The biophysical chemistry of nucleic acids & proteins:
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| Main Author: | |
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| Format: | Book |
| Language: | English |
| Published: |
[Eastbourne]
Helvetian Press
2010
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXXVII, 774 S. Ill., graph. Darst. |
| ISBN: | 9780956478115 |
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| 100 | 1 | |a Creighton, Thomas E. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a The biophysical chemistry of nucleic acids & proteins |c Thomas E. Creighton |
| 246 | 1 | 3 | |a Nucleic acids & proteins |
| 264 | 1 | |a [Eastbourne] |b Helvetian Press |c 2010 | |
| 300 | |a XXXVII, 774 S. |b Ill., graph. Darst. | ||
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| adam_text | THE BIOPHYSICAL CHEMISTRY OF NUCLEIC ACIDS & PROTEINS THOMAS E.
CREIGHTON HELVETIAN PRESS CONTENTS PREFACE XIX COMMON ABBREVIATIONS XXI
GLOSSARY XXV SECTION I: MACROMOLECULES 1. CONFIGURATIONS AND
CONFORMATIONS 1 1.1. STEREOCHEMISTRY 2 1.1.A. CHIRALITY 3 1. ENANTIOMERS
5 2. RACEMIC MIXTURES 6 3. DIASTEREOMERS 7 4. EPIMERS AND EPIMERIZATION
8 5. CIS AND TRANS ISOMERS 9 1.1.B. PROCHIRAL 10 L.L.C. TAUTOMERS 12
1.2. CONFORMATIONS 13 1.2.A. TORSION ANGLE 15 I.2.B. DIHEDRAL ANGLE 16
1.3. CONFORMATIONS OF IDEALIZED POLYMERS 17 1.3.A. RANDOM COILS 18 1.
END-TO-END DISTANCES 19 2. RADIUS OF GYRATION 21 3. CHARACTERISTIC RATIO
, 21 I.3.B. EXCLUDED VOLUME EFFECTS AND THETA SOLVENTS 22 1. COVALENT
CROSS-LINKS 23 1.4. STRUCTURE DATABASES: STRUCTURES ON THE WEB 24
SECTION II: NUCLEIC ACIDS 2. DNA STRUCTURE 25 2.1. POLYNUCLEOTIDES 26 VI
CONTENTS 2.1.A. THE DEOXYRIBOSE GROUP 29 2.I.B. PROPERTIES OF THE BASES
31 2. L.C. MODIFICATIONS OF THE BASES 37 2.2. DNA THREE-DIMENSIONAL
STRUCTURES 40 2.2.A. BASE PAIRING AND STACKING 42 2.2.B. DOUBLE HELICES
46 1. B-DNA 52 2. A-DNA 53 3. Z-DNA 54 2.2.C. OTHER DNA STRUCTURES 56 1.
HOOGSTEEN BASE PAIRS 56 2. TRIPLE HELICES 57 3. H-DNA: INTRAMOLECULAR
TRIPLE HELICES 60 4. FOUR-STRANDED STRUCTURES: GUANINE QUARTET 60 5. I-
MOTIF 63 6. INVERTED REPEAT SEQUENCES AND PALINDROMES 64 7. HELICAL
JUNCTIONS: CRUCIFORMS, HOLLIDAY JUNCTIONS 66 8. PARALLEL-STRANDED DNA
DUPLEXES 66 2.3. DNA AS A POLYELECTROLYTE: HYDRATION AND COUNTERIONS 68
2.4. DNA FLEXIBILITY AND DYNAMICS: CURVING, TWISTING, STRETCHING 71
2.4.A. LOCAL FLEXIBILITY 74 2.4.B. HYDROGEN EXCHANGE 75 2.5. BINDING OF
SMALL MOLECULES 77 2.5.A. BINDING TO THE MINOR GROOVE 77 2.5.B.
INTERCALATION 78 1. ETHIDIUM BROMIDE 78 2. PSORALEN PHOTO CROSS-LINKING
79 2.6. CHEMICAL MODIFICATION AS A PROBE OF STRUCTURE 80 2.6.A.
CROSS-LINKING 85 3. DNA TOPOLOGY 86 3.1. SUPERCOILING AND SUPERHELICES:
TOPOISOMERS 90 3.2. LINKING NUMBER, LK 92 3.2.A. LINKING DIFFERENCE ,
ALK 92 1. RELAXED DUPLEX DNA 93 3.2.B. SUPERHELIX DENSITY, A 94 3.3.
TOPOISOMERASES 95 3.4. TWIST AND WRITHE 96 3.4.A. TWIST, TW 96 3.4.B.
WRITHE, WR 97 3.5. DNA TOPOLOGY AND GEOMETRY 98 3.5.A. EXPERIMENTAL
CHARACTERIZATION OF DNA TOPOLOGY 99 1. ELECTRON MICROSCOPY 99 2. GEL
ELECTROPHORESIS TO SEPARATE TOPOISOMERS 101 CONTENTS VII 3.
INTERCALATION BY ETHIDIUM BROMIDE 101 4. TWO-DIMENSIONAL GEL
ELECTROPHORESIS 101 3.6. ENERGETICS OF SUPERCOILING 103 3.6. B. ENERGY
DISTRIBUTION OF TOPOISOMERS 104 3.6. C. TOPOLOGY-DEPENDENT BINDING OF
LIGANDS 105 3.7. DNA WRAPPED AROUND THE NUCLEOSOME 106 4. RNA STRUCTURE
108 4.1. SECONDARY STRUCTURE OF RNA 112 4. LA. HAIRPIN LOOPS 116 4.I.B.
TETRALOOPS 117 4.L.C. BULGES AND INTERNAL LOOPS 118 4.2. TERTIARY
STRUCTURE OF RNA 118 4.2.A. COMMON STRUCTURAL MOTIFS 120 1. PSEUDOKNOTS
120 2. COAXIAL HELICES: INTERHELICAL STACKING 121 3. A-MINOR MOTIF 122
4. DINUCLEOTIDE PLATFORM 123 5. KISSING HAIRPIN LOOPS 123 6. RIBOSE
ZIPPER 124 7. URIDINE TURN 125 8. TETRALOOP/RECEPTOR INTERACTIONS 126 9.
ROLES OF IONS 126 4.2.B. TRANSFER RNA STRUCTURES 127 4.2.C. RIBOZYME
STRUCTURES 129 4.3. QUATERNARY STRUCTURE OF RNA 133 4.4. RNA STRUCTURE
PREDICTION 134 4.4.A. PREDICTION OF SECONDARY STRUCTURE 134 1.
THERMODYNAMIC APPROACH 134 2. PHYLOGENETIC APPROACH 135 4.4.B.
PREDICTION OF TERTIARY STRUCTURE 136 5. DENATURATION, RENATURATION, AND
HYBRIDIZATION OF NUCLEIC ACIDS 139 5.1. DENATURATION OF DOUBLE-STRANDED
NUCLEIC ACIDS 139 5. LA. METHODS FOR MONITORING DENATURATION 140 5.I.B.
DOUBLE-STRANDED DNA 142 1. THERMAL MELTING 143 2. DENATURANTS 144 3. PH
145 4. SALT EFFECTS 145 5. PREDICTION OF THE T M 146 5.1.C
DOUBLE-STRANDED RNA 148 5.1 .D. DNA . RNA HETERODUPLEXES 149 5.I.E.
SINGLE-STRANDED NUCLEIC ACIDS 149 1. PHYSICAL STRETCHING 150 5.2.
UNFOLDING AND REFOLDING OF SINGLE-STRANDED RNA MOLECULES 150 VIII
CONTENTS 5.2.A. TRANSFER RNA UNFOLDING/REFOLDING 153 5.2.B. RIBOZYME
UNFOLDING/REFOLDING 154 5.2.C. UNFOLDING USING MECHANICAL FORCE 155 5.3.
RENATURATION, ANNEALING, AND HYBRIDIZATION 157 5.3.A. COMPETING
INTRAMOLECULAR STRUCTURES IN INDIVIDUAL SINGLE STRANDS 162 5.3.B. C O T
AND R Q T CURVES 163 5.3.C. PROBE HYBRIDIZATION 165 1. STRINGENCY 167 2.
ANALYZING THE EXTENT OF COMPLEMENTARITY 168 3. IN SITU HYBRIDIZATION 170
5.4. DNA MIMICS: PEPTIDE NUCLEIC ACIDS 170 5.4.A. CHEMISTRY AND
SYNTHESIS 172 5.4.B. HYBRIDIZATION PROPERTIES 172 1. PNA.DNA AND PNA.RNA
DUPLEXES 173 2. (PNA) 2 .DNA TRIPLEXES 173 3. STRAND INVASION: BINDING
TO DOUBLE-STRANDED DNA 173 4. PNA DUPLEXES AND TRIPLEXES 175 5.4.C.
STRUCTURES OF PNA COMPLEXES 175 6. MANIPULATING NUCLEIC ACIDS 177 6.1.
REPLICATING DNA 177 6. LA. DNA POLYMERASE 178 6.I.B. DNALIGASE 181
6.L.C. POLYMERASE CHAIN REACTION (PCR) 182 6.2. PRODUCING RNA 185 6.2.A.
RNA REPLICATION: RNA REPLICASES 185 6.2.B. TRANSCRIPTION: DNA-DEPENDENT
RNA POLYMERASES 186 1. SINGLE-SUBUNIT PHAGE DNA-DEPENDENT RNA
POLYMERASES 188 6.2.C. REVERSE TRANSCRIPTION: RNA INTO DNA 189 6.2.D.
ANTISENSE OLIGONUCLEOTIDES 190 6.3. CLONING 191 6.3.A. EXPRESSION
VECTORS 193 6.3.B. CDNA LIBRARIES 194 6.3.C. RESTRICTION ENZYMES 195
6.3.D. RESTRICTION MAPS 196 6.4. SEQUENCING DNA 198 6.4.A. ISOLATING THE
DNA FRAGMENTS TO BE SEQUENCED 199 6.4.B. CHAIN-TERMINATION, SANGER
METHOD 199 6.4.C. SEPARATING THE DNA FRAGMENTS BY SIZE 203 6.4.D.
ALTERNATIVE APPROACHES 204 6.5. SEQUENCING RNA 205 6.5.A. DIRECT
SEQUENCING OF OLIGORIBONUCLEOTIDES 205 6.5.B. IDENTIFYING MODIFIED
NUCLEOTIDES 207 6.6. CHEMICAL SYNTHESIS OF DNA 208 6.6.A. PROTECTING
GROUPS FOR 2 -DEOXYNUCLEOSIDES 211 6.6.B. COUPLING METHODS 211 CONTENTS
1. PHOSPHOTRIESTER PROCEDURE 2. PHOSPHORAMIDITE PROCEDURE 3.
H-PHOSPHONATE PROCEDURE 6.6.C. SOLUTION-PHASE DNA SYNTHESIS 6.6.D.
SOLID-PHASE DNA SYNTHESIS 6.6.E. SITE-DIRECTED MUTAGENESIS 6.7. CHEMICAL
SYNTHESIS OF RNA 6.7.A. PROTECTING THE 2 -HYDROXYL GROUP 6.7.B. RNA
SYNTHESIS IN SOLUTION 6.7.C. SOLID-PHASE RNA SYNTHESIS SECTION III:
PROTEINS 7. POLYPEPTIDE STRUCTURE 7.1. POLYPEPTIDE CHAINS 7.2. AMINO
ACID RESIDUES 7.2.A. GLYCINE (GLY) 7.2.B. NONPOLAR AMINO ACID RESIDUES
(ALA, LEU, HE, VAL) 7.2.C. HYDROXYL RESIDUES (SER, THR) 7.2.D. ARGININE
(ARG) 7.2.E. LYSINE (LYS) 1. ACETYLATION BY ANHYDRIDES 2. AMIDINATION 3.
GUANIDINATION 4. SCHIFF BASE FORMATION 5. CARBAMYLATION 7.2.F. HISTIDINE
(HIS) 7.2.G. ACIDIC RESIDUES (ASP, GLU) 7.2.H. AMIDE RESIDUES (ASN, GIN)
1. DEAMIDATION 7.2.1. CYSTEINE (CYS) 1. ALKYLATION OF THIOL GROUPS 2.
THIOL ADDITION ACROSS DOUBLE BONDS 3. BINDING OF METAL IONS 4. OXIDATION
OF THIOL GROUPS 5. DISULFIDE BONDS 6. THIOL-DISULFIDE EXCHANGE 7.
DITHIOTHREITOL, DITHIOERYTHRITOL 8. ELLMAN S REAGENT 7.2.J. METHIONINE
(MET) 7.2.K. PHENYLALANINE (PHE) 7.2.L. TYROSINE (TYR) 7.2.M. TRYPTOPHAN
(TRP) 7.2.N. IMINO ACID (PRO) 7.2.0. SELENOCYSTEINE (SEC) 7.2.P.
PHYSICAL PROPERTIES AND HYDROPHOBICITIES OF AMINO ACID RESIDUES IX 211
212 213 215 216 218 220 220 222 223 227 227 229 230 232 232 233 234 236
236 237 238 239 239 241 242 243 245 245 246 247 247 248 249 252 253 254
255 256 257 258 259 260 CONTENTS 1. HYDROPHILICITIES 261 2.
HYDROPHOBICITIES 261 7.3. PROTEIN DETECTION 267 7.3.A. BIURET REACTION
267 7.3.B. LOWRY ASSAY 268 7.3.C. NINHYDRIN 268 7.3.D. FLUORESCAMINE 269
7.3.E. COOMASSIE BRILLIANT BLUE 270 7.3.F. PONCEAU S 271 7.4. PEPTIDE
SYNTHESIS 271 7.4.A. CHEMISTRY OF POLYPEPTIDE CHAIN ASSEMBLY 272 1.
CHEMICAL LIGATION OF PEPTIDE FRAGMENTS 275 7.4.B. SOLUTION OR SOLID
PHASE? 276 7.4.C. PEPTIDE LIBRARIES 278 7.5. PEPTIDE AND PROTEIN
SEQUENCING 280 7.5.A. AMINO ACID ANALYSIS 280 1. PEPTIDE BOND HYDROLYSIS
281 2. QUANTIFYING AMINO ACIDS 282 3. COUNTING RESIDUES 283 7.5.B.
FRAGMENTATION OF A PROTEIN INTO PEPTIDES 285 1. PROTEOLYTIC ENZYMES 285
2. CHEMICAL METHODS OF CLEAVAGE 288 7.5.C. PEPTIDE MAPPING 289 7.5.D.
DIAGONAL MAPS 291 1. ISOLATING PEPTIDES CONTAINING CERTAIN AMINO ACIDS
291 2. IDENTIFYING DISULFIDE BONDS 292 7.5.E. SEQUENCING 293 1.
AMINO-TERMINAL AND CARBOXYL-TERMINAL RESIDUES 294 2. SEQUENCING FROM THE
N-TERMINUS: THE EDMAN DEGRADATION 295 3. SEQUENCING FROM THE C-TERMINUS
298 4. SEQUENCING BY MASS SPECTROMETRY 299 7.5.F. PROTEIN SEQUENCES FROM
GENE SEQUENCES 301 1. POST-TRANSLATIONAL MODIFICATIONS 302 7.6. PRIMARY
STRUCTURES OF NATURAL PROTEINS: EVOLUTION AT THE MOLECULAR LEVEL 306
7.6.A. HOMOLOGOUS GENES AND PROTEINS. 307 1. DETECTING SEQUENCE HOMOLOGY
310 2. ALIGNING HOMOLOGOUS SEQUENCES 313 3. ORTHOLOGOUS / PARALOGOUS
GENES AND PROTEINS 314 4. NATURE OF AMINO ACID SEQUENCE DIFFERENCES 315
5. RATES OF DIVERGENCE 318 6. ROLES OF SELECTION. 321 A. NEUTRAL
MUTATIONS AND NEGATIVE SELECTION 322 B. POSITIVE SELECTION FOR
FUNCTIONAL MUTATIONS 323 7.6.B. GENE REARRANGEMENTS AND THE EVOLUTION OF
PROTEIN COMPLEXITY. 324 1. GENE DUPLICATIONS 324 CONTENTS XI 2. PROTEIN
ELONGATION BY INTRA-GENE DUPLICATION 3. GENE FUSION AND DIVISION 7.6.C.
PROTEIN ENGINEERING 8. POLYPEPTIDE CONFORMATION 8.1. LOCAL FLEXIBILITY
OF THE POLYPEPTIDE BACKBONE: THE RAMACHANDRAN PLOT 8.2. RANDOM-COIL
POLYPEPTIDE CHAINS 8.2.A. STATISTICAL PROPERTIES 8.2.B. RATES OF
CONFORMATIONAL CHANGE 1. X-PRO PEPTIDE BOND CIS/TRANS ISOMERIZATION 8.3.
REGULAR STRUCTURES 8.3.A. CT-HELIX 1. 3 10 - AND LL-HELICES 8.3.B.
(3-SHEET 8.3.C. POLYGLYCINE 8.3.D. POLYPROLINE 8.4 A-HELIX FORMATION
FROM A RANDOM COIL 8.4.A. FACTORS STABILIZING THE A-HELIX 8.4.B.
HELIX-COIL TRANSITIONS 8.4.C. HELIX-COIL MODELS 1. ZIMM-BRAGG MODEL 2.
LIFSON-ROIG MODEL 8.4.D. TRIFLUOROETHANOL 8.5. FIBROUS PROTEINS 8.5.A
A-FIBROUS STRUCTURES: COILED COILS 8.5.B. (3-FIBROUS STRUCTURES 8.5.C.
COLLAGENS 9. PROTEIN STRUCTURE 9.1. THREE-DIMENSIONAL STRUCTURES OF
GLOBULAR PROTEINS: MOLECULAR COMPLEXITY 9. LA. TERTIARY STRUCTURE: THE
OVERALL FOLD 9.I.B. SECONDARY STRUCTURE: REGULAR LOCAL STRUCTURES 1.
HELICES 2. (3-STRUCTURE 3. (3-BULGE 9.L.C. REVERSE TURNS: CHANGING
DIRECTION 1. (3-TURNS. 2. Y-TURNS. 3. OMEGA LOOPS 9.I.D. SUPERSECONDARY
STRUCTURES: COMMON MOTIFS 1. (3-HAIRPIN AND (3-MEANDER 2. (3-HELIX AND
(3-ROLL: (3-SOLENOIDS 3. CYSTINE KNOT 4. GREEK KEY MOTIF 5. JELLY ROLL
MOTIF 6. FOUR-HELIX BUNDLE 325 326 326 329 329 334 334 336 337 338 339
342 342 344 344 346 347 348 351 351 352 353 353 354 358 359 362 363 366
369 371 372 374 375 376 377 378 378 379 380 381 381 382 383 XII CONTENTS
7. EPIDERMAL GROWTH FACTOR (EGF) MOTIF 384 8. INTERLEUKIN-1 MOTIF:
TREFOILS 384 9. KRINGLE DOMAIN 385 9.I.E. CONTACT MAPS 386 9.I.F.
INTERIORS AND EXTERIORS. 388 9.I.G. THE SOLVENT: INTERACTIONS WITH WATER
393 9.I.H. QUATERNARY STRUCTURE: INITIATING MACROMOLECULAR ASSEMBLY 394
1. SYMMETRY 398 2. ASYMMETRY AND APPROXIMATE SYMMETRY 400 3. INTERFACES
402 4. OLIGOMERIZATION AND DOMAIN SWAPPING 403 5. FILAMENTOUS ARRAYS 405
9.1.1. CLASSIFICATION OF TERTIARY STRUCTURES: ORDER OUT OF DIVERSITY 405
1. A STRUCTURES 405 2. (3 STRUCTURES 406 3. A(3 STRUCTURES 407 A. TIM,
(A/(3) 8 BARRELS 407 4. A + (3 AND OTHER STRUCTURES 408 5. PROTEIN
STRUCTURE CLASSIFICATION DATABASES 408 9.2. MEMBRANE PROTEINS: AVOIDING
WATER 409 9.2.A. HELICAL SUPERFOLDS 411 9.2.B. (3-BARREL MEMBRANE
PROTEINS 413 9.2.C. MONOTOPIC AND BITOPIC MEMBRANE PROTEINS 414 9.2.D.
INTERACTIONS WITH THE MEMBRANE 414 9.3. PROTEINS WITH SIMILAR FOLDED
CONFORMATIONS: EVOLUTION IN 3-D 415 9.3.A. HOMOLOGOUS PROTEINS: PROTEIN
FAMILIES 415 1. STRUCTURAL HOMOLOGY WITHIN A POLYPEPTIDE CHAIN 421
9.3.B. STRUCTURAL SIMILARITY WITHOUT APPARENT SEQUENCE HOMOLOGY:
SURPRISES 421 9.3.C. SEQUENCE SIMILARITY WITHOUT STRUCTURAL HOMOLOGY:
NEW FOLDS? 422 9.4. PROTEIN STRUCTURE PREDICTION 424 9.4.A. AB INITIO
PREDICTIONS: THE ULTIMATE GOAL 425 9.4.B. SECONDARY STRUCTURE
PREDICTION: A ONE-DIMENSIONAL PROBLEM 426 1. IDENTIFYING TRANSMEMBRANE
HELICES: HYDROPATHY 427 9.4.C. HOMOLOGY MODELING 429 1. INVERSE FOLDING
PROBLEM 430 2. THREADING PROTEIN SEQUENCES 430 9.4.D. DE NOVO PROTEIN
DESIGN 432 10. PHYSICAL PROPERTIES OF FOLDED PROTEINS 434 10.1.
SOLUBILITIES AND VOLUMES OF PROTEINS IN WATER 436 10.1.A. HYDRATION
LAYER 437 10.1.B. PARTIAL VOLUMES 438 10.2. CHEMICAL REACTIVITIES 441
10.2.A. IONIZATION: ELECTROSTATIC EFFECTS 445 10.3. ISOTOPE (HYDROGEN)
EXCHANGE 447 CONTENTS XIII 10.3.A. EXCHANGE IN MACROMOLECULES 447
10.3.B. SOLVENT PENETRATION MODEL 449 10.3.C. LOCAL UNFOLDING MECHANISM
449 1. EX1 MECHANISM 450 2. EX2 MECHANISM 450 10.4. FLEXIBILITY DETECTED
CRYSTALLOGRAPHICALLY 451 10.4. A. EFFECTS OF DIFFERENT CRYSTAL LATTICES
451 10.4.B. THE TEMPERATURE FACTOR: MOBILITY OR DISORDER? 452 10.5.
FLEXIBILITY DETECTED BY NMR 453 10.5.A. NMR TIME SCALES 453 10.5.B.
AROMATIC RING FLIPPING 454 10.6. VARYING THE TEMPERATURE 456 10.7.
EFFECTS OF HIGH PRESSURE 457 10.7.A. ADIABATIC COMPRESSIBILITY 457
10.7.B. ISOTHERMAL COMPRESSIBILITY 458 10.7.C. STRUCTURAL EFFECTS OF
HIGH PRESSURE 458 10.8. SPECTRAL PROPERTIES 459 10.9. INTEGRAL MEMBRANE
PROTEINS 460 11. PROTEIN DENATURATION: UNFOLDING AND REFOLDING 462 11.1.
REVERSIBLE UNFOLDING AT EQUILIBRIUM 463 11.1. A. REVERSIBILITY OF
DENATURATION 463 LL.L.B. COOPERATIVITY OF UNFOLDING 465 LL.L.C.
DENATURANTS 468 11.1 .D. HEAT DENATURATION 472 11.I.E. COLD DENATURATION
474 11.L.F. PH DENATURATION 476 11.1 .G. DENATURATION BY HIGH PRESSURE
478 11.1 .H. BREAKAGE OF DISULFIDE BONDS 480 11.2. UNFOLDED PROTEINS 480
11.2.A. MOLTEN GLOBULE 484 11.2.B. CONFORMATIONAL EQUILIBRIA IN
POLYPEPTIDE FRAGMENTS 486 11.3. PROTEIN STABILITY 488 11.3.A. PHYSICAL
BASIS OF PROTEIN STABILITY 491 1. WATER AND CO-SOLVENTS 496 A.
STABILIZERS 496 B. DESTABILIZERS I 497 C. THE ROLE OF WATER 497 11.3.B.
EFFECTS OF VARYING THE PRIMARY STRUCTURE 498 1. NATURAL PROTEINS OF
EXCEPTIONAL STABILITY 498 2. MUTAGENIC STUDIES 499 11.3.C. STRUCTURAL
STABILITY OF MEMBRANE PROTEINS 503 11.4. PROTEIN REFOLDING IN VITRO 504
11.4.A. REFOLDING OF SINGLE-DOMAIN PROTEINS 505 1. CHARACTERIZING THE
TRANSITION STATE FOR FOLDING 507 2. KINETIC SCHEMES FOR FOLDING 509 XIV
CONTENTS 11.4.B. KINETIC DETERMINATION OF FOLDING 510 1. BACTERIAL
PROTEINASES 511 2. SERPIN PROTEINASE INHIBITORS 512 11.4.C. FOLDING
COUPLED TO DISULFIDE FORMATION 513 11.4.D. PROTEINS WITH MULTIPLE
DOMAINS 516 11.4.E. PROTEINS WITH MULTIPLE SUBUNITS 516 11.4.F.
COMPETITION WITH AGGREGATION AND PRECIPITATION 517 11.4.G. DIFFERENCES
WITH FOLDING IN VIVO 518 SECTION IV: FUNCTIONS 12. LIGAND BINDING BY
PROTEINS 519 12.1. GENERAL PROPERTIES OF PROTEIN-LIGAND INTERACTIONS 520
12.2.METALLOPROTEINS 525 12.2.A. CHELATION: SYNERGY BETWEEN LIGANDS 527
12.2.B. ZINC-BINDING PROTEINS 529 12.2.C. METALLOTHIONEINS 531 12.2.D.
IRON-TRANSPORT AND STORAGE PROTEINS 532 12.2.E. BLUE-COPPER PROTEINS 534
12.3. CALCIUM-BINDING PROTEINS 535 12.3.A. EF-HAND CALCIUM-BINDING
PROTEINS 536 1. CALMODULIN AND TROPONIN C 538 12.3.B. CARBOXYLATION AND
HYDROXYLATION OF ASP, ASN AND GLU RESIDUES 539 12.4. NAD- AND
NUCLEOTIDE-BINDING PROTEINS 540 12.4.A. DINUCLEOTIDE BINDING MOTIF 541
12.4.B. MONONUCLEOTIDE-BINDING MOTIF 543 12.5. ALLOSTERY: INTERACTIONS
BETWEEN DIFFERENT BINDING SITES 543 12.5.A . STRUCTURAL MODELS 544 1.
SEQUENTIAL MODEL: DIRECT INTERACTIONS 544 2. CONCERTED MODEL: QUATERNARY
STRUCTURE CHANGES 545 3. COMPARISON OF THE SEQUENTIAL AND CONCERTED
MODELS 546 12.5.B. HEMOGLOBIN AND MYOGLOBIN 547 1. STRUCTURE 548 2.
OXYGEN BINDING 549 3. COOPERATIVITY OF OXYGEN BINDING 552 4.
HETEROTROPIC INTERACTIONS 554 5. BOHR EFFECT 555 6. ALLOSTERIC MECHANISM
OF HEMOGLOBIN 557 12.5.C. NEGATIVE COOPERATIVITY 560 1. NEGATIVE
COOPERATIVITY OR HETEROGENEITY OF SITES? 562 13. NUCLEIC ACID/PROTEIN
INTERACTIONS 564 13.1. TECHNIQUES FOR MEASURING PROTEIN-DNA INTERACTIONS
566 13.LA. FILTER-BINDING ASSAYS 567 13.1.B. GEL RETARDATION ASSAY 568
13.L.C. FOOTPRINTING 570 13.2. PRINCIPLES OF PROTEIN-DNA RECOGNITION 572
CONTENTS XV 13.2.A. SPECIFICITY OF DNA-PROTEIN BINDING 573 1. SPECIFIC
INTERACTIONS 576 2. NONSPECIFIC COMPLEXES 578 3. WATER-MEDIATED CONTACTS
579 4. DEHYDRATION EFFECTS 579 5. RELEASE OF CONDENSED COUNTERIONS 581
13.2.B. CHANGES IN THE PROTEIN CONFORMATION 582 13.2.C. CHANGES IN THE
DNA CONFORMATION 582 13.3. DNA-BINDING STRUCTURAL MOTIFS 585 13.3.A.
HELIX-TURN-HELIX MOTIF 587 1. LAC REPRESSOR 590 2. LAMBDA CI AND CRO
REPRESSORS 591 3. HOMEODOMAINS 592 4. POU DOMAINS 593 5. TRP REPRESSOR
595 6. CYCLIC AMP RECEPTOR PROTEIN (CRP) / CATABOLITE GENE ACTIVATOR
PROTEIN (CAP) 596 13.3.B. TATA-BINDING PROTEIN (TBP) 598 13.3.C.
ZINC-CONTAINING DNA-BINDING MOTIFS 599 1. ZINC FINGERS 599 2. STEROID
HORMONE RECEPTORS 602 3. GAL4 TYPE 603 13.3.D. BZIP AND HELIX-LOOP-HELIX
DOMAINS 604 13.3.E. (3-SHEETS: METHIONINE REPRESSOR 605 13.3.F. HISTONE
FOLD 607 13.3.G. BACTERIAL TYPE-II DNA-BINDING PROTEINS: HEAT-UNSTABLE
(HU) AND INTEGRATION HOST FACTOR (IHF) 608 13.3.H. SINGLE-STRAND
DNA-BINDING PROTEINS 609 1. PROKARYOTIC SINGE-STRAND DNA BINDING
PROTEINS 609 2. EUKARYOTIC REPLICATION PROTEIN A 610 3. OB
(OLIGONUCLEOTIDE/OLIGOSACCHARIDE BINDING) FOLD 611 13.4. RNA-BINDING
PROTEINS 613 13.4.A. RIBONUCLEOPROTEIN (RNP) DOMAIN 616 13.4.B.
DOUBLE-STRANDED RNA-BINDING DOMAIN 616 13.4.C. KH DOMAIN 618 13.4.D. MS2
BACTERIOPHAGE COAT PROTEIN 619 13.4.E. RECOGNIZING TRANSFER RNAS 620 1.
CLASS-I GLUTAMINYL-TRNA SYNTHETASE 621 2. CLASS-II ASPARTYL-TRNA
SYNTHETASE 622 3. CLASS-II SERYL-TRNA SYNTHETASE 623 4. ELONGATION
FACTOR EF-TU 624 13.4.F. THE RIBOSOME 625 14. CATALYSIS 628 14.1.
CHEMICAL CATALYSIS 630 XVI CONTENTS 14.2. ENZYME KINETICS:
MICHAELIS-MENTEN 630 14.2.A. THE MICHAELIS-MENTEN EQUATION 633 14.2.B. K
M (MICHAELIS CONSTANT) 635 14.2.C. TURNOVER NUMBER (K ) 635 V CAT
14.2.D. LINEWEAVER-BURKE PLOT 635 1. EADIE-HOFSTEE PLOT 636 2.
LINEWEAVER-BURKE VERSUS EADIE-HOFSTEE 637 14.2.E. KINETICS OF INDIVIDUAL
ENZYME MOLECULES 637 14.3. ENZYME KINETIC MECHANISMS WITH MULTIPLE
SUBSTRATES 638 14.3.A. SEQUENTIAL MECHANISMS 639 1. ORDERED MECHANISMS
640 2. RANDOM MECHANISMS 640 14.3.B. NON-SEQUENTIAL MECHANISMS:
PING-PONG 640 14.3.C. INITIAL RATE EQUATIONS 641 1. STEADY-STATE ORDERED
AND RAPID-EQUILIBRIUM MECHANISMS 641 2. EQUILIBRIUM ORDERED MECHANISM
643 3. PING-PONG MECHANISM 643 14.3.D. DEAD-END INHIBITORS 645 14.3.E.
COMPETITIVE INHIBITION 646 1. LINEAR COMPETITIVE INHIBITION 647 2.
HYPERBOLIC COMPETITIVE INHIBITION 649 14.3.F. NONCOMPETITIVE INHIBITION
649 1. LINEAR NONCOMPETITIVE INHIBITION 649 2. HYPERBOLIC NONCOMPETITIVE
INHIBITION 650 14.3.G. UNCOMPETITIVE INHIBITION 651 14.3.H. SUBSTRATE
INHIBITION 652 14.3.1. PRODUCT INHIBITION 654 14.3.J. HALDANE
RELATIONSHIP 655 14.3.K. ISOTOPE EXCHANGE AT EQUILIBRIUM 656 1.
PING-PONG MECHANISM 657 2. SEQUENTIAL REACTIONS 658 14.3.L. SLOW- AND
TIGHT-BINDING ENZYME INHIBITORS 659 14.4. MECHANISMS OF ENZYME CATALYSIS
662 14.4A. REACTIONS ON THE ENZYME 666 14.4.B. STABILIZING THE
TRANSITION STATE 668 1. TRANSITION STATE ANALOGUES 669 14.4.C. ENTROPIC
CONTRIBUTIONS 672 14.4.D. BISUBSTRATE ANALOGUES 675 LAP 5 A 675 2.
N-PHOSPHONACETYL-L-ASPARTATE (PALA ) 676 14.4.E. INDUCED FIT 677 14.4.F.
COVALENT CATALYSIS 680 14.4.G. COFACTORS, COENZYMES, AND PROSTHETIC
GROUPS 681 1. PYRIDOXAL PHOSPHATE 681 14.4.H. SUICIDE SUBSTRATES 683
CONTENTS XVII 14.4.1. CRYOENZYMOLOGY 685 14.4.J. TIME-RESOLVED
CRYSTALLOGRAPHY 685 14.4.K. POLYMERIC SUBSTRATES: PROCESSIVITY 686
14.4.L. ENZYME FUNCTION IN VIVO: TOWARD PERFECTION 688 14.4.M. ONE
EXAMPLE: TYROSYL TRNA SYNTHETASE 691 1. EDITING OF AMINO ACID ACTIVATION
695 14.5. CATALYTIC ANTIBODIES 696 14.6. CATALYTIC NUCLEIC ACIDS:
RIBOZYMES AND DEOXYRIBOZYMES (DNAZYMES). 698 14.6.A. NATURAL REACTIONS
698 14.6.B. RIBOZYME STRUCTURE AND CATALYSIS 701 14.6.C. SELECTION FOR
NOVEL RIBOZYMES AND DEOXYRIBOZYMES 702 14.6.D. LIGAND-BINDING NUCLEIC
ACIDS: APTAMERS 704 15. ENZYME REGULATION 706 15.1. ALLOSTERIC ENZYMES
707 15.1.A. ALLOSTERIC MODELS 708 15.1.B. STRUCTURAL ASPECTS 709 15.L.C.
ASPARTATE TRANSCARBAMOYLASE 710 15.1.D. PHOSPHOFRUCTOKINASE 717 1.
MECHANISM OF PHOSPHORYL TRANSFER 718 2. ALLOSTERIC PROPERTIES OF E. COLI
PFK 719 15.I.E. THREONINE SYNTHASE 720 15.2. COVALENT REGULATION 721
15.2.A. PHOSPHORYLATION 721 1. PHOSPHORYLATION IN EUKARYOTES 722 2.
PHOSPHORYLATION IN PROKARYOTES 724 3. PROTEIN PHOSPHORYLATION IN SIGNAL
TRANSDUCTION NETWORKS 725 4. SPECIFICITY OF PROTEIN PHOSPHORYLATION 725
5. EFFECTS OF PHOSPHORYLATION ON THE PROPERTIES OF PROTEINS 726 6.
METHODS TO CHARACTERIZE PROTEIN PHOSPHORYLATION 727 15.2.B. GLYCOGEN
PHOSPHORYLASE 728 1. REGULATION BY PHOSPHORYLATION 731 2. ALLOSTERIC
PROPERTIES OF GLYCOGEN PHOSPHORYLASE 733 15.2.C. ADENYLYLATION 735 1.
GLUTAMINE SYNTHETASE 736 15.2.D. PROTEOLYSIS: TURNING ZYMOGENS INTO
PROTEINASES 738 1. TRYPSIN FAMILY OF SERINE PROTEINASES 738 2. CARBOXYL
PROTEINASES 740 3. METALLOPROTEINASES 742
|
| any_adam_object | 1 |
| author | Creighton, Thomas E. |
| author_facet | Creighton, Thomas E. |
| author_role | aut |
| author_sort | Creighton, Thomas E. |
| author_variant | t e c te tec |
| building | Verbundindex |
| bvnumber | BV036613798 |
| classification_rvk | WD 5000 WD 5100 |
| classification_tum | PHY 821f CHE 860f CHE 802f |
| ctrlnum | (OCoLC)699543912 (DE-599)BVBBV036613798 |
| discipline | Physik Biologie Chemie |
| format | Book |
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| id | DE-604.BV036613798 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:44:12Z |
| institution | BVB |
| isbn | 9780956478115 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-020533987 |
| oclc_num | 699543912 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM |
| owner_facet | DE-M49 DE-BY-TUM DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM |
| physical | XXXVII, 774 S. Ill., graph. Darst. |
| publishDate | 2010 |
| publishDateSearch | 2010 |
| publishDateSort | 2010 |
| publisher | Helvetian Press |
| record_format | marc |
| spelling | Creighton, Thomas E. Verfasser aut The biophysical chemistry of nucleic acids & proteins Thomas E. Creighton Nucleic acids & proteins [Eastbourne] Helvetian Press 2010 XXXVII, 774 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Proteine (DE-588)4076388-2 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 gnd rswk-swf Biophysikalische Chemie (DE-588)4291844-3 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 s Proteine (DE-588)4076388-2 s Biophysikalische Chemie (DE-588)4291844-3 s b DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020533987&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Creighton, Thomas E. The biophysical chemistry of nucleic acids & proteins Proteine (DE-588)4076388-2 gnd Nucleinsäuren (DE-588)4172117-2 gnd Biophysikalische Chemie (DE-588)4291844-3 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4172117-2 (DE-588)4291844-3 |
| title | The biophysical chemistry of nucleic acids & proteins |
| title_alt | Nucleic acids & proteins |
| title_auth | The biophysical chemistry of nucleic acids & proteins |
| title_exact_search | The biophysical chemistry of nucleic acids & proteins |
| title_full | The biophysical chemistry of nucleic acids & proteins Thomas E. Creighton |
| title_fullStr | The biophysical chemistry of nucleic acids & proteins Thomas E. Creighton |
| title_full_unstemmed | The biophysical chemistry of nucleic acids & proteins Thomas E. Creighton |
| title_short | The biophysical chemistry of nucleic acids & proteins |
| title_sort | the biophysical chemistry of nucleic acids proteins |
| topic | Proteine (DE-588)4076388-2 gnd Nucleinsäuren (DE-588)4172117-2 gnd Biophysikalische Chemie (DE-588)4291844-3 gnd |
| topic_facet | Proteine Nucleinsäuren Biophysikalische Chemie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020533987&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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