Encyclopedia of Biological Chemistry

[1].pdf......Page 1
Volume 4 (S-Z)......Page 0
Phylogeny......Page 2
Cover Page......Page 896
Editors-in-Chief......Page 830
Associate Editors......Page 832
Preface......Page 835
Notes on the Subject Index......Page 836
Volume 1......Page 837
Volume 2......Page 845
Volume 3......Page 853
Volume 4......Page 861
Lipids, Carbohydrates, Membranes and Membrane Proteins......Page 866
Metabolism, Vitamins and Hormones......Page 868
Cell Architecture and Function......Page 870
Protein/Enzyme Structure Function and Degradation......Page 873
Bioenergetics......Page 876
Molecular Biology......Page 882
Signaling......Page 888
Techniques and Methodology......Page 895
Function and Diseases......Page 3
Structure and Biochemical Mechanism......Page 4
The Substrate Specificity of the ABC Multidrug Exporters......Page 5
Further Reading......Page 6
ABA Biosynthesis......Page 7
Role of ABA in Seed Development and Maturation......Page 8
Stomatal Closure Meditated by ABA......Page 9
ABA-Induced Modulation of Gene Expression......Page 11
Further Reading......Page 12
General Concepts in Actin Assembly/Disassembly......Page 13
Capping Proteins......Page 15
Cellular Aspects of Actin Assembly/Disassembly......Page 16
Further Reading......Page 18
Actin......Page 20
Pointed-End Binding and Branching......Page 21
Evolutionary and Structural Relationships between Some Severing and Severing/Barbed-End-Capping Proteins......Page 22
The Six Segment Proteins: Gelsolin, Villin, and Adseverin/Scinderin......Page 23
The Single Domain ADF/Cofilin Family......Page 24
Barbed-End-Capping Proteins......Page 25
Further Reading......Page 26
Prokaryotic Arps......Page 28
Conventional Actin......Page 31
Arp2 and Arp3......Page 32
Chromatin-Associated Conventional Actin......Page 33
Further Reading......Page 34
Sequence Similarity......Page 35
A1 Receptors......Page 36
Signaling Downstream of Adenosine Receptors......Page 37
A2A Receptors......Page 38
Glossary......Page 39
Further Reading......Page 40
Members of the Family......Page 41
Regulation of Adenylyl Cyclase Activity by G Proteins and Calcium......Page 42
Physiological Roles of Adenylyl Cyclases......Page 43
See Also the Following Articles......Page 45
Further Reading......Page 46
Classification and Mechanism of Action of Adrenergic Receptors......Page 47
Pharmacological and Molecular Characteristics of Alpha-1 Adrenergic Receptors......Page 48
Pharmacological and Molecular Characteristics of Beta Adrenergic Receptors......Page 49
Adrenergic Receptor Polymorphisms......Page 50
Further Reading......Page 51
Why and Where AC Works......Page 52
Activation of and Coupling to Carriers......Page 53
Adsorption......Page 54
AC and DNA Recombinant Techniques......Page 55
Glossary......Page 56
Further Reading......Page 57
Linker Peptide Composition......Page 58
Protein-Ligand Interaction Affinity Tags......Page 59
Antibody-Epitope Interaction Affinity Tags......Page 60
Glossary......Page 63
Further Reading......Page 64
The PKA Anchoring Hypothesis......Page 65
Anchoring Protein Targeting Regions......Page 66
Alternatively Spliced Scaffolds......Page 67
Further Reading......Page 68
The Hill n, a Measure of Cooperativity......Page 69
Two-State Models to Explain Cooperativity in Allosteric Proteins......Page 70
Ribonucleotide Reductase (RR)......Page 72
Further Reading......Page 73
Alternative Splicing of FGF-R2 Transcripts......Page 75
Exonic Splicing Enhancers......Page 76
Layers of Regulation......Page 77
Further Reading......Page 78
Details of the Hierarchy......Page 79
TRA: A Simple Blockage Model......Page 80
Sxl Autoregulation......Page 82
Alternative Splicing and Sex Determination in Other Species......Page 83
Further Reading......Page 84
FAD-Containing Monoamine Oxidases......Page 86
Cu/TPQ Amine Oxidases......Page 87
Further Reading......Page 89
Intestinal Metabolism......Page 91
Liver Metabolism......Page 92
Inter-Organ Exchanges......Page 93
Ureagenesis......Page 94
Catabolic Hormones......Page 95
Further Reading......Page 96
N-Terminal Cotranslational Processing......Page 97
Properties of MetAPs......Page 98
Further Reading......Page 99
History......Page 100
Physiological Factors in Amyloid Formation......Page 101
Evolved Amyloid......Page 102
Amyloid Assembly......Page 103
Glossary......Page 104
Further Reading......Page 105
Entry at Malate and Oxaloacetate......Page 106
Exit of Intermediates: Balancing Anaplerosis......Page 107
Expression and Activity of Proteins Regulating Anaplerosis......Page 108
Renal Ammonia Formation during Starvation......Page 109
Summary and Perspective......Page 110
Further Reading......Page 111
Ang I Binding Protein......Page 112
Ang II Receptors......Page 113
Ang IV......Page 115
Further Reading......Page 116
Control of DNA Looping......Page 117
The Discovery and Demonstration of DNA Looping......Page 118
History and Historical Significance......Page 119
Further Reading......Page 120
ARF-Related Proteins......Page 121
Regulators of ARF Activity......Page 122
Further Reading......Page 123
Structure......Page 124
Overall Structure......Page 125
Cancer......Page 126
Naturally Occurring Inhibitors......Page 127
Further Reading......Page 128
Mitochondrial Electron Transport Chain in Plants......Page 129
Substrates for ATP Synthesis......Page 130
Inhibitors of ATP Synthesis......Page 131
Nonphosphorylating Respiration......Page 132
Further Reading......Page 133
Cyanide-Resistant Respiration......Page 134
AOX Structure......Page 135
Physiological Role(s) of AOX......Page 137
Further Reading......Page 138
Macroautophagy in Mammals......Page 139
Macroautophagy in Yeast......Page 140
Glossary......Page 143
Further Reading......Page 144
The Cobalamin Cofactor......Page 145
Radical-Mediated Rearrangement Reactions......Page 146
Cobalamin-Dependent Methionine Synthase......Page 149
Further Reading......Page 150
Structure of Bcl2 Family Proteins......Page 152
Role of the Mitochondria......Page 153
Further Reading......Page 154
B-Cell Antigen Receptor Diversity......Page 155
Early Signaling Events......Page 156
The B-Cell Antigen Receptor and the Immune Response......Page 157
Further Reading......Page 158
Bile Salt Synthesis and its Regulation......Page 159
Bile Salt Transport and its Regulation......Page 161
Further Reading......Page 162
Mitochondrial Antigens and the Cellular Immune System......Page 164
Pathology......Page 165
Clinical Findings......Page 166
Treatment of the Underlying Disease Process......Page 167
Further Reading......Page 168
Gibbs Free Energy......Page 170
Redox Potentials......Page 171
The Thermodynamics of Bioenergetic Interconversions......Page 172
Further Reading......Page 173
Biotin Enzymes......Page 174
Biotin Domains......Page 175
Biotin Domain Structure......Page 176
E. coli Biotin Ligase, BirA......Page 177
Further Reading......Page 178
Biosynthesis and Degradation of Natively Biotinylated Proteins......Page 179
Clinical Application of Biotinylated Antibodies......Page 180
Further Reading......Page 181
B1 Receptor......Page 182
Regulation of B1 Receptor Induction......Page 183
B2 Receptor Knockout Animals......Page 184
Further Reading......Page 185
Interorgan Relationships......Page 186
The Macromolecular Organization of the BCKD Complex......Page 188
Brain Neuropathology of BCKAs......Page 189
Further Reading......Page 190
Brassinosteroid Biosynthesis......Page 192
Campesterol to Brassinolide......Page 193
Receptor Kinases and BR Perception......Page 195
Downstream Components......Page 196
Further Reading......Page 197
Signaling Triggered by Cell-Cell Contact......Page 198
Mechanisms of Cadherin Signaling......Page 199
Rho Family GTPase Signaling......Page 200
Wnt/Beta-Catenin Signaling......Page 201
Phosphorylation and Dephosphorylation......Page 202
Further Reading......Page 203
Protocadherins......Page 204
Extracellular Domain Structure (cis- and trans-Dimers)......Page 205
Linkage to Beta-Catenin Family Members......Page 206
Roles of Cadherins in Cell and Tissue Morphogenesis......Page 207
See Also The Following Articles......Page 209
Further Reading......Page 210
CGRP Receptor-Selective Drugs and their Pharmacological Properties......Page 211
Cellular Signaling and RCP......Page 212
The Pathophysiology of CGRP and Adrenomedullin Receptors......Page 214
Further Reading......Page 215
Protein Structure......Page 216
Signaling......Page 217
CTR-Like Receptor (CTRLR)......Page 218
Further Reading......Page 219
Distribution and Localization......Page 220
Distribution and Localization......Page 221
Knockout Animals......Page 222
Further Reading......Page 223
Ca2+ Buffering in the ER Lumen......Page 225
Grp94 (Glucose-Regulated Protein)......Page 226
The Protein Disulfide Isomerase (PDI) Family of Proteins......Page 227
See Also the Following Articles......Page 228
Further Reading......Page 229
Mechanism of [Ca2+]c Oscillations......Page 230
Role and Functional Significance of [Ca2+]c Oscillations......Page 232
Further Reading......Page 233
Structure......Page 234
Intracellular Signaling Pathways Used by the CaR......Page 236
CaR in Hypercalcemia......Page 237
Further Reading......Page 238
Structure......Page 240
Substrate Specificity......Page 241
Regulation of Gene Expression......Page 242
Neuronal Functions......Page 243
Further Reading......Page 244
Cell-Cycle Regulators......Page 245
Oocyte Prophase and Metaphase Arrest......Page 246
Calcium and Meiosis......Page 247
Further Reading......Page 248
Tropomyosin Shift and Steric Blocking Model......Page 249
Molecular Organization of Troponin and its Ca2+-Induced Changes......Page 250
Ca2+-Induced Troponin Shift on the Thin Filaments......Page 252
Molecular Mechanism of Ca2+ Regulation......Page 253
Further Reading......Page 254
Calmodulin Interactions with Ca2+ and with NOS......Page 255
Ca2+/CaM Regulation of NOS......Page 256
Further Reading......Page 259
The Origins and the Fundamental Principles......Page 260
The Renaissance......Page 261
One (or Many) Roles......Page 262
Further Reading......Page 264
Mechanisms......Page 266
History, Roles, and Visualization......Page 267
Further Reading......Page 268
Soluble Complex Ions and Their Binding Strengths......Page 269
Concentrations and Selectivity of Binding in Organisms......Page 270
Overall Functional Fitness of Calcium Ions in Evolution......Page 271
Further Reading......Page 272
Neuronal CaMKII: Localization and Substrates......Page 273
Activation, Autoregulation, and Structure of CaMKII......Page 274
Ca2+/CaM-Dependent Autophosphorylation......Page 275
Autophosphorylation as an Index of Neuronal Activity......Page 276
CaMKII in LTP and Learning and Memory......Page 277
Glossary......Page 278
Further Reading......Page 279
Ca2+ Signaling......Page 280
Myosin Light Chain Kinase......Page 281
Ca2+/Calmodulin-Dependent Protein Kinase II......Page 282
Ca2+/Calmodulin-Dependent Protein Kinase IV......Page 283
Summary......Page 284
Further Reading......Page 285
Annexins......Page 286
Gelsolin......Page 287
C2-Domain Proteins......Page 289
Further Reading......Page 291
Temporal Buffering......Page 293
Structure of the EF-Hand......Page 294
Distribution of EF-Hand Domains......Page 295
Further Reading......Page 298
Structure and Function of Conventional Calpains......Page 299
Classifications......Page 302
Structure and Functions of Calpain Superfamily Members......Page 303
Further Reading......Page 304
Enzymatic Synthesis of Oligosaccharides......Page 306
Carbohydrate Chain Synthesis Utilizing Glycotransferases......Page 307
Chemical Synthesis of Oligosaccharides......Page 308
Solution Phase Chemical Oligosaccharide Synthesis......Page 309
See Also the Following Articles......Page 311
Further Reading......Page 312
Mitochondrial Beta-Oxidation......Page 313
Further Reading......Page 316
Structure and Active Site......Page 318
Mechanism of Action......Page 319
Sequence of Action......Page 320
Substrates during Apoptosis......Page 321
Inhibitors......Page 323
Pathological Implications......Page 324
Further Reading......Page 325
Regulators of G0 Exit and G1-S Progression......Page 327
Cell Growth Regulation......Page 329
Further Reading......Page 330
Initiation......Page 331
Cdc7 (DDK)......Page 332
Coupling Replication to the Cell-Cycle Engine......Page 333
CDK Inhibitors and Proteolysis......Page 334
Conclusions......Page 335
Further Reading......Page 336
G2/M Checkpoint......Page 337
Intra-S Checkpoint......Page 339
G1/S Checkpoint......Page 340
Protein Kinase of the PI3K Family......Page 341
Glossary......Page 342
Further Reading......Page 343
Molecular Components of the Mitotic Checkpoint......Page 344
Sequestration Model......Page 346
Direct Inhibitor Model......Page 347
Checkpoint Proteins Can Have Dual Functions......Page 348
Further Reading......Page 349
Executors of Ca2+ Death Signals......Page 351
Apoptosis, Necrosis, and Other Ca2+-Dependent Forms of Cell Death in Brain Ischemia......Page 352
See Also the Following Articles......Page 353
Further Reading......Page 354
The Actin Cytoskeleton......Page 355
Adhesion......Page 356
Microtubules and Cell Guidance......Page 358
Microtubules and Contractility......Page 359
Further Reading......Page 360
Adhesive Motifs......Page 361
Structure......Page 362
Conformational Changes......Page 363
Further Reading......Page 364
Heterochromatin Domain......Page 366
The Centromere as DNA......Page 367
The Centromere as Chromatin......Page 368
Further Reading......Page 370
Structure of the Centrosome......Page 371
GammaTuRC......Page 372
GammaTuRC-Mediated Microtubule Nucleation in Vivo......Page 373
Centrosome Abnormalities in Cancer......Page 374
Further Reading......Page 375
N-Terminal Region......Page 376
Myeloid Differentiation......Page 377
Small G Proteins......Page 378
PI3-K Pathway......Page 379
Further Reading......Page 380
Why the Need for Metal Trafficking?......Page 382
Delivering Copper to the Golgi: Pathways Involving the ATX1 Copper Chaperone......Page 383
Delivery of Copper to Mitochondrial Cytochrome Oxidase......Page 384
Further Reading......Page 385
Clp/Hsp100 Chaperones......Page 386
Structure of Clp ATPases and Their Associated Proteases......Page 387
Mechanism of Action of Clp Chaperones and Proteases......Page 388
Hsp90 Chaperones......Page 389
Further Reading......Page 390
Overall Mechanism......Page 392
Architecture......Page 394
Polypeptide Binding by Type I Chaperonins......Page 395
Substrate Proteins......Page 396
Further Reading......Page 397
Chemiluminescence: Fluorescence from a Chemical Reaction......Page 398
Bioluminescence: Chemiluminescence from a Biological Source......Page 401
Further Reading......Page 403
Protonmotive Force......Page 404
The Protonmotive Circuit......Page 405
Behavior of the Protonmotive Circuit......Page 406
Uncoupling Proteins......Page 407
Fourth Postulate - Ion Carriers and Channels......Page 408
The Sodium-Calcium Cycle......Page 409
Further Reading......Page 410
Structure......Page 412
Signal Transduction......Page 413
Internalization......Page 414
HIV Entry......Page 415
Tumor Growth and Metastasis......Page 416
Further Reading......Page 417
Categories of Growth Based on the Nature of the Growth-Supporting Reductant......Page 418
Nitrifying Bacteria......Page 419
Generation of the Electrochemical Gradient and ATP Synthesis......Page 420
Release and Uptake of Protons in Chemolithotrophic Reactions......Page 421
Ecology......Page 422
Further Reading......Page 423
Receptors......Page 424
Chemotactic Peptide Receptors......Page 425
Effector Proteins......Page 426
Receptor Regulation......Page 427
Further Reading......Page 428
Spectroscopy......Page 429
Chemical Properties......Page 431
Spectroscopy......Page 432
Occurrence and Functions......Page 433
Glossary......Page 435
Further Reading......Page 436
The Hill Reaction......Page 437
Chloroplast Function......Page 438
Cyclic Electron Transport and Photophosphorylation......Page 439
State Transitions......Page 440
Transcriptional Control......Page 441
Mechanisms and Evolutionary Implications......Page 442
See Also The Following Articles......Page 443
Further Reading......Page 444
Envelope......Page 445
Thylakoid System......Page 446
Etioplasts......Page 447
Glossary......Page 448
Further Reading......Page 449
Diet and Lipoproteins......Page 450
Cholesterol Synthesis......Page 451
Statins......Page 453
Further Reading......Page 454
Remodeling Enzymes......Page 455
Remodeling Mechanisms......Page 456
Acetylation......Page 457
Methylation......Page 458
Ubiquitination......Page 459
Modification Crosstalk and the ‘‘Histone Code’’ Hypothesis......Page 460
Further Reading......Page 461
Posttranslational Modifications of Core Histones......Page 463
NHCPs......Page 464
Global Primary Structures-The Nucleosome Repeat Length (NRL)......Page 465
Tertiary and Higher Level Features......Page 466
Further Reading......Page 467
The Structure of Chromatin......Page 468
The Mitotic Chromosome......Page 471
Further Reading......Page 472
CoA as Donor of 4-Phosphopantetheine for Fatty Acid Synthase......Page 474
Metabolic Roles/Functions......Page 475
Further Reading......Page 476
Revised Definition of ‘‘Collagenases’’......Page 477
The Collagenases......Page 478
See Also the Following Articles......Page 479
Further Reading......Page 480
The Two Subtypes: The Fibrillar and Non-Fibrillar Collagens......Page 481
Why the Hydroxyproline......Page 484
Evolutionary Origins and Selective Pressures on (Gly-XY-)n Sequences......Page 485
Further Reading......Page 486
Identification and Properties of cAMP Receptors......Page 487
G Protein-Dependent Pathways......Page 489
G Protein-Independent Pathways......Page 490
See Also the Following Articles......Page 491
Further Reading......Page 492
Domain Structure of Class I PDEs......Page 493
C Domains of Class I PDEs......Page 494
Characteristics of cGMP-Specific Class I PDEs (PDEs 5, 6, and 9)......Page 496
Regulation of Class II PDEs......Page 497
Further Reading......Page 498
Molecular Diversity......Page 500
PDEs: Components of Spatially Organized Signaling Networks and Microdomains......Page 501
PDEs: Signal Integrators......Page 502
Glossary......Page 503
Further Reading......Page 504
Overall Structure of Cyclic Nucleotide-Dependent Protein Kinases......Page 505
PKA......Page 506
Cyclic Nucleotide-Binding Specificity and Affinity......Page 508
Negative Feedback and Feed-Forward Control of Cyclic Nucleotide Pathways......Page 509
Further Reading......Page 510
CNG Channels......Page 511
HCN Channels......Page 512
Further Reading......Page 513
Activation......Page 515
Bone Turnover......Page 517
Parasitic Proteinases......Page 518
Further Reading......Page 519
Composition and Structure......Page 520
The Rieske FeS-Protein......Page 521
Plastoquinol Oxidation - Q-Cycle and Fes-Domain Movement......Page 523
Genes, Biogenesis, and Phylogeny......Page 524
Further Reading......Page 525
Protein Subunits......Page 527
Three-Dimensional Structure of the bc1 Complex......Page 529
The Protonmotive Q Cycle......Page 530
Proton Conduction Pathways......Page 531
Inhibitors......Page 532
Further Reading......Page 533
Attachment of the Heme Prosthetic Group to Cytochrome c Apoprotein......Page 534
Evolutionary Aspects......Page 535
Cytochrome c and Apoptosis......Page 536
Further Reading......Page 537
Structures......Page 538
Oxygen Binding and Reduction......Page 540
Proton Pumping......Page 541
Further Reading......Page 542
Cytochrome P-450-General Aspects......Page 543
Structural Organization of Cytochrome P-450 Systems......Page 544
Reaction Cycle......Page 545
Regulation of Cytochrome P-450 Systems......Page 546
Further Reading......Page 547
Regulated Expression......Page 549
Cytokines and the Innate Immune Response......Page 550
Cytokines and the Adaptive Immune Response......Page 551
JAK/STAT Signaling......Page 552
Glossary......Page 553
Further Reading......Page 554
Making the Plans: Coordinating Nuclear and Cytoplasmic Division in Animal Cells......Page 555
Assembling the Parts 2: Building the Central Spindle......Page 557
Pushing the Envelope: Membrane Fusion......Page 558
Getting the Timing Right......Page 559
Further Reading......Page 560
Biosynthesis......Page 561
Conjugation......Page 562
Signal Transduction......Page 563
Cell Cycle......Page 564
Further Reading......Page 565
Structure and Molecular Components of the Desmosome......Page 567
Desmosome Assembly and Maintenance......Page 568
Desmosome Function......Page 569
Structure and Molecular Components of the Hemidesmosome......Page 570
BP180......Page 571
Conclusion......Page 573
Further Reading......Page 574
Hydrophilic Groups (Headgroups)......Page 575
Critical Micelle Concentration (CMC)......Page 576
Temperature Effects......Page 577
Membrane Proteins......Page 578
Further Reading......Page 579
Type 1 Diabetes Mellitus......Page 580
Type 2 Diabetes Mellitus......Page 581
Other Specific Types......Page 583
Acute......Page 585
Chronic......Page 586
Weight Loss and Exercise......Page 588
Further Reading......Page 589
Regulation of DGK Activity......Page 591
PA as a Signal......Page 593
Further Reading......Page 594
Disulfide Bond Formation During Protein Folding......Page 596
Catalysis of Disulfide Formation......Page 597
The Thioredoxin Family......Page 598
Disulfide Formation as a Regulatory Mechanism......Page 599
Further Reading......Page 600
DNA Base Excision......Page 601
Backbone Incision......Page 603
Base Excision Repair in Mitochondria......Page 604
Further Reading......Page 605
Alkylating Agents and Mechanism of the Reaction with DNA......Page 607
Effect of DNA Conformation on the Alkylation......Page 608
Methods of Identification of Alkyl Derivatives of Nucleic Acids......Page 609
Cytotoxic and Mutagenic Effects of Alkylation: Methylation......Page 610
Further Reading......Page 611
Structural Superfamilies of DNA Glycosylases......Page 612
Base Flipping......Page 613
Catalytic Strategies for Glycosidic Bond Hydrolysis......Page 614
Further Reading......Page 615
Primary Structures......Page 616
‘‘Open’’ And ‘‘Closed’’ Conformations......Page 617
Single-Stranded DNA Translocation by Monomers of SF1 Helicases......Page 618
Active Versus Passive Mechanisms of DNA Unwinding......Page 619
Summary......Page 620
Further Reading......Page 621
Nucleic Acid Strand Separation Activity of Helicases......Page 622
Brownian Motor Model......Page 623
Mechanisms of Nucleic Acid Strand Separation......Page 624
Ring Structure......Page 625
Nucleic Acid Binding in the Central Channel......Page 626
Mechanism and Role of NTP Hydrolysis......Page 627
Conclusion......Page 628
Further Reading......Page 629
Structure......Page 630
Domains Constituting the Core Catalytic Domain......Page 631
Biological Functions......Page 632
Genetic Recombination and Recombinational Repair......Page 633
Further Reading......Page 634
Overall Structure of DNA Ligases......Page 635
Mechanism of Nucleotidyl Transfer......Page 638
Glossary......Page 640
Further Reading......Page 641
Molecular Recognition of the Presence of the Methyl Groups on the DNA......Page 642
The Molecular Logic of DNA Methylation......Page 643
Chemistry of DNA Methylation......Page 644
Reaction Mechanism of N-MTases......Page 645
Mechanism of Base Flipping......Page 646
Mechanism of DNA Recognition......Page 647
Mechanism of Target Site Location and Processivity of DNA Methylation......Page 648
Further Reading......Page 649
Prokaryotes......Page 650
Eukaryotes......Page 651
Tertiary Structure......Page 653
Chemistry......Page 654
AdoMet and DNA Binding......Page 656
Further Reading......Page 657
Dam-Directed Mismatch Repair......Page 658
Altered Gene Expression......Page 660
See Also the Following Articles......Page 661
Further Reading......Page 662
Generalized Mismatch Repair in Eukaryotes......Page 663
Anti-Recombination Activity in Escherichia coli......Page 664
Anti-Recombination Activity in Saccharomyces cerevisae......Page 665
DNA Sequence Divergence, Mismatch Repair, Loss of Heterozygosity, and Cancer......Page 666
Evolutionary Role of the Control of Homologous Recombination by Mismatch Repair......Page 667
Further Reading......Page 668
Mismatch Repair Function is Required for Drug Cytotoxicity......Page 669
Mismatch Repair Proteins Promote DNA Damage-Induced Cell Cycle Arrest and Apoptosis......Page 670
Mismatch Repair-Mediated Apoptosis Eliminates Damaged Cells from Tumorigenesis......Page 671
Further Reading......Page 672
MutS Homologue Proteins Involved in Mismatch Repair......Page 673
Other Proteins Implicated in Mismatch Repair......Page 675
Defects in Mismatch Repair Cause Increased Cancer Susceptibility......Page 676
Glossary......Page 678
Further Reading......Page 679
Mechanism of E. coli Long-Patch Mismatch Repair......Page 680
Initiation of Mismatch Repair......Page 681
Excision and Repair Synthesis of Mismatch Repair......Page 682
MutY Repair Pathway......Page 683
Further Reading......Page 684
MutS and Some of Its Homologs Recognize Mismatches......Page 685
Orchestration of Mismatch Correction in Mammals......Page 686
How is Directional Excision Initiated and Controlled......Page 687
Further Reading......Page 688
Biochemistry of Vsr......Page 689
Structure and Biochemistry of MBD4......Page 690
Further Reading......Page 691
Oxidants and Antioxidants......Page 692
Carcinogenesis......Page 693
GO System......Page 694
Further Reading......Page 695
Primary Structure and Chromophores......Page 696
Reaction Mechanism......Page 697
See Also The Following Articles......Page 699
Further Reading......Page 700
DNA Primase Activity and Mechanisms of Primer Synthesis......Page 701
Residues Responsible for Interactions with the Metal Ion-dNTP Complex......Page 702
Checkpoint Activation......Page 703
Glossary......Page 704
Further Reading......Page 705
Pol  Domain Organization......Page 706
Lyase Domain......Page 707
Polymerase Domain......Page 708
Glossary......Page 709
Further Reading......Page 710
Processivity Factor......Page 711
Further Reading......Page 712
Biochemical Character......Page 714
Role at Replication Fork......Page 715
Glossary......Page 716
Further Reading......Page 717
Domain Structure and Relation to Other Polymerases......Page 718
Substrate Binding......Page 719
DNA Polymerase Reaction Specificity......Page 720
3-5 Exonuclease......Page 721
Glossary......Page 722
Further Reading......Page 723
DNA Polymerase II: Structure and Biochemical Functions......Page 724
Biological Function: Replication Restart......Page 725
Further Reading......Page 726
Subunits and Subassembly of Pol III Holoenzyme......Page 727
Tau-Subunit and Pol III......Page 728
Concurrent DNA Synthesis of Leading and Lagging Strands......Page 729
Further Reading......Page 731
Selectivity Contributions of Each Step......Page 732
Measurement of the Kinetics of Incorporation......Page 733
Structural Determinants of Fidelity......Page 734
Selectivity of the Proofreading Exonuclease......Page 735
Glossary......Page 736
Further Reading......Page 737
DNA Polymerase Holoenzymes......Page 738
Primosomes......Page 739
Lagging-Strand Synthesis......Page 740
Further Reading......Page 742
Replication Protein A (RPA)......Page 743
Polymerase Accessory Proteins......Page 744
Topoisomerases......Page 745
Further Reading......Page 746
Protein......Page 747
Mammalian mtDNA......Page 748
Glossary......Page 749
Further Reading......Page 750
The Generic DNA Replication Origin......Page 751
Metazoan Replication Origins......Page 753
The Origin Recognition Complex......Page 754
Regulating ORC Activity: The ORC Cycle......Page 755
Further Reading......Page 757
The E. coli Replication Origin, oriC......Page 759
DnaA Protein and the DnaA Box......Page 760
Functional Domains of DnaA Protein......Page 761
Regulation of DNA Replication in E. coli......Page 762
Interaction of DnaA with Hda and the -Subunit of DNA Polymerase III Holoenzyme......Page 763
Further Reading......Page 764
Genes and Protein Structure......Page 765
The Sequence Specificity Subunit......Page 766
Assembly and Control of the Type I Restriction Enzyme......Page 767
Cleavage of DNA......Page 768
Further Reading......Page 769
Discovery of New Restriction-Modification Systems......Page 770
Recognition Sequences......Page 771
Protein Structures......Page 772
Subsets of Type II Restriction Enzymes......Page 773
The Methyltransferase Enzymes......Page 774
Further Reading......Page 775
Substrate Requirements......Page 776
Organization of Genes and Regulation of Restriction Activity......Page 777
Other Type III RM Systems......Page 778
Further Reading......Page 779
Structure......Page 780
Biology......Page 781
Biology......Page 782
Cruciforms......Page 783
Further Reading......Page 784
Reading Heads......Page 786
The Helix-Turn-Helix Motif......Page 787
The Leucine Zipper Motif......Page 789
Diverse Structural Strategies are Employed by Proteins for DNA Recognition......Page 790
Further Reading......Page 791
Quantitative Relationship between Twist and Supercoil......Page 792
Handedness and the Sign of Tw and Wr......Page 793
Biological Effects of Supercoiling and Enzymes That Can Change DNA Supercoiling......Page 794
Further Reading......Page 795
Classification, Nomenclature and General Properties......Page 796
Protein Domains......Page 797
Reverse Gyrase Mechanism......Page 798
Crystal Structure of Human Topoisomerase I......Page 799
Cellular Roles......Page 800
Transcription......Page 801
Glossary......Page 802
Further Reading......Page 803
DNA Topoisomerases......Page 804
Enzyme Mechanism......Page 805
Enzyme Domain Structures and Isoforms......Page 806
Topoisomerase IV......Page 807
Anticancer Drugs......Page 808
Further Reading......Page 809
RecQ Helicases......Page 810
Physical Association......Page 811
The Recombination Connection......Page 812
RecQ Helicases and Human Disease......Page 813
Further Reading......Page 814
D1-Like and D2-Like Receptor Subfamilies......Page 815
Dopamine Receptor Signaling......Page 816
Dopamine Receptor Variants......Page 819
Further Reading......Page 820
Functions Associatedwith Dynein-Based Motility......Page 821
Dynein-Independent Functions......Page 822
Binding Activities......Page 823
Further Reading......Page 824
The Dynein Heavy Chain......Page 825
Cytoplasmic Dynein......Page 826
Flagellar Dyneins......Page 827
Glossary......Page 828
Further Reading......Page 829
Academic.Press,.Encyclopedia.of.Biological.Chemistry.Vol..2.(2004).pdf......Page 897
Academic.Press,.Encyclopedia.of.Biological.Chemistry.Vol..3.(2004).pdf......Page 1739
Academic.Press,.Encyclopedia.of.Biological.Chemistry.Vol..4.(2004).pdf......Page 2586