 416
Categories of Growth Based on the Nature of the Growth-Supporting Reductant......Page 417
Nitrifying Bacteria......Page 418
Generation of the Electrochemical Gradient and ATP Synthesis......Page 419
Release and Uptake of Protons in Chemolithotrophic Reactions......Page 420
Ecology......Page 421
Further Reading......Page 422
Receptors......Page 423
Chemotactic Peptide Receptors......Page 424
Effector Proteins......Page 425
Receptor Regulation......Page 426
Further Reading......Page 427
Spectroscopy......Page 428
Chemical Properties......Page 430
Spectroscopy......Page 431
Occurrence and Functions......Page 432
Glossary......Page 434
Further Reading......Page 435
The Hill Reaction......Page 436
Chloroplast Function......Page 437
Cyclic Electron Transport and Photophosphorylation......Page 438
State Transitions......Page 439
Transcriptional Control......Page 440
Mechanisms and Evolutionary Implications......Page 441
See Also The Following Articles......Page 442
Further Reading......Page 443
Envelope......Page 444
Thylakoid System......Page 445
Etioplasts......Page 446
Glossary......Page 447
Further Reading......Page 448
Diet and Lipoproteins......Page 449
Cholesterol Synthesis......Page 450
Statins......Page 452
Further Reading......Page 453
Remodeling Enzymes......Page 454
Remodeling Mechanisms......Page 455
Acetylation......Page 456
Methylation......Page 457
Ubiquitination......Page 458
Modification Crosstalk and the ‘‘Histone Code’’ Hypothesis......Page 459
Further Reading......Page 460
Posttranslational Modifications of Core Histones......Page 462
NHCPs......Page 463
Global Primary Structures-The Nucleosome Repeat Length (NRL)......Page 464
Tertiary and Higher Level Features......Page 465
Further Reading......Page 466
The Structure of Chromatin......Page 467
The Mitotic Chromosome......Page 470
Further Reading......Page 471
CoA as Donor of 4-Phosphopantetheine for Fatty Acid Synthase......Page 473
Metabolic Roles/Functions......Page 474
Further Reading......Page 475
Revised Definition of ‘‘Collagenases’’......Page 476
The Collagenases......Page 477
See Also the Following Articles......Page 478
Further Reading......Page 479
The Two Subtypes: The Fibrillar and Non-Fibrillar Collagens......Page 480
Why the Hydroxyproline......Page 483
Evolutionary Origins and Selective Pressures on (Gly-XY-)n Sequences......Page 484
Further Reading......Page 485
Identification and Properties of cAMP Receptors......Page 486
G Protein-Dependent Pathways......Page 488
G Protein-Independent Pathways......Page 489
See Also the Following Articles......Page 490
Further Reading......Page 491
Domain Structure of Class I PDEs......Page 492
C Domains of Class I PDEs......Page 493
Characteristics of cGMP-Specific Class I PDEs (PDEs 5, 6, and 9)......Page 495
Regulation of Class II PDEs......Page 496
Further Reading......Page 497
Molecular Diversity......Page 499
PDEs: Components of Spatially Organized Signaling Networks and Microdomains......Page 500
PDEs: Signal Integrators......Page 501
Glossary......Page 502
Further Reading......Page 503
Overall Structure of Cyclic Nucleotide-Dependent Protein Kinases......Page 504
PKA......Page 505
Cyclic Nucleotide-Binding Specificity and Affinity......Page 507
Negative Feedback and Feed-Forward Control of Cyclic Nucleotide Pathways......Page 508
Further Reading......Page 509
CNG Channels......Page 510
HCN Channels......Page 511
Further Reading......Page 512
Activation......Page 514
Bone Turnover......Page 516
Parasitic Proteinases......Page 517
Further Reading......Page 518
Composition and Structure......Page 519
The Rieske FeS-Protein......Page 520
Plastoquinol Oxidation - Q-Cycle and Fes-Domain Movement......Page 522
Genes, Biogenesis, and Phylogeny......Page 523
Further Reading......Page 524
Protein Subunits......Page 526
Three-Dimensional Structure of the bc1 Complex......Page 528
The Protonmotive Q Cycle......Page 529
Proton Conduction Pathways......Page 530
Inhibitors......Page 531
Further Reading......Page 532
Attachment of the Heme Prosthetic Group to Cytochrome c Apoprotein......Page 533
Evolutionary Aspects......Page 534
Cytochrome c and Apoptosis......Page 535
Further Reading......Page 536
Structures......Page 537
Oxygen Binding and Reduction......Page 539
Proton Pumping......Page 540
Further Reading......Page 541
Cytochrome P-450-General Aspects......Page 542
Structural Organization of Cytochrome P-450 Systems......Page 543
Reaction Cycle......Page 544
Regulation of Cytochrome P-450 Systems......Page 545
Further Reading......Page 546
Regulated Expression......Page 548
Cytokines and the Innate Immune Response......Page 549
Cytokines and the Adaptive Immune Response......Page 550
JAK/STAT Signaling......Page 551
Glossary......Page 552
Further Reading......Page 553
Making the Plans: Coordinating Nuclear and Cytoplasmic Division in Animal Cells......Page 554
Assembling the Parts 2: Building the Central Spindle......Page 556
Pushing the Envelope: Membrane Fusion......Page 557
Getting the Timing Right......Page 558
Further Reading......Page 559
Biosynthesis......Page 560
Conjugation......Page 561
Signal Transduction......Page 562
Cell Cycle......Page 563
Further Reading......Page 564
Structure and Molecular Components of the Desmosome......Page 566
Desmosome Assembly and Maintenance......Page 567
Desmosome Function......Page 568
Structure and Molecular Components of the Hemidesmosome......Page 569
BP180......Page 570
Conclusion......Page 572
Further Reading......Page 573
Hydrophilic Groups (Headgroups)......Page 574
Critical Micelle Concentration (CMC)......Page 575
Temperature Effects......Page 576
Membrane Proteins......Page 577
Further Reading......Page 578
Type 1 Diabetes Mellitus......Page 579
Type 2 Diabetes Mellitus......Page 580
Other Specific Types......Page 582
Acute......Page 584
Chronic......Page 585
Weight Loss and Exercise......Page 587
Further Reading......Page 588
Regulation of DGK Activity......Page 590
PA as a Signal......Page 592
Further Reading......Page 593
Disulfide Bond Formation During Protein Folding......Page 595
Catalysis of Disulfide Formation......Page 596
The Thioredoxin Family......Page 597
Disulfide Formation as a Regulatory Mechanism......Page 598
Further Reading......Page 599
DNA Base Excision......Page 600
Backbone Incision......Page 602
Base Excision Repair in Mitochondria......Page 603
Further Reading......Page 604
Alkylating Agents and Mechanism of the Reaction with DNA......Page 606
Effect of DNA Conformation on the Alkylation......Page 607
Methods of Identification of Alkyl Derivatives of Nucleic Acids......Page 608
Cytotoxic and Mutagenic Effects of Alkylation: Methylation......Page 609
Further Reading......Page 610
Structural Superfamilies of DNA Glycosylases......Page 611
Base Flipping......Page 612
Catalytic Strategies for Glycosidic Bond Hydrolysis......Page 613
Further Reading......Page 614
Primary Structures......Page 615
‘‘Open’’ And ‘‘Closed’’ Conformations......Page 616
Single-Stranded DNA Translocation by Monomers of SF1 Helicases......Page 617
Active Versus Passive Mechanisms of DNA Unwinding......Page 618
Summary......Page 619
Further Reading......Page 620
Nucleic Acid Strand Separation Activity of Helicases......Page 621
Brownian Motor Model......Page 622
Mechanisms of Nucleic Acid Strand Separation......Page 623
Ring Structure......Page 624
Nucleic Acid Binding in the Central Channel......Page 625
Mechanism and Role of NTP Hydrolysis......Page 626
Conclusion......Page 627
Further Reading......Page 628
Structure......Page 629
Domains Constituting the Core Catalytic Domain......Page 630
Biological Functions......Page 631
Genetic Recombination and Recombinational Repair......Page 632
Further Reading......Page 633
Overall Structure of DNA Ligases......Page 634
Mechanism of Nucleotidyl Transfer......Page 637
Glossary......Page 639
Further Reading......Page 640
Molecular Recognition of the Presence of the Methyl Groups on the DNA......Page 641
The Molecular Logic of DNA Methylation......Page 642
Chemistry of DNA Methylation......Page 643
Reaction Mechanism of N-MTases......Page 644
Mechanism of Base Flipping......Page 645
Mechanism of DNA Recognition......Page 646
Mechanism of Target Site Location and Processivity of DNA Methylation......Page 647
Further Reading......Page 648
Prokaryotes......Page 649
Eukaryotes......Page 650
Tertiary Structure......Page 652
Chemistry......Page 653
AdoMet and DNA Binding......Page 655
Further Reading......Page 656
Dam-Directed Mismatch Repair......Page 657
Altered Gene Expression......Page 659
See Also the Following Articles......Page 660
Further Reading......Page 661
Generalized Mismatch Repair in Eukaryotes......Page 662
Anti-Recombination Activity in Escherichia coli......Page 663
Anti-Recombination Activity in Saccharomyces cerevisae......Page 664
DNA Sequence Divergence, Mismatch Repair, Loss of Heterozygosity, and Cancer......Page 665
Evolutionary Role of the Control of Homologous Recombination by Mismatch Repair......Page 666
Further Reading......Page 667
Mismatch Repair Function is Required for Drug Cytotoxicity......Page 668
Mismatch Repair Proteins Promote DNA Damage-Induced Cell Cycle Arrest and Apoptosis......Page 669
Mismatch Repair-Mediated Apoptosis Eliminates Damaged Cells from Tumorigenesis......Page 670
Further Reading......Page 671
MutS Homologue Proteins Involved in Mismatch Repair......Page 672
Other Proteins Implicated in Mismatch Repair......Page 674
Defects in Mismatch Repair Cause Increased Cancer Susceptibility......Page 675
Glossary......Page 677
Further Reading......Page 678
Mechanism of E. coli Long-Patch Mismatch Repair......Page 679
Initiation of Mismatch Repair......Page 680
Excision and Repair Synthesis of Mismatch Repair......Page 681
MutY Repair Pathway......Page 682
Further Reading......Page 683
MutS and Some of Its Homologs Recognize Mismatches......Page 684
Orchestration of Mismatch Correction in Mammals......Page 685
How is Directional Excision Initiated and Controlled......Page 686
Further Reading......Page 687
Biochemistry of Vsr......Page 688
Structure and Biochemistry of MBD4......Page 689
Further Reading......Page 690
Oxidants and Antioxidants......Page 691
Carcinogenesis......Page 692
GO System......Page 693
Further Reading......Page 694
Primary Structure and Chromophores......Page 695
Reaction Mechanism......Page 696
See Also The Following Articles......Page 698
Further Reading......Page 699
DNA Primase Activity and Mechanisms of Primer Synthesis......Page 700
Residues Responsible for Interactions with the Metal Ion-dNTP Complex......Page 701
Checkpoint Activation......Page 702
Glossary......Page 703
Further Reading......Page 704
Pol  Domain Organization......Page 705
Lyase Domain......Page 706
Polymerase Domain......Page 707
Glossary......Page 708
Further Reading......Page 709
Processivity Factor......Page 710
Further Reading......Page 711
Biochemical Character......Page 713
Role at Replication Fork......Page 714
Glossary......Page 715
Further Reading......Page 716
Domain Structure and Relation to Other Polymerases......Page 717
Substrate Binding......Page 718
DNA Polymerase Reaction Specificity......Page 719
3-5 Exonuclease......Page 720
Glossary......Page 721
Further Reading......Page 722
DNA Polymerase II: Structure and Biochemical Functions......Page 723
Biological Function: Replication Restart......Page 724
Further Reading......Page 725
Subunits and Subassembly of Pol III Holoenzyme......Page 726
Tau-Subunit and Pol III......Page 727
Concurrent DNA Synthesis of Leading and Lagging Strands......Page 728
Further Reading......Page 730
Selectivity Contributions of Each Step......Page 731
Measurement of the Kinetics of Incorporation......Page 732
Structural Determinants of Fidelity......Page 733
Selectivity of the Proofreading Exonuclease......Page 734
Glossary......Page 735
Further Reading......Page 736
DNA Polymerase Holoenzymes......Page 737
Primosomes......Page 738
Lagging-Strand Synthesis......Page 739
Further Reading......Page 741
Replication Protein A (RPA)......Page 742
Polymerase Accessory Proteins......Page 743
Topoisomerases......Page 744
Further Reading......Page 745
Protein......Page 746
Mammalian mtDNA......Page 747
Glossary......Page 748
Further Reading......Page 749
The Generic DNA Replication Origin......Page 750
Metazoan Replication Origins......Page 752
The Origin Recognition Complex......Page 753
Regulating ORC Activity: The ORC Cycle......Page 754
Further Reading......Page 756
The E. coli Replication Origin, oriC......Page 758
DnaA Protein and the DnaA Box......Page 759
Functional Domains of DnaA Protein......Page 760
Regulation of DNA Replication in E. coli......Page 761
Interaction of DnaA with Hda and the -Subunit of DNA Polymerase III Holoenzyme......Page 762
Further Reading......Page 763
Genes and Protein Structure......Page 764
The Sequence Specificity Subunit......Page 765
Assembly and Control of the Type I Restriction Enzyme......Page 766
Cleavage of DNA......Page 767
Further Reading......Page 768
Discovery of New Restriction-Modification Systems......Page 769
Recognition Sequences......Page 770
Protein Structures......Page 771
Subsets of Type II Restriction Enzymes......Page 772
The Methyltransferase Enzymes......Page 773
Further Reading......Page 774
Substrate Requirements......Page 775
Organization of Genes and Regulation of Restriction Activity......Page 776
Other Type III RM Systems......Page 777
Further Reading......Page 778
Structure......Page 779
Biology......Page 780
Biology......Page 781
Cruciforms......Page 782
Further Reading......Page 783
Reading Heads......Page 785
The Helix-Turn-Helix Motif......Page 786
The Leucine Zipper Motif......Page 788
Diverse Structural Strategies are Employed by Proteins for DNA Recognition......Page 789
Further Reading......Page 790
Quantitative Relationship between Twist and Supercoil......Page 791
Handedness and the Sign of Tw and Wr......Page 792
Biological Effects of Supercoiling and Enzymes That Can Change DNA Supercoiling......Page 793
Further Reading......Page 794
Classification, Nomenclature and General Properties......Page 795
Protein Domains......Page 796
Reverse Gyrase Mechanism......Page 797
Crystal Structure of Human Topoisomerase I......Page 798
Cellular Roles......Page 799
Transcription......Page 800
Glossary......Page 801
Further Reading......Page 802
DNA Topoisomerases......Page 803
Enzyme Mechanism......Page 804
Enzyme Domain Structures and Isoforms......Page 805
Topoisomerase IV......Page 806
Anticancer Drugs......Page 807
Further Reading......Page 808
RecQ Helicases......Page 809
Physical Association......Page 810
The Recombination Connection......Page 811
RecQ Helicases and Human Disease......Page 812
Further Reading......Page 813
D1-Like and D2-Like Receptor Subfamilies......Page 814
Dopamine Receptor Signaling......Page 815
Dopamine Receptor Variants......Page 818
Further Reading......Page 819
Functions Associatedwith Dynein-Based Motility......Page 820
Dynein-Independent Functions......Page 821
Binding Activities......Page 822
Further Reading......Page 823
The Dynein Heavy Chain......Page 824
Cytoplasmic Dynein......Page 825
Flagellar Dyneins......Page 826
Glossary......Page 827
Further Reading......Page 828
Academic.Press,.Encyclopedia.of.Biological.Chemistry.Vol..2.(2004);.BM.OCR.7.0-2.5.pdf......Page 896
Atrial Natriuretic Peptide......Page 1738
Cover Page......Page 2585
Editors-in-Chief......Page 2519
Associate Editors......Page 2521
Preface......Page 2524
Notes on the Subject Index......Page 2525
Volume 1......Page 2526
Volume 2......Page 2534
Volume 3......Page 2542
Volume 4......Page 2550
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 2555
Metabolism, Vitamins and Hormones......Page 2557
Cell Architecture and Function......Page 2559
Protein/Enzyme Structure Function and Degradation......Page 2562
Bioenergetics......Page 2565
Molecular Biology......Page 2571
Signaling......Page 2577
Techniques and Methodology......Page 2584
Brain Natriuretic Peptide......Page 1739
Natriuretic Peptide Receptors......Page 1740
Guanylyl Cyclase-Linked Natriuretic Peptide Receptors......Page 1741
Further Reading......Page 1742
The N-End Rule Pathway......Page 1743
Further Reading......Page 1746
Using Synthetic Carbohydrate Derivatives......Page 1748
Use of Glycosyl Transferases......Page 1749
Conjugation of Glycopeptides......Page 1750
Further Reading......Page 1751
Spatial Calcium Signaling in Synapse-to-Nucleus Communication......Page 1753
NFAT and DREAM......Page 1754
Nuclear Calcium Signals......Page 1755
See Also the Following Articles......Page 1756
Further Reading......Page 1757
The Neurofilament Triplet Proteins......Page 1758
Peripherin......Page 1761
Further Reading......Page 1762
The NPY Y1 Receptor......Page 1763
The NPY Y2 Receptor......Page 1764
The NPY Y4 Receptor......Page 1765
The NPY Y5 Receptor......Page 1766
Further Reading......Page 1767
NTS1......Page 1769
NTS3......Page 1770
Neurotensin Receptor Implication in Brain Functions......Page 1771
Glossary......Page 1772
Further Reading......Page 1773
Reuptake......Page 1774
Structure and Function......Page 1775
Further Reading......Page 1776
Neurotrophin Activation of Trk Receptors......Page 1778
Neurotrophin Activation of the p75NTR Receptor......Page 1780
Interaction Between p75NTR and the Nogo Receptor......Page 1781
Further Reading......Page 1782
Structure-Function of the Substrate-Binding Domains......Page 1783
Mechanism of Hydride Transfer......Page 1785
The Proton Channel......Page 1787
Physiological Role......Page 1788
Further Reading......Page 1789
The Extracellular Domain......Page 1790
The Pore......Page 1791
Central Nervous System......Page 1792
Epilepsy......Page 1793
Further Reading......Page 1794
Nitric Oxide Synthase......Page 1795
Chemistry of NO......Page 1796
Non-cGMP NO-Signaling Pathways......Page 1797
Further Reading......Page 1798
Classification and Properties of Processing Alpha-Mannosidases......Page 1799
Class-I Golgi Alpha1,2-Mannosidases......Page 1800
Class II Golgi Alpha-Mannosidases......Page 1801
Further Reading......Page 1802
DNA-PKcs......Page 1803
Roles of NHEJ......Page 1804
Repair of Radiation Induced DSBs......Page 1805
Role in Maintaining Genomic Stability......Page 1806
Further Reading......Page 1807
Types of Transposable Elements......Page 1808
DDE Enzymes......Page 1810
Non-DDE Transposases......Page 1812
Target Choice......Page 1813
Regulation......Page 1814
Further Reading......Page 1815
Transposons......Page 1817
‘‘Cut-and-Paste’’ versus ‘‘Copy-and-Paste’’ Transposition......Page 1818
Retrotransposons......Page 1819
Site-Specific Non-LTR Retrotransposons......Page 1821
Glossary......Page 1822
Further Reading......Page 1823
PML Nuclear Bodies, ND10......Page 1824
Cajal (Coiled) Bodies and Gems......Page 1826
The Compartmentalized Nucleus......Page 1827
Further Reading......Page 1828
Lamin Genes......Page 1829
Nuclear Size......Page 1830
Proteolysis......Page 1831
Further Reading......Page 1832
Regulation of NFB Activity......Page 1833
NFAlphaB and Disease......Page 1835
Further Reading......Page 1836
Origin of Nuclear Gene Products with Functions in Mitochondria......Page 1837
Nonessential PET Genes......Page 1838
Essential PET Genes......Page 1839
Glossary......Page 1840
Further Reading......Page 1841
Establishing a Zone......Page 1842
Changes in Gene Expression Correlate with Shifting Zones......Page 1843
Glossary......Page 1844
Further Reading......Page 1845
Targeting Signals......Page 1846
Transport Receptors......Page 1847
Transport Mechanisms: RNA Trafficking......Page 1848
mRNA Export......Page 1849
Further Reading......Page 1850
DNA Supercoiling......Page 1852
The Domain Structure of the Nucleoid......Page 1853
Nucleoid-Associated Proteins......Page 1854
Further Reading......Page 1855
Amplified Nucleoli and Missing Nucleoli......Page 1856
The Plurifunctional Nucleolus......Page 1857
Further Reading......Page 1859
Types of Damage Repaired by NER......Page 1860
Excision of the Damaged Strand......Page 1861
Replication of Damaged DNA......Page 1862
Clinical Consequences of NER Deficiencies - Cancer......Page 1863
Mouse Models of NER Deficiencies......Page 1864
Glossary......Page 1865
Further Reading......Page 1866
Mechanism of Nucleotide Excision Repair......Page 1867
Damage Recognition and Transcription-Coupled Repair......Page 1868
Glossary......Page 1869
Further Reading......Page 1870
Genetics and Evolutionary Conservation of uvr Genes......Page 1871
Properties of UvrA, UvrB, and UvrC Proteins......Page 1873
Molecular Mechanism of Damage Recognition......Page 1875
Dual Incision......Page 1876
UvrD......Page 1877
Transcription-Coupled Repair......Page 1878
Further Reading......Page 1879
Distribution in Nature......Page 1880
Detection of NER in vivo and in vitro......Page 1881
Kinetics of NER......Page 1882
Further Reading......Page 1883
Olfactory Receptors Segregate in Several Highly Divergent Groups......Page 1885
Monogenic and Monoallelic Expression of Olfactory Receptor Genes......Page 1886
Olfactory Receptor Gene Expression is Regulated by Proximal and Distal Control Regions......Page 1887
Signal Transduction of Olfactory Receptors......Page 1888
Further Reading......Page 1890
Obtaining and Preparing Glycans for Mass Spectrometry......Page 1891
Instrumentation for Glycoconjugate Mass Spectrometry......Page 1892
Tandem Mass Spectrometry (MS/MS) and Sequential Mass Spectrometry (MSn)......Page 1893
Further Reading......Page 1896
Free Oligosaccharide Transport System from the Endoplasmic Reticulum to the Cytosol......Page 1897
Free Oligosaccharides Formed in the Cytosol: Its Connection with Endoplasmic-Reticulum-Associated Degradation......Page 1898
Concluding Remarks......Page 1899
Further Reading......Page 1900
Mitochondrial Biochemistry......Page 1901
Further Reading......Page 1902
Discovery of Multiple Opioid Receptors......Page 1903
Distribution and Pharmacology of Multiple Opioid Receptors......Page 1904
Opioid Ligands Selectivity for the Multiple Opioid Receptors......Page 1905
Summary and Future Direction......Page 1906
Further Reading......Page 1907
Chemistry of the Cycle......Page 1908
Physiological Aspects of the Cycle......Page 1909
Short-Term Regulation......Page 1910
Extra-Hepatic Expression of Ornithine Cycle Enzymes......Page 1911
Inborn Errors of the Ornithine Cycle......Page 1912
Further Reading......Page 1913
Dioxygenases......Page 1914
Molecular Oxygen as a Substrate......Page 1915
Biological Function of Oxygenases......Page 1916
Glossary......Page 1917
Further Reading......Page 1918
Release of ATP onto P2X Receptors......Page 1919
Activation of P2X Receptor Ion Channels (P2X1 through P2X6)......Page 1920
P2X Receptors and Sympathetic Neurotransmission (P2X1 and P2X2 Receptors)......Page 1921
P2X Receptors and Sensory Pathways (P2X3 and P2X2/3)......Page 1922
Further Reading......Page 1923
Extracellular Nucleotides as Signaling Molecules......Page 1924
Functional Classification of the P2Y Receptors......Page 1925
Important Physiological or Pathological Functions of P2Y Receptor Subtypes......Page 1926
Further Reading......Page 1927
Growth Arrest and Apoptosis......Page 1928
p53 Regulation......Page 1929
Protein-Protein Interactions......Page 1930
Further Reading......Page 1931
Roles of Nutrients and mTOR in Regulating p70 S6 Kinase......Page 1932
Mechanisms Involved in the Activation of p70 S6 Kinase......Page 1933
mTOR Signaling is Inhibited by the Immunosuppressant Drug, Rapamycin......Page 1934
mTOR Signaling Is Regulated by Hormones and Nutrients......Page 1935
Further Reading......Page 1936
PTH......Page 1937
Functional Domains of PTH(1-34) and PTHrP(1-34)......Page 1939
The Ligand Interaction Mechanism in the PPR......Page 1940
Blomstrand’s Chondrodysplasia......Page 1942
Further Reading......Page 1943
Applications......Page 1944
Further Reading......Page 1946
Shunt or Cycle......Page 1947
Methods......Page 1948
Further Reading......Page 1951
Background......Page 1952
Early Discoveries......Page 1953
Post Second World War Discoveries of Reactions in the Nonoxidative Segment of the Pentose Pathway......Page 1955
Finding a Reaction Sequence for the Nonoxidative Pentose Pathway......Page 1956
The Search for a New Reaction Scheme for the Pentose Pathway......Page 1957
Exposing the Problem of Assigning a Reaction Scheme to the Nonoxidative PP......Page 1959
Glossary......Page 1960
Further Reading......Page 1961
Peptidylglycine Alpha-Hydroxylating Monooxygenase - PHM......Page 1962
Evolutionary Relationships......Page 1964
Impaired Peptide Amidation......Page 1965
Further Reading......Page 1966
Respiratory Electron Transport Systems......Page 1967
Bacterial Periplasmic Respiratory Electron Transport Systems that are Dependent on the Cytochrome bc1 Complex......Page 1968
Periplasmic Electron Transport Systems that do not Depend on the Cytochrome bc1 Complex......Page 1969
Formate Dehydrogenase N......Page 1970
Nitrate Reductase A......Page 1971
Multi-Heme c-Type Cytochromes......Page 1972
Synthesis of Periplasmic Electron Transport Systems......Page 1973
Further Reading......Page 1974
Peroxisome Proliferator-Activated Receptors......Page 1975
PPAR (NR1C1)......Page 1976
PPAR (NR1C3)......Page 1979
PPAR (NR1C2)......Page 1980
Further Reading......Page 1981
Functions of Peroxisomes......Page 1982
Peroxisomal Matrix Protein Import......Page 1983
Glossary......Page 1985
Further Reading......Page 1986
Phagemid Vectors......Page 1987
Construction of Libraries......Page 1988
Design of Diversity Libraries......Page 1989
Phage-Binding Analysis......Page 1990
Further Reading......Page 1991
Pheromone Receptors Stimulate a Signal Transduction Pathway......Page 1992
Pheromone Receptor Synthesis Requires the Secretory Pathway......Page 1994
Pheromone Receptors Bind Ligand via Contacts with the Extracellular Ends of the Transmembrane Segments......Page 1995
Pheromone Receptors Promote G-Protein Activation via the Third Intracellular Loop......Page 1996
Further Reading......Page 1997
The PHO Genes and their Regulation......Page 1998
Further Reading......Page 2001
Synthesis......Page 2002
Hydrolysis......Page 2003
Cellular Function......Page 2004
PtdIns-3,4,5-P3-Binding Proteins......Page 2005
Cellular Function......Page 2006
Further Reading......Page 2007
Dephosphorylation of PtdIns(3)P......Page 2008
Protein Domains that Bind to PtdIns(3)P......Page 2009
PtdIns(3)P in Phagocytosis and Bacterial Invasion......Page 2010
Further Reading......Page 2011
Enzymology of PFK-2......Page 2013
Regulation and Physiological Roles of Specific Isoforms in Specific Tissues......Page 2014
Glossary......Page 2015
Further Reading......Page 2016
Activation and Regulation of PI 3-Kinases......Page 2017
Class I PI 3-Kinases......Page 2018
Signaling Downstream of PI 3-Kinases......Page 2020
Inflammatory Disease......Page 2021
Further Reading......Page 2022
Cellular Functions......Page 2023
Type II PIP Kinases......Page 2024
Type III PIP Kinases......Page 2025
Phosphoinositide 5-Phosphatases......Page 2026
Further Reading......Page 2027
Protein Kinase B/Akt......Page 2028
PDK1 and the Regulation of the AGC Kinases......Page 2029
Regulators of Cellular Growth - mTOR and S6K1......Page 2030
Further Reading......Page 2031
PLA2 Enzymes Using a Catalytic Histidine (sPLA2s)......Page 2033
PLA2 Enzymes Utilizing a Catalytic Serine......Page 2034
Further Reading......Page 2035
Structure of PLC......Page 2037
PLC-Beta......Page 2038
PLC-Gamma......Page 2039
See Also the Following Articles......Page 2040
Further Reading......Page 2041
PLD Structure......Page 2042
Regulation of Mammalian Phospholipase D......Page 2043
Biophysical role......Page 2046
Mammals......Page 2047
Further Reading......Page 2048
Diacylglycerophospholipids......Page 2050
Biosynthesis of Ether Glycerophospholipids......Page 2053
Glossary......Page 2055
Further Reading......Page 2056
CDP-DAG Pathway......Page 2057
CDP-Choline and CDP-Ethanolamine (Kennedy) Pathways......Page 2058
Regulation of Phospholipid Synthesis......Page 2059
Biochemical Regulation......Page 2060
Further Reading......Page 2061
Phototransduction......Page 2062
Pineal Photoreceptors......Page 2064
Further Reading......Page 2065
Energy Capture......Page 2066
Electron Transport and ATP Synthesis......Page 2067
Benson-Calvin Cycle......Page 2068
C4 Photosynthesis......Page 2069
Further Reading......Page 2070
Carboxylation Phase......Page 2072
Regeneration Phase......Page 2073
Regulation of the Calvin Cycle......Page 2074
Direct Targeting of Calvin Cycle......Page 2075
Glossary......Page 2076
Further Reading......Page 2077
Function of PS I......Page 2078
The Proteins......Page 2079
The Electron Transport Chain......Page 2080
The Antenna System......Page 2081
Further Reading......Page 2083
Photosystem I: The Best-Studied Type I Reaction Center......Page 2084
Geometry and Oxidation States......Page 2085
FX, the Interpolypeptide [4Fe-4S] Cluster Bound by PsaA and PsaB......Page 2087
FA and FB, the [4Fe-4S] Clusters Bound by PsaC......Page 2088
Resolution of the Sequence of Electron Transfer: FX>FA>FB......Page 2089
Further Reading......Page 2091
Structure and Function of LHCII......Page 2093
The Need for Control of the Light Reactions of Photosynthesis......Page 2094
Energy-Dependent Quenching, qE......Page 2095
The Nature of the Quenched State of LHCII......Page 2096
See Also the Following Articles......Page 2097
Further Reading......Page 2098
Cooperation Between Chloroplast and Nucleus......Page 2099
PSII Photoinactivation and the D1 Protein Damage......Page 2100
PSII Photoinhibition Repair Cycle......Page 2101
Further Reading......Page 2102
QA......Page 2103
PsbC-CP43......Page 2104
PsbE and PsbF......Page 2105
PsbH......Page 2106
PsbO......Page 2107
PsbV......Page 2108
Further Reading......Page 2109
The Photosystem II Complex......Page 2111
The Water Splitting Enzyme......Page 2112
The Redox Potential of the Different S States......Page 2113
The Mechanism of Water Oxidation......Page 2114
Glossary......Page 2115
Further Reading......Page 2116
Tomato and Tobacco Hydroxyproline-Rich Glycosylated Defense Signals......Page 2117
CLAVATA3......Page 2118
Concluding Remarks......Page 2119
Further Reading......Page 2120
Plasma-Membrane Calcium Pump Structure......Page 2121
Mechanistic Aspects......Page 2122
Regulation......Page 2123
Glossary......Page 2124
Further Reading......Page 2125
The Structure of Cyt f......Page 2126
The Structure of PSI......Page 2127
Involvement of The PsaF Subunit in Electrostatic Interaction Between PC and PSI in Higher Plants and Green Algae......Page 2128
Further Reading......Page 2129
Platelet-Activating Factor......Page 2130
PAF Receptor Structure......Page 2131
PAF Receptor Signal Transduction......Page 2133
Further Reading......Page 2134
PDGF Receptors......Page 2135
Proteins Associated with the PDGF Receptors and PDGF-Driven Signaling Pathways......Page 2136
Proliferation......Page 2137
Chemotaxis......Page 2139
Dephosphorylation by PTPs......Page 2140
Further Reading......Page 2141
Polysialic Acid inMolecular Medicine......Page 2143
Embryonic and Adult Forms of N-CAM......Page 2144
Expression and Function of Polysialic Acid on Extraneural Cells......Page 2145
Prokaryotic-Derived Reagentsfor the Detection and Analysisof PolySia......Page 2146
Evidence for the Role of Polysialic Acid in Cancer Metastasis......Page 2147
Rationale for Chemotherapeutic Inhibition of PolySia Biosynthesis......Page 2148
Further Reading......Page 2149
-Aminolevulinic Acid to Uroporphyrinogen III......Page 2151
Heme and Chlorophyll Biosynthesis......Page 2152
Regulation......Page 2153
Herbicides......Page 2154
Further Reading......Page 2155
Enzymatic Processing of tRNA Precursors......Page 2156
Primary Processing......Page 2157
Generation of Mature rRNAs......Page 2158
Processing Differences among Various Bacterial Species......Page 2159
Further Reading......Page 2160
Removal of Precursor-Specific Sequences......Page 2161
Changes in Nucleotide Sequence of the Mature Domain......Page 2162
Removal of the Spacer Regions......Page 2163
Further Reading......Page 2167
Prion Domains and Functional Domains......Page 2168
Yeast, Fungal Prions [PSI+], [URE3], and [Het-s] are Self-Propagating Amyloidoses......Page 2169
Prion Generation......Page 2170
Chaperones and Prion Propagation......Page 2171
Further Reading......Page 2172
Replication Cycle......Page 2173
Physiopathology of Prion Diseases......Page 2174
Glossary......Page 2175
Further Reading......Page 2176
Processivity Clamp Loaders......Page 2177
E. Coli Clamp Loader, Gama-Complex......Page 2178
See Also the Following Articles......Page 2181
Further Reading......Page 2182
Propionyl CoA Carboxylase......Page 2183
Propionic Acidemia/Aciduria (PA)......Page 2184
Further Reading......Page 2186
PGHS Catalysis and Inhibition......Page 2188
PGHS-1 and PGHS-2 Gene Expression......Page 2189
5-Lipoxygenase Activating Protein (FLAP)......Page 2190
Leukotriene Metabolism......Page 2191
Further Reading......Page 2192
The Role of Thrombin......Page 2193
Similarity to Trypsin......Page 2195
Further Reading......Page 2198
Subunit Composition......Page 2200
Structure......Page 2201
The 19S Regulator and its Subcomplexes......Page 2202
Glossary......Page 2203
Further Reading......Page 2204
The 26S Proteasome......Page 2205
Physiological Importance......Page 2206
REGs or PA28s......Page 2207
PA200......Page 2208
Further Reading......Page 2209
Introduction......Page 2210
Ras-Related and Heterotrimeric G Protein......Page 2211
Protein Phosphatase 2A......Page 2212
Further Reading......Page 2213
Primary Data Acquisition - The PDB......Page 2214
Data Dissemination......Page 2215
Secondary Sources......Page 2216
Data Reduction......Page 2217
The Future......Page 2218
Further Reading......Page 2219
Endocytic-Lysosomal Pathway......Page 2220
Lysosomes......Page 2221
Ubiquitin-Proteasome Pathway......Page 2222
Ubiquitin Conjugation......Page 2223
Protein Degradation......Page 2224
Proteolysis in Mitochondria......Page 2226
Selection of Substrates......Page 2227
Further Reading......Page 2228
Levinthal’s Paradox......Page 2229
Folding Intermediates......Page 2230
More Complex Folding Reactions......Page 2231
Disulfide-Coupled Folding......Page 2232
Assembly of Oligomeric Proteins......Page 2233
Protein Folding Pathologies......Page 2234
Further Reading......Page 2235
Mechanism of Action of Glycosylation Inhibitors......Page 2236
Mechanism of Action and Effect of Glycoprotein Processing Inhibitors......Page 2237
Further Reading......Page 2239
The Protein Carbohydrate Linkage......Page 2240
O-Linked Glycosylation......Page 2241
Protective......Page 2243
Glossary......Page 2244
Further Reading......Page 2245
Transport to and Across the Outer Membrane......Page 2246
The TOM Translocase......Page 2247
The TIM23 Complex......Page 2248
Protein Folding and Assembly......Page 2249
Further Reading......Page 2250
The PI3K/PKB Signaling Pathway......Page 2252
Apoptosis and Cell Survival......Page 2254
Regulation of proliferation......Page 2256
Further Reading......Page 2257
Protein Kinase C Phosphorylation......Page 2259
Protein Kinase C Translocation......Page 2260
Protein Kinase C Signaling......Page 2261
Further Reading......Page 2262
Function of N-Myristoylation......Page 2263
Reaction Mechanism......Page 2264
Therapeutics......Page 2265
Further Reading......Page 2266
Palmitoyltransferases......Page 2268
Palmitoylation and Protein Function......Page 2269
Further Reading......Page 2270
Intracellular PTPs......Page 2272
Involvement of PTPs in Mammalian Biology and Disease......Page 2273
PTPs as Drug Targets......Page 2276
Further Reading......Page 2277
Agonist Peptides......Page 2279
Northern Blot Analysis......Page 2280
In SituHybridization to Detect Receptor mRNA......Page 2281
Tissue Bioassays (Contraction or Relaxation)......Page 2282
See Also the Following Articles......Page 2283
Further Reading......Page 2284
Glycosaminoglycans......Page 2285
Secreted And Matrix Proteoglycans......Page 2287
Membrane-Bound Proteoglycans......Page 2289
Glossary......Page 2290
Further Reading......Page 2291
Distribution of Pterins in Nature......Page 2292
The Aromatic Amino Acid Hydroxylases (AAHs)......Page 2293
Molybdopterin-Containing Enzymes......Page 2294
Tetrahydrobiopterin and Human Disease......Page 2295
Further Reading......Page 2296
General Structure of Group IB P-Type ATPases......Page 2297
Physiological Roles......Page 2298
Regulation......Page 2299
Further Reading......Page 2300
The Alpha-Subunit of Gastric H+, K+-ATPase......Page 2301
The Beta-Subunit of Gastric H+, K+-ATPase......Page 2302
Kinetics and Conformational Changes of the Gastric H+, K+-ATPase......Page 2303
Functional Residues of the H+, K+-ATPase......Page 2304
See Also the Following Articles......Page 2305
Further Reading......Page 2306
E1- and E2-Conformations of the Na+/K+ Pump......Page 2307
Na+/K+ Pumps in Epithelial Cells of Kidney, Intestine, Lung, and Glands......Page 2309
Na+/K+ Pump Isoform Expression and Regulation in Muscle and Central Nervous System......Page 2310
Further Reading......Page 2311
Structure......Page 2313
Reaction Mechanism......Page 2314
Biogenesis......Page 2315
Regulation......Page 2316
Further Reading......Page 2317
Reaction Center......Page 2318
Properties of Reaction Center Cofactors......Page 2319
Ubiquinol-Cytochrome c Oxidoreductase (Cytochrome bc1 Complex)......Page 2320
Further Reading......Page 2321
Subunit Composition and Molecular Characterization......Page 2322
Kinetics......Page 2325
Mutants......Page 2326
Quinone Reduction and Protonation......Page 2328
Cytochrome c2 Oxidation......Page 2329
Further Reading......Page 2330
The Variety of PLP-Dependent Reactions......Page 2331
Chemical Mechanisms......Page 2333
Further Reading......Page 2334
Regulation......Page 2336
Deficiency and Interference......Page 2337
Formation of Cytidine and Thymidine Nucleotides......Page 2338
Regulation......Page 2339
Deficiency and Interference......Page 2340
Further Reading......Page 2341
Control of Gluconeogenesis......Page 2342
Control by Substrate Supply......Page 2344
Breakdown of Amino Acids in Muscle and the ‘‘Glucose-Alanine Cycle’’......Page 2345
Further Reading......Page 2346
Components and Structure of PDH......Page 2347
Role of PDH in Metabolism......Page 2348
Regulation of Activity by Phosphorylation......Page 2349
Extrinsic Regulation of PDH......Page 2350
Further Reading......Page 2351
Phosphorylation/Dephosporylation......Page 2352
Crystallographic Studies......Page 2353
Regulation of ChREBP in Response to Glucose and cAMP......Page 2354
Further Reading......Page 2355
Chemistry and Distribution......Page 2356
Functions of Coenzyme Q......Page 2358
Biological Naphthoquinones: Menaquinone and Vitamin K......Page 2361
Further Reading......Page 2362
Primary Structure and Evolution......Page 2363
Cellular Localization......Page 2364
Functional Cycle......Page 2365
Rabs and Diseases......Page 2366
Further Reading......Page 2368
The Cellular Gradient of RanGTP......Page 2369
Nuclear Transport......Page 2370
Regulation of Spindle and Nuclear Envelope Assembly at Mitosis......Page 2372
Further Reading......Page 2373
The GDP/GTP Cycle and Ras Mutations......Page 2374
H-, K-, and N-Ras......Page 2375
Rap1 and 2......Page 2376
Other Ras Family Members......Page 2377
Further Reading......Page 2378
RecA Strand Transfer......Page 2379
Mismatch Repair Mediates Heteroduplex Formation......Page 2380
Glossary......Page 2381
Further Reading......Page 2382
Structure......Page 2383
Three-Strand Exchange Reaction......Page 2384
Mediator Proteins......Page 2385
Further Reading......Page 2386
RDR Pathways in Bacteriophage......Page 2388
Demonstration of RDR in Escherichia coli and Yeast......Page 2389
RDR as a Backup Mechanism to Complete DNA Replication......Page 2390
Replication Fork Failure and Direct Restart Pathways......Page 2391
Further Reading......Page 2393
Bloom Syndrome......Page 2394
Functional Clues Provided by In vitro Studies......Page 2395
Potential Functions for recQ Helicases in Replication-Associated DNA Repair......Page 2396
Glossary......Page 2397
Further Reading......Page 2398
Sterol Regulatory Element-Binding Proteins (SREBPs)......Page 2399
ATF6 and RseA......Page 2401
Amyloid Precursor Protein (APP)......Page 2402
Rip Mediated by Rhomboid......Page 2403
Further Reading......Page 2404
Complex I (NADH-Ubiquinone Oxidoreductase)......Page 2405
Complex IV (Ferrocytochrome c - Oxygen Oxidoreductase or Cytochrome c Oxidase)......Page 2406
Other Ubiquinol Oxidizing Enzymes (The Alternative Oxidase)......Page 2407
Mechanism of ATP Synthesis......Page 2408
Further Reading......Page 2409
Assembly Factors......Page 2410
The Hydrogenase Module......Page 2411
Proton Pumping......Page 2412
Poisoning of Complex I......Page 2413
Further Reading......Page 2414
Structural Classification......Page 2415
Overall Description of the Structure......Page 2416
The Integral Membrane Subunit(s) C (and D) and the Sites of Quinol Oxidation/Quinone Reduction......Page 2418
Electron Transfer......Page 2419
Glossary......Page 2420
Further Reading......Page 2421
Background......Page 2422
Prosthetic Groups......Page 2423
Protein Structure......Page 2424
Proton Transfer Pathways......Page 2425
The Catalytic Cycle and Proton Pumping......Page 2426
Further Reading......Page 2428
Electron Transport Chains......Page 2429
Genetic Regulation of Respiration and Photosynthesis in Facultative Phototrophs......Page 2430
Electron Transport Pathways in Oxygenic Phototrophs......Page 2431
Further Reading......Page 2433
The RB Tumor Suppressor......Page 2434
The Rb Pathway......Page 2435
Glossary......Page 2436
Further Reading......Page 2437
Retinoic Acid-Binding Domain......Page 2438
Retinoic Acid Receptor Function......Page 2439
Glossary......Page 2440
Further Reading......Page 2441
Retrovirus Genome......Page 2442
Activities Associated with the Reverse Transcriptase......Page 2443
Fidelity......Page 2444
The Role of RT in Reverse Transcription......Page 2445
See Also the Following Articles......Page 2446
Further Reading......Page 2447
GTPase-Activating Proteins......Page 2448
Rho Effectors......Page 2449
Rac Effectors......Page 2450
Cell Migration......Page 2451
Further Reading......Page 2452
Assembly of Bacterial Ribosomes in vitro......Page 2453
Synthesis, Modification, and Processing of rRNA......Page 2454
Ribosome Assembly......Page 2456
See Also the Following Articles......Page 2457
Further Reading......Page 2458
Fundamental Activities of the Ribosome......Page 2459
Distinguishing Structural Features of the Ribosome......Page 2460
Struggling with Ribosome Structure......Page 2461
General Features of Ribosomal Architecture Revealed from the Subunit Structures......Page 2462
High-Resolution Structure of the Small Subunit......Page 2463
Medium-Resolution Structure of the 70S Ribosome......Page 2464
Further Reading......Page 2465
Chemical Structure of RNA......Page 2467
Ribonuclease P......Page 2468
Small Ribozymes that do not Require Divalent Metals......Page 2469
Further Reading......Page 2471
Secondary Structure......Page 2472
The Guanosine-Binding Site......Page 2473
Helix P1 and 5 Splice-Site Recognition......Page 2474
Further Reading......Page 2476
Tertiary Structure......Page 2477
Comparison with Other Ribozymes......Page 2479
Further Reading......Page 2480
Classes of Natural Ribozymes......Page 2481
Unnatural Ribozymes......Page 2483
SELEX......Page 2485
Further Reading......Page 2486
RNA Substrates that Undergo A-to-I Editing......Page 2487
Adenosine Deaminases that Act on RNA......Page 2488
Editosome Complex......Page 2489
Substitution Editing of Viral RNAs......Page 2490
Roles of RNA Editing......Page 2491
Further Reading......Page 2492
The RNA Polymerase Molecules......Page 2493
Alu Genes and Retrotransposition......Page 2494
Glossary......Page 2495
Further Reading......Page 2496
Structure and Catalytic Activity of RNA Polymerase II......Page 2497
Roles of the Basal Factors in Transcription Initiation by Pol II......Page 2498
Further Reading......Page 2499
Elongation Maintenance Factors......Page 2500
N-TEFs and Termination Factors......Page 2501
Integration of Elongation Control and Gene Expression......Page 2502
Further Reading......Page 2503
Transcription Cycle......Page 2504
Initiation......Page 2505
Elongation......Page 2506
Glossary......Page 2507
Further Reading......Page 2508
Transcription Initiation......Page 2509
Transcription Elongation......Page 2511
Transcription Termination......Page 2512
Further Reading......Page 2513
Structure of the Core Enzyme......Page 2515
Structure of the Holoenzyme......Page 2516
Structure of a Single Subunit Phage RNAP......Page 2517
Further Reading......Page 2518
Repetitive Secondary Structure: The -Helix......Page 2586
Cover Page......Page 3088
Editors-in-Chief......Page 3022
Associate Editors......Page 3024
Preface......Page 3027
Notes on the Subject Index......Page 3028
Volume 1......Page 3029
Volume 2......Page 3037
Volume 3......Page 3045
Volume 4......Page 3053
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 3058
Metabolism, Vitamins and Hormones......Page 3060
Cell Architecture and Function......Page 3062
Protein/Enzyme Structure Function and Degradation......Page 3065
Bioenergetics......Page 3068
Molecular Biology......Page 3074
Signaling......Page 3080
Techniques and Methodology......Page 3087
Repetitive Secondary Structure: The 310-Helix......Page 2587
Repetitive Secondary Structure: The Polyproline II Helix (PII)......Page 2588
Programs to Identify Structure from Coordinates......Page 2589
Neural Networks......Page 2590
Further Reading......Page 2591
Beta-Secretase......Page 2592
Gama-Secretase......Page 2594
Further Reading......Page 2595
Soluble and Integral Membrane Proteins......Page 2596
Chaperones and the ER Quality Control System......Page 2597
Vesicular Transport between the ER and Golgi......Page 2598
Protein Localization in the ER......Page 2599
Protein Exit from the Golgi......Page 2600
Further Reading......Page 2601
Selenocysteine Biosynthesis......Page 2602
Formation of the SelBx GTPxSelenocysteyl-tRNAx SECIS Complex......Page 2603
Archaeal and Eukaryal Selenoprotein Synthesis......Page 2605
Further Reading......Page 2606
Septins Bind Guanine Nucleotide and Form Complexes and Filaments......Page 2607
Septin Filaments Can Form Higher-Order Assemblies......Page 2608
Septins Interact with Inositol Phospholipids......Page 2609
Metazoa......Page 2610
Further Reading......Page 2611
Three-Dimensional Structures......Page 2612
Interaction of PP1 with Diverse Regulatory Subunits......Page 2613
PP5......Page 2614
PPP Family......Page 2615
See Also The Following Articles......Page 2616
Further Reading......Page 2617
Serotonin Receptors that Inhibit Adenylyl Cyclase......Page 2618
Serotonin Receptors Linked to Activation of Adenylate Cyclase......Page 2619
RNA Editing Produces Multiple Functional 5-HT2C Receptor Isoforms......Page 2620
Summary: Potential Role of Receptor Diversity......Page 2621
Further Reading......Page 2622
Cell-Type Specific Expression......Page 2623
Known and Putative Functions of the Siglecs......Page 2624
Further Reading......Page 2625
Bacterial RNA Polymerase and the Transcription Cycle......Page 2626
Biochemical Properties......Page 2627
Phylogenetic Distribution......Page 2628
Further Reading......Page 2629
Clamp Structure and Function......Page 2630
Clamp Loader Structure......Page 2631
Further Reading......Page 2632
The Small GTPase Cycle and Its Regulation......Page 2633
Small GTPase Structure......Page 2636
Ras Proteins as Signaling Nodes and Regulators of Cell Proliferation......Page 2637
Further Reading......Page 2639
Somatostatin Receptor Subtypes......Page 2640
Somatostatin Receptor Structure......Page 2641
Pharmacology of Somatostatin Receptor Subtypes......Page 2642
Somatostatin Receptor Signaling......Page 2643
Further Reading......Page 2644
SPG7/Paraplegin......Page 2646
SPG10/KIF5A......Page 2648
SPG20/Spartin......Page 2649
Myelin-Associated Genes......Page 2650
Further Reading......Page 2651
Dual-Wavelength Technology......Page 2652
Photochemical Action Spectra......Page 2653
Control Of Respiration......Page 2654
The Ruby Laser and Electron Tunneling......Page 2655
NADH as an Oximeter......Page 2656
NIR Imaging......Page 2657
Brain Functional Activation......Page 2658
Glossary......Page 2659
Further Reading......Page 2660
More Complex Phospho- and Glyco-Sphingolipids......Page 2661
Serine Palmitoyltransferase......Page 2662
Dihydroceramide Desaturase......Page 2663
Glycosphingolipids......Page 2664
Glossary......Page 2665
Further Reading......Page 2666
Neutral Sphingomyelinase (nSMase)......Page 2667
Neutral Ceramidase......Page 2668
Glycosphingolipid Catabolism......Page 2669
Arylsulfatase A......Page 2670
Beta-Glucocerebrosidase......Page 2671
Further Reading......Page 2672
Splicing Takes Place via Consecutive Transesterification Reactions......Page 2673
Spliceosome Assembly and the Splicing Cycle......Page 2674
Why is the Spliceosome so Complex......Page 2675
Glossary......Page 2676
Further Reading......Page 2677
History of Src......Page 2678
Other Vertebrate Src Family Kinases: Redundant and Specific Functions......Page 2679
Regulation of Src Kinase Activity......Page 2680
Summary: Integration of Many Inputs and Regulation of Many Outputs......Page 2682
Further Reading......Page 2683
Background......Page 2684
Obesity and Starvation, and Clinical Features of Starvation......Page 2685
Weight Loss, Body Composition, and Energy Requirements......Page 2686
The Nature and Quantity of Fuels Oxidized during Starvation......Page 2687
Changes in the Concentration of Substrates and Hormones in the Blood......Page 2688
Hormonal Changes......Page 2689
Control of Fatty Acid Release During Starvation......Page 2690
Proteolysis and Amino Acid Metabolism......Page 2691
Ketogenesis......Page 2692
Urinary Nitrogen Excretion......Page 2693
Fuel Consumption during Starvation......Page 2694
Further Reading......Page 2695
Overview of Nuclear Receptor Ligands and Mechanism of Action......Page 2696
Receptor Structure......Page 2697
Receptor Binding to DNA......Page 2698
Steroid Receptor Coregulators......Page 2699
Functional Interactions between Nuclear Receptors and Signal-Regulated Transcription Factors......Page 2700
Further Reading......Page 2701
Characteristics of SOCE......Page 2702
Molecular Candidates for SOCC......Page 2703
Conformational Coupling......Page 2704
Ca2+ Signaling Microdomains......Page 2705
Further Reading......Page 2707
Catalysis......Page 2708
Free-Energy Profiles......Page 2709
Rate-Limiting Steps for V......Page 2710
Further Reading......Page 2711
Structure of Golgi Nucleotide Sugar Transporters......Page 2712
Topography of Nucleotide Sugar Transporters in the Golgi Membrane......Page 2713
Further Reading......Page 2714
Conjugation......Page 2715
Deconjugation......Page 2717
See Also the Following Articles......Page 2718
Further Reading......Page 2719
The Cu, Zn SODs......Page 2720
E. coli......Page 2721
See Also the Following Articles......Page 2722
Further Reading......Page 2723
Interaction of ZAP-70 with the TCR ITAM......Page 2724
Tyrosine Phosphorylation of ZAP-70......Page 2726
Tyrosine Phosphorylation of Syk......Page 2727
T Lymphocyte Development......Page 2728
ZAP-70 and Syk in Integrin-Mediated Functions......Page 2729
Further Reading......Page 2730
Similarities to Other Polymerases......Page 2731
Promoter Release and Elongation......Page 2733
Regulation......Page 2734
Further Reading......Page 2735
SP......Page 2736
Full-Length SPR......Page 2737
Role of the Carboxyl-Tail in SPR Function......Page 2739
SPR in Emesis......Page 2740
Further Reading......Page 2741
T1R Receptors......Page 2742
Transduction Cascades......Page 2744
Further Reading......Page 2745
T Cell Antigen Receptor......Page 2746
Invariant Chains: CD3, CD247, and Pre-TAlpha......Page 2749
Cell Biology......Page 2750
Further Reading......Page 2751
PH Domain......Page 2753
Tec Family Kinase Functions......Page 2754
Tec Family Kinases in Signal Transduction......Page 2755
Further Reading......Page 2756
Telomeric DNA......Page 2758
Telomerase......Page 2759
Telomere Proteins......Page 2760
A Negative Regulatory Loop Stabilizes Telomere Length......Page 2761
See Also the Following Articles......Page 2762
Further Reading......Page 2763
The Luteinizing Hormone Receptor......Page 2764
Extracellular Domains......Page 2765
Naturally Occurring Mutations of the Glycoprotein Hormone Receptors......Page 2768
Further Reading......Page 2769
Peripheral Membrane Proteins......Page 2771
Glossary......Page 2772
Further Reading......Page 2773
MyD88-Dependent Signaling Pathway......Page 2774
Structural and Functional Homologues of TLRs......Page 2776
Further Reading......Page 2778
Intrinsic Termination......Page 2779
Rho-Mediated Termination......Page 2780
Regulated Termination and Antitermination......Page 2781
Further Reading......Page 2782
Budding Yeast, S. cerevisiae......Page 2784
Metazoans......Page 2786
Further Reading......Page 2787
E. coli......Page 2788
Alkylation Damage......Page 2790
Oxidative Damage......Page 2791
Further Reading......Page 2792
Receptor-Ligand Interactions......Page 2793
Accessory Receptors......Page 2794
Receptor Activation......Page 2795
See Also The Following Articles......Page 2796
Further Reading......Page 2797
The Three Basic Reactions of Elongation......Page 2798
The Hybrid Site Model......Page 2799
Selection of the Ternary Complex: Decoding and A Site Occupation......Page 2801
An Additional Role of EF-Tu......Page 2802
Peptide-Bond Formation......Page 2803
Translocation......Page 2806
Further Reading......Page 2807
The Traditional Elongation Cycle: The A and P Sites......Page 2808
Molecular Mimicry......Page 2810
Influence of Other Sites......Page 2811
Glossary......Page 2812
Further Reading......Page 2813
The Translation Initiation Region of Prokaryotic mRNAs......Page 2814
Initiation Complex Formation......Page 2815
IF1......Page 2816
IF2......Page 2817
IF3......Page 2818
Further Reading......Page 2820
Recruitment of Initiator tRNA to the 40S Ribosomal Subunit......Page 2821
Attachment of 43S Preinitiation Complexes to mRNA......Page 2822
Regulation of Translation Initiation......Page 2824
Further Reading......Page 2825
Prokaryotic Polypeptide Chain Release Factors......Page 2826
Eukaryotic Chain Release Factors......Page 2827
Bypassing Stop Codons: The Causes and Consequences......Page 2829
Further Reading......Page 2830
Structural Features......Page 2831
Lesion Bypass Specificity......Page 2832
Cellular Role(s)......Page 2833
Further Reading......Page 2834
Occurrence of Trehalose in the Biological World......Page 2835
As a Stabilizer and Protectant of Proteins and Membranes Against Various Stresses......Page 2836
Glossary......Page 2838
Further Reading......Page 2839
History of the Discovery of the TCA Cycle......Page 2840
Into the Wilderness and Back Again......Page 2842
The TCA Cycle Today......Page 2843
Glossary......Page 2845
Further Reading......Page 2846
tRNAs......Page 2847
tRNA Dependent Amidation......Page 2848
Novel Functions of tRNA Synthetases......Page 2849
Further Reading......Page 2850
Attenuation Control of the E. coli trp Operon......Page 2851
The B. subtilis trp Leader......Page 2853
The Role of Pausing in TRAP Mediated Attenuation......Page 2854
Further Reading......Page 2855
Physical Properties......Page 2856
Tubulin Polymerization......Page 2857
Gamma-Tubulin and Microtubule Nucleation......Page 2858
Further Reading......Page 2859
Expression......Page 2861
TRAF Signaling......Page 2862
Death Receptor Signaling......Page 2864
Costimulation......Page 2865
Further Reading......Page 2866
2D PAGE in the Future......Page 2868
Second Dimension: SDS-PAGE......Page 2869
Applications of 2D PAGE......Page 2870
Differential Analysis......Page 2871
Further Reading......Page 2872
The Yeast Two-Hybrid System......Page 2874
Advanced Applications......Page 2875
Role in Proteomics......Page 2876
Further Reading......Page 2877
The Tyrosine Sulfation Reaction......Page 2878
Properties of TPST......Page 2879
TPST-1- and TPST-2-Deficient Mice......Page 2880
Further Reading......Page 2881
Degradation......Page 2882
Substrate Recognition......Page 2883
Diseases......Page 2884
Drug Development......Page 2885
Further Reading......Page 2886
Proteins Modified by Sentrin......Page 2887
Rub1/NEDD8 Modification of CDC53/Cullins......Page 2889
Further Reading......Page 2890
The Discovery of Pol V......Page 2891
The Fidelity of Pol V......Page 2892
In vivo Function of Pol V......Page 2893
Eukaryotic Homologues of Pol V......Page 2894
Further Reading......Page 2895
Brown Adipose Tissue and UCP1: History of a True Respiration Uncoupling......Page 2896
Respiration Uncoupling is the Thermogenic Mechanism in Brown Adipocytes......Page 2897
The Novel UCPs......Page 2898
Role and Function of UCPs other than UCP1: A Role in Controlling the Level of Reactive Oxygen Species......Page 2899
UCP1, UCP2, and UCP3, Conclusions and Perspectives......Page 2900
Further Reading......Page 2901
Physiological and Pathological ER Stress......Page 2902
Unconventional Splicing of HAC1 mRNA......Page 2903
Conservation of the IRE1 Pathway......Page 2904
PERK Couples ER Stress to eIF2 Phosphorylation and Translational Repression......Page 2905
Gene Expression, eIF2 Phosphorylation and Integration of Signals in the UPR, and Other Stress Pathways......Page 2906
See Also the Following Articles......Page 2907
Further Reading......Page 2908
Urea Cycle Defects......Page 2909
Other Hyperammonemia States due to Amino Acid Transporter Defects......Page 2910
Long-Term Management......Page 2912
Further Reading......Page 2913
Vacuole Function in Yeast......Page 2914
Vacuole Biogenesis and Transport Pathways to the Vacuole in Yeast......Page 2915
Cytoplasm to Vacuole Transport and Macro-Autophagy......Page 2916
Glossary......Page 2918
Further Reading......Page 2919
VEGFR-2......Page 2920
VEGF Structure and Receptor Binding......Page 2921
Coreceptors......Page 2922
Signal Transduction Cascades......Page 2923
Nonmitogenic Functions......Page 2924
Further Reading......Page 2925
The Functions of Vasopressin and Oxytocin......Page 2926
Vasopressin and Oxytocin Receptors......Page 2930
Further Reading......Page 2931
Function of Plasma Membrane V-ATPases......Page 2932
V-ATPase Structure......Page 2933
Glossary......Page 2935
Further Reading......Page 2936
The Chemistry of atROH Generation, Storage, and Metabolic Activation......Page 2937
Retinoid Binding-Proteins and their Contributions to Retinoid Homeostasis......Page 2938
Control of Vitamin A Homeostasis......Page 2941
Further Reading......Page 2942
B12-Derivatives in Electron Transfer Reactions......Page 2943
Organometallic Reactions of B12-Derivatives......Page 2944
Coenzyme B12-Dependent Enzymes......Page 2946
Further Reading......Page 2948
Chemistry......Page 2950
Nutritional and Biochemical Importance......Page 2951
Defining Ascorbic Acid Status......Page 2952
Glossary......Page 2953
Further Reading......Page 2954
The N-Terminal DNA-Binding Domain (DBD)......Page 2955
Ligand-Binding Domain (LBD)......Page 2956
VDR Interaction with Vitamin D Responsive Elements......Page 2957
Communication between VDR and the Transcriptional Machinery......Page 2958
Further Reading......Page 2959
Conversion of Vitamin D to its Hormonal Form......Page 2961
The Vitamin D Endocrine System......Page 2962
Molecular Mechanism......Page 2963
New and Nonclassical Roles of the Vitamin D Hormone......Page 2964
Glossary......Page 2965
Further Reading......Page 2966
Dietary Sources and Recommended Intake of Vitamin E......Page 2967
Uptake, Distribution, and Metabolism of Vitamin E......Page 2968
Effects of Vitamin E on Cell Signaling and Gene Expression......Page 2969
Recognition of Vitamin E Deficiency Diseases and the Beneficial Effects of Vitamin E Supplements in Human Health.........Page 2970
Further Reading......Page 2971
Biochemical Role of Vitamin K......Page 2972
The Vitamin K-Dependent Carboxylase......Page 2973
Metabolic Interconversion of Vitamin K......Page 2974
Nutritional Aspects of Vitamin K......Page 2975
Further Reading......Page 2976
Blood Coagulation......Page 2977
Nutrition......Page 2980
Further Reading......Page 2981
Voltage-Dependent K+ Channel Structure and Diversity......Page 2982
Ether-a-go-go K+ Channels......Page 2983
Calcium-Activated K+ Channel......Page 2984
Further Reading......Page 2986
Calmodulin Binding......Page 2988
Physiology......Page 2989
Further Reading......Page 2991
The Alpha-Subunits of Sodium Channels......Page 2992
The Outer Pore and Selectivity Filter......Page 2993
Modulation of Channel Activity......Page 2994
Genetic Defects Affecting Voltage-Gated Sodium Channels......Page 2995
Toxins and Channel Modifiers......Page 2996
Glossary......Page 2997
Further Reading......Page 2998
Structure of the VHL Ubiquitin Ligase......Page 2999
Regulation of HIF Ubiquitylation by the VHL Ubiquitin Ligase......Page 3000
Further Reading......Page 3001
Catalytic Activity......Page 3002
Localization......Page 3003
Further Reading......Page 3004
Diffraction Measurements......Page 3005
Fitting Electron Density Maps......Page 3006
Studies of Molecular Complexes and Conformational Changes......Page 3007
The Importance of Resolution......Page 3008
Structures at Very High Resolution......Page 3009
Further Reading......Page 3011
The Gene-Specific Regulatory Factors......Page 3012
Chromosomal Organization......Page 3013
How Gal4p Activates Transcription......Page 3014
Glossary......Page 3015
Further Reading......Page 3016
Classical Zinc Fingers......Page 3017
Interactions with DNA and RNA......Page 3019
Non-Nucleic Acid Interactions......Page 3020
Further Reading......Page 3021