The Biophysical Chemistry of Nucleic Acids & Proteins Helvetian Press © Thomas E Creighton 2010 Published by Helvetian Press 2010 www.HelvetianPress.com HelvetianPress@gmail.com All rights reserved No part of this book may be reproduced, adapted, stored in a retrieval system or transmitted by any means, electronic, mechanical, photocopying, or otherwise without the prior written permission of the author ISBN 978-0-9564781-1-5 ~ PREFACE ~ The field of molecular biology continues to be the most exciting and dynamic area of science and is predicted to dominate the 21st century Only by investigating biological phenomena at the molecular level is it possible to understand them in detail Such understanding is vital for advances in medicine, and the pharmaceutical industry that produces new drugs and cures is greatly dependent upon molecular biology But molecular biology also contributes to the understanding of what human beings are and how they fit into this universe This volume builds on its companion volume, The Physical and Chemical Basis of Molecular Biology It will be most intelligible and useful if the reader is aware of the information in that volume Proteins and nucleic acids are the primary subjects of molecular biology They carry, transmit, and express the genetic information that defi nes each living organism It is vital to understand how these molecules function The first chapter is an introduction to the covalent structures and conformations of macromolecules The next four chapters deal with the nucleic acids The structural and chemical properties of DNA are the basis of its central role in storing and transmitting the genetic information (Chapter 2) DNA molecules tend to be immensely long, equivalent to a rope that is many kilometers long, which gives them special topological properties that must be accommodated (Chapter 3) The structure of RNA differs from DNA only very slightly, but this gives it remarkably diff erent properties and functions (Chapter 4) The abilities of individual strands of DNA and RNA to base-pair with other strands with complementary nucleotide sequences are central to many techniques of molecular biology and increasingly to molecular medicine (Chapter 5) Th e ability to manipulate nucleic acids is central to molecular biology and described in Chapter The next six chapters deal with proteins, starting with the chemical properties of polypeptide chains and the implications of their covalent structures (Chapter 7) The conformational properties of polypeptides determine the structures that proteins can adopt (Chapter 8), to produce threedimensional structures of incredible diversity and amazing functional properties (Chapter 9) Proteins in solution have very important dynamic properties that are crucial for their biological activities (Chapter 10) They also have a propensity to lose their folded structures and unfold, and how proteins this and how they manage to fold to their native three-dimensional structure remains a major question (Chapter 11) The final four chapters describe the most fundamental functional properties of proteins and nucleic acids Central to the functions of proteins is their interactions with other molecules (Chapter 12) xx 20 PREFACE Some of the physiologically most important interactions are those between proteins and nucleic acids (Chapter 13) The most impressive and important property of proteins and nucleic acids is their ability of catalyze the rates of chemical reactions by many orders of magnitude, and usually incredibly specifically (Chapter 14) Such potent chemical capabilities must be controlled very closely (Chapter 15) The references listed were chosen to be those that would best provide the interested reader with entry to the literature They should not be assumed to be those most important for the subject No one person can be expert in all the areas of molecular biology, so I have made ample use of the work of many others more expert than me, but too numerous to specify Very special thanks are due to Eric Martz of the University of Massachusetts for making available the program Firstglance in Jmol (http://firstglance.jmol.org) It is incredibly useful for examining protein structures and, at least as important, is very easy to use Of course, shortcomings and errors in this volume are totally my responsibility, for which I apologize in advance Criticisms and suggestions would be welcome and can be sent to me at HelvetianPress@ gmail.com Thomas E Creighton CONTENTS Preface xix Common Abbreviations xxi Glossary xxv Section I: Macromolecules Configurations and conformations 1.1 Stereochemistry 1.1.A Chirality Enantiomers Racemic mixtures Diastereomers Epimers and epimerization Cis and trans isomers 1.1.B Prochiral 1.1.C Tautomers 1.2 Conformations 1.2.A Torsion angle 1.2.B Dihedral angle 1.3 Conformations of idealized polymers 1.3.A Random coils End-to-end distances Radius of gyration Characteristic ratio 1.3.B Excluded volume effects and theta solvents Covalent cross-links 1.4 Structure databases: structures on the WEB 10 12 13 15 16 17 18 19 21 21 22 23 24 Section II: Nucleic acids DNA structure 2.1 Polynucleotides 25 26 vi CONTENTS 2.1.A The deoxyribose group 2.1.B Properties of the bases 2.1.C Modifications of the bases 2.2 DNA three-dimensional structures 2.2.A Base pairing and stacking 2.2.B Double helices B-DNA A-DNA Z-DNA 2.2.C Other DNA structures Hoogsteen base pairs Triple helices H-DNA: intramolecular triple helices Four-stranded structures: guanine quartet i- motif Inverted repeat sequences and palindromes Helical junctions: cruciforms, Holliday junctions Parallel-stranded DNA duplexes 2.3 DNA as a polyelectrolyte: hydration and counterions 2.4 DNA flexibility and dynamics: curving, twisting, stretching 2.4.A Local flexibility 2.4.B Hydrogen exchange 2.5 Binding of small molecules 2.5.A Binding to the minor groove 2.5.B Intercalation Ethidium bromide Psoralen photo cross-linking 2.6 Chemical modification as a probe of structure 2.6.A Cross-linking DNA topology 3.1 Supercoiling and superhelices: topoisomers 3.2 Linking number, Lk 3.2.A Linking difference , ΔLk Relaxed duplex DNA 3.2.B Superhelix density, σ 3.3 Topoisomerases 3.4 Twist and writhe 3.4.A Twist, Tw 3.4.B Writhe, Wr 3.5 DNA topology and geometry 3.5.A Experimental characterization of DNA topology Electron microscopy Gel electrophoresis to separate topoisomers 29 31 37 40 42 46 52 53 54 56 56 57 60 60 63 64 66 66 68 71 74 75 77 77 78 78 79 80 85 86 90 92 92 93 94 95 96 96 97 98 99 99 101 CONTENTS vii Intercalation by ethidium bromide Two-dimensional gel electrophoresis 3.6 Energetics of supercoiling 3.6 B Energy distribution of topoisomers 3.6 C Topology-dependent binding of ligands 3.7 DNA wrapped around the nucleosome 101 101 103 104 105 106 RNA structure 4.1 Secondary structure of RNA 4.1.A Hairpin loops 4.1.B Tetraloops 4.1.C Bulges and internal loops 4.2 Tertiary structure of RNA 4.2.A Common structural motifs Pseudoknots Coaxial helices: interhelical stacking A-minor motif Dinucleotide platform “Kissing” hairpin loops Ribose zipper Uridine turn Tetraloop/receptor interactions Roles of ions 4.2.B Transfer RNA structures 4.2.C Ribozyme structures 4.3 Quaternary structure of RNA 4.4 RNA structure prediction 4.4.A Prediction of secondary structure Thermodynamic approach Phylogenetic approach 4.4.B Prediction of tertiary structure 108 112 116 117 118 118 120 120 121 122 123 123 124 125 126 126 127 129 133 134 134 134 135 137 Denaturation, renaturation, and hybridization of nucleic acids 5.1 Denaturation of double-stranded nucleic acids 5.1.A Methods for monitoring denaturation 5.1.B Double-stranded DNA Thermal melting Denaturants pH Salt effects Prediction of the Tm 5.1.C Double-stranded RNA 5.1.D DNA • RNA heteroduplexes 5.1.E Single-stranded nucleic acids Physical stretching 5.2 Unfolding and refolding of single-stranded RNA molecules 139 139 140 142 143 144 145 145 146 148 149 149 150 150 viii CONTENTS 5.2.A Transfer RNA unfolding/refolding 5.2.B Ribozyme unfolding/refolding 5.2.C Unfolding using mechanical force 5.3 Renaturation, annealing, and hybridization 5.3.A Competing intramolecular structures in individual single strands 5.3.B C0t and R0t curves 5.3.C Probe hybridization Stringency Analyzing the extent of complementarity In situ hybridization 5.4 DNA mimics: peptide nucleic acids 5.4.A Chemistry and synthesis 5.4.B Hybridization properties PNA•DNA and PNA•RNA duplexes (PNA)2•DNA triplexes Strand invasion: binding to double-stranded DNA PNA duplexes and triplexes 5.4.C Structures of PNA complexes 153 154 155 157 162 163 165 167 168 170 170 172 172 173 173 173 175 175 Manipulating nucleic acids 6.1 Replicating DNA 6.1.A DNA polymerase 6.1.B DNA ligase 6.1.C Polymerase chain reaction (PCR) 6.2 Producing RNA 6.2.A RNA replication: RNA replicases 6.2.B Transcription: DNA-dependent RNA polymerases Single-subunit phage DNA-dependent RNA polymerases 6.2.C Reverse transcription: RNA into DNA 6.2.D Antisense oligonucleotides 6.3 Cloning 6.3.A Expression vectors 6.3.B cDNA libraries 6.3.C Restriction enzymes 6.3.D Restriction maps 6.4 Sequencing DNA 6.4.A Isolating the DNA fragments to be sequenced 6.4.B Chain-termination, Sanger method 6.4.C Separating the DNA fragments by size 6.4.D Alternative approaches 6.5 Sequencing RNA 6.5.A Direct sequencing of oligoribonucleotides 6.5.B Identifying modified nucleotides 6.6 Chemical synthesis of DNA 6.6.A Protecting groups for 2´-deoxynucleosides 6.6.B Coupling methods 177 177 178 181 182 185 185 186 188 189 190 191 193 194 195 196 198 199 199 203 204 205 205 207 208 211 211 CONTENTS Phosphotriester procedure Phosphoramidite procedure 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 ix 211 212 213 215 216 218 220 220 222 223 Section III: Proteins 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, Ile, Val) 7.2.C Hydroxyl residues (Ser, Thr) 7.2.D Arginine (Arg) 7.2.E Lysine (Lys) Acetylation by anhydrides Amidination Guanidination Schiff base formation Carbamylation 7.2.F Histidine (His) 7.2.G Acidic residues (Asp, Glu) 7.2.H Amide residues (Asn, Gln) Deamidation 7.2.I Cysteine (Cys) Alkylation of thiol groups Thiol addition across double bonds Binding of metal ions Oxidation of thiol groups Disulfide bonds Thiol-disulfide exchange Dithiothreitol, dithioerythritol 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.O Selenocysteine (Sec) 7.2.P Physical properties and hydrophobicities of amino acid residues 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 x10 CONTENTS Hydrophilicities Hydrophobicities 7.3 Protein detection 7.3.A Biuret reaction 7.3.B Lowry assay 7.3.C Ninhydrin 7.3.D Fluorescamine 7.3.E Coomassie brilliant blue 7.3.F Ponceau S 7.4 Peptide synthesis 7.4.A Chemistry of polypeptide chain assembly Chemical ligation of peptide fragments 7.4.B Solution or solid phase? 7.4.C Peptide libraries 7.5 Peptide and protein sequencing 7.5.A Amino acid analysis Peptide bond hydrolysis Quantifying amino acids Counting residues 7.5.B Fragmentation of a protein into peptides Proteolytic enzymes Chemical methods of cleavage 7.5.C Peptide mapping 7.5.D Diagonal maps Isolating peptides containing certain amino acids Identifying disulfide bonds 7.5.E Sequencing Amino-terminal and carboxyl-terminal residues Sequencing from the N-terminus: the Edman degradation Sequencing from the C-terminus Sequencing by mass spectrometry 7.5.F Protein sequences from gene sequences Post-translational modifications 7.6 Primary structures of natural proteins: evolution at the molecular level 7.6.A Homologous genes and proteins Detecting sequence homology Aligning homologous sequences Orthologous / paralogous genes and proteins Nature of amino acid sequence differences Rates of divergence Roles of selection a Neutral mutations and negative selection b Positive selection for functional mutations 7.6.B Gene rearrangements and the evolution of protein complexity Gene duplications 261 261 267 267 268 268 269 270 271 271 272 275 276 278 280 280 281 282 283 285 285 288 289 291 291 292 293 294 295 298 299 301 302 306 307 310 313 314 315 318 321 322 323 324 324 Index Terms Links rubredoxin 522 Ruhemann's purple 268 S 35 S (sulfur-35) 202 S-adenosyl-methionine 37 S1 domain 614 S1 nuclease 84 605 718 142 164 S1 ribosomal protein 613 salt bridges 338 392 395 443 500 556 607 740 Sanger DNA sequencing method 199 207 sarcosine 144 496 satellite RNA 129 698 701 scaffolding proteins 343 668 725 scanning calorimetry 467 472 scanning force microscopy 100 scanning transmission electron microscopyy 567 Scatchard plot 636 Schiff base 13 SCOP database 408 SCOR (structural classification of RNA) data base 120 screw rotation 17 238 667 445 477 682 697 729 498 398 SdaI restriction enzyme 195 SDS-PAGE 290 569 second messengers 535 724 731 secondary structure, nucleic acid xxxv 111 127 150 160 165 327 xxxv 338 344 353 362 369 380 386 392 395 404 418 421 425 458 460 484 503 514 542 611 xxxvi 99 567 625 712 selection, natural 307 317 321 421 497 501 511 selection marker gene 193 selenocysteine 128 136 259 SELEX 703 625 secondary structure, protein 615 secretory vesicles, granules sedimentation 304 This page has been reformatted by Knovel to provide easier navigation Index Terms Links self-splicing introns 120 127 129 151 699 seminal ribonuclease 404 sensor kinase/response regulator 723 sequence alignment 136 158 312 317 429 sequencing DNA 198 sequencing peptides 280 sequencing RNA 205 sequential allosteric model 544 559 708 734 sequential enzyme mechanism 639 658 Ser/Thr protein kinases 194 722 serine (Ser) residues 232 260 264 282 288 302 305 317 340 347 355 358 376 390 417 419 426 436 441 446 615 663 678 718 721 729 737 738 441 467 511 535 serine carboxypeptidase 422 serine hydroxymethylase 682 serine proteinases 286 305 417 540 667 738 serine stack 380 serpins 325 512 serum albumin 326 439 serum response factor (SRF) 584 seryl-tRNA synthetase 620 623 seven-helix fold 358 412 SH2 domains 725 shear number 373 sheared base pair 162 shearing DNA β-sheets 457 406 71 163 338 339 342 351 358 369 372 396 405 418 423 447 456 458 491 503 512 514 541 543 605 615 721 720 Shine-Dalgarno sequence 192 shotgun DNA sequencing 203 207 300 23 175 227 227 329 364 406 427 446 452 469 477 483 500 522 525 530 side-chain side chains, amino acid This page has been reformatted by Knovel to provide easier navigation Index Terms Links side chains, amino acid (Cont.) 533 535 547 556 577 582 599 662 682 693 709 718 721 725 732 739 602 704 705 sigma factor 187 signal peptide 303 signal recognition particle (SRP) 118 614 28 423 537 544 709 721 724 737 signal transduction silica gel 215 silk 357 silver 247 silver stain 267 similarity index 310 simulated annealing 429 single-strand DNA-binding proteins 609 single-stranded oligonucleotides site-directed mutagenesis 270 22 28 40 60 72 75 77 79 81 84 108 111 113 141 149 175 178 182 190 195 204 208 218 567 609 687 704 218 327 498 548 577 663 728 skatole skin 258 289 79 359 sliding clamps 687 slot blot 166 slow-binding enzyme inhibitors 659 Sm domain 614 Smad 588 small nuclear RNP (snRNP) 133 small-angle neutron scattering 438 small-angle X-ray scattering 484 snake venom phosphodiesterase 207 snake venom toxins 320 snRNA (small nuclear RNA) 186 614 sodium dodecyl sulfate (SDS) 497 503 β-solenoids 380 solid-phase folding 517 671 684 186 614 728 This page has been reformatted by Knovel to provide easier navigation 693 Index Terms Links solid-phase sequencing 296 solid-phase synthesis 172 212 216 220 222 272 274 22 144 261 269 353 436 464 469 498 532 211 215 220 222 271 13 17 22 31 69 127 245 263 333 338 341 344 353 375 388 392 432 436 440 445 456 473 467 475 482 492 494 521 577 580 630 697 12 22 54 491 solvent, cryogenic 456 502 685 solvent, crystalline 394 452 solvent, denaturation 145 474 solvent, theta 22 481 solvent exchange 76 240 438 447 484 solvent exposure 44 52 68 79 130 138 181 245 347 348 372 388 392 402 412 432 436 440 447 459 469 473 484 492 494 521 523 532 540 549 552 564 579 611 623 662 740 solvent penetration 438 446 449 458 solvent perturbation 459 666 383 solubility solution-phase synthesis solvation solvent sonication 496 71 sorbitol 496 southern bean mosaic virus 401 Southern blot 166 soybean trypsin inhibitor 439 SP6 phage 188 457 specific linking difference 94 spectral properties, nucleic acid 33 140 255 459 481 spermidine 54 126 130 spermine 54 69 126 spine, hydration 53 68 77 614 701 spectral properties, protein spliceosome 742 This page has been reformatted by Knovel to provide easier navigation Index Terms Links splicing RNA xxxvi 108 205 699 Src 725 SRP (signal recognition particle) 118 SRY 588 stabilizers 496 120 127 129 151 190 614 stacked X structure 66 stacking, base 42 49 52 55 57 66 72 74 78 112 116 118 125 127 131 134 140 143 150 154 163 165 175 583 610 615 617 621 141 169 267 293 361 476 483 487 535 629 656 660 666 691 623 701 623 staggered end 195 stain 99 stammer 357 staphylococcal nuclease 445 star activity 196 starch 686 start codon 193 statistical segment 302 22 staufen 614 617 steady-state enzyme kinetics 633 640 648 711 718 732 125 133 168 621 13 171 87 184 192 195 29 55 90 103 248 251 404 492 495 511 694 342 358 396 404 413 418 422 500 512 514 521 534 541 588 600 605 611 616 729 740 71 150 155 stellacyanin 535 stem-loop 113 stereochemistry stereoisomers xxxvi steroid hormone receptors 602 sticky ends xxxvi stop codons 192 strain, conformational β-strand strand invasion 173 streptavidin 168 stretching 31 This page has been reformatted by Knovel to provide easier navigation Index Terms Links stringency 161 167 structural proteins 305 325 363 397 423 structure prediction, protein 424 structure prediction, RNA 134 stutter 357 submaxillary proteinase 287 substrate enzyme inhibition 652 657 659 675 707 subtilisin 422 445 535 665 subtractive hybridization 195 succinic anhydride 235 283 succinimides 235 244 257 289 292 suicide substrates 683 sulfate-binding protein 523 sulfates 496 sulfation 304 sulfenate 248 235 237 240 277 282 286 464 480 sulfhydryl (thiol) group 436 520 245 259 275 291 305 348 442 492 513 525 531 534 87 357 423 712 sulfinate 248 sulfite 249 sulfones 255 291 sulfonic acid 172 235 248 282 sulfonium salts 246 254 258 292 sulfoxides 145 255 685 sulfur atoms 207 393 530 704 SULT1A1 654 60 64 66 90 354 406 423 superoxide dismutase 397 403 522 superoxide ion 532 supersecondary structures 362 378 422 supershift 569 surface plasmon resonance 567 supercoiling 55 supercooled water superhelix 476 This page has been reformatted by Knovel to provide easier navigation Index Terms Links surface areas 37 44 52 260 263 342 366 388 392 395 402 440 457 470 473 475 491 494 561 579 583 37 44 50 53 68 97 103 144 564 322 341 354 360 364 366 372 375 378 388 402 409 429 434 452 456 460 469 480 484 486 490 508 515 521 525 534 538 572 575 582 586 597 599 602 606 610 613 615 622 662 687 709 736 738 740 surfaces, RNA 127 138 SV-11 RNA 154 SV40 virus 101 SWI5 600 SWISS-PROT 306 surfaces, DNA surfaces, proteins symmetry 610 20 29 41 47 61 64 66 106 114 118 137 195 228 232 256 332 344 384 395 407 411 421 435 452 455 460 545 560 575 584 589 596 603 619 622 640 687 693 715 718 720 730 733 736 syn conformation 14 27 30 55 synclinal conformation 14 527 640 694 synergy 500 synperiplanar conformation synthesizers 715 14 216 272 T arm, loop, tRNA 119 127 624 T loop, kinase 723 T state, allosteric 544 712 730 734 204 420 194 201 T T-even bacteriophages 38 T4 bacteriophage 38 182 T4 lysozyme 452 477 T7 phage 186 188 280 This page has been reformatted by Knovel to provide easier navigation Index Terms Links TAF (TBP-associated factor) 588 598 608 Taq DNA polymerase 200 TAR RNA 157 574 579 581 584 588 598 xxxvi 12 29 33 42 75 238 240 TBDMS protecting group 220 222 224 TBP (TATA binding protein) 574 579 581 584 588 598 TCF-1 588 665 tartaric acid TATA box, binding protein (TBP) 193 tau protein 484 taurinomethyluridine 220 tautomers telomerase, telomere 60 220 613 temperature factor 74 393 452 456 471 359 361 xxxvi 47 90 111 118 136 151 236 353 362 366 385 400 405 415 427 431 434 458 484 503 511 516 558 615 620 397 526 530 534 712 153 617 tendon tertiary structures 625 tetrahedral atoms tetrahedral intermediates tetrahedral symmetry tetrahydrofuran tetrahydrofuryl group 670 xxxvi 214 35 tetrahydrophthaloyl anhydride 236 Tetrahymena ribozyme 130 154 156 tetraloops 117 120 126 tetramethyl guanidine 211 215 223 tetranitromethane 257 441 tetrazole 212 216 TF1 588 608 TGGE (transverse gradient gel electrophoresis) 224 95 Theorell-Chance mechanism 640 thermal expansion 456 thermochromism 238 thermodynamic approach, RNA structure 134 thermolysin 286 458 422 671 This page has been reformatted by Knovel to provide easier navigation Index Terms Links thermophiles 182 190 200 498 501 583 677 691 theta solvent 22 thiacytidine 39 481 thiamine pyrophosphate 111 thin-layer chromatography 207 291 thin-layer electrophoresis 291 728 thio-dATP 202 thioguanine 39 thiohydantoins thiol (sulfhydryl) group 296 298 235 237 240 245 259 275 277 282 286 291 305 348 442 464 480 492 513 525 531 534 513 712 thiol-disulfide exchange 246 248 492 thiolate ion 245 275 534 thiophosphate 204 207 thiouracil 38 thiouridine (s U) 110 Thp protecting group 220 threading protein sequences 425 three-hybrid system 615 threonine (Thr) residues 229 231 260 262 264 282 288 302 305 317 336 340 347 355 376 390 419 446 457 470 542 695 721 732 401 720 417 540 threonine synthase threose 208 430 thrombin, prothrombin 309 thymine phosphorylase 651 322 385 thymine, thymidine 26 56 60 tilt, base-pair 43 47 53 373 405 422 TIM barrel tipping, base-pair 92 43 tissue plasminogen activator 309 titin 405 titration curve, pH 445 476 This page has been reformatted by Knovel to provide easier navigation Index Terms Links Tm (melting temperature) 116 142 146 184 471 489 TNBS (trinitrobenzene sulfonate) 235 tobacco mosaic virus (TMV) 397 toluene 255 261 tomato bushy stunt virus 185 382 401 95 100 107 158 168 173 175 329 334 337 344 topoisomers 86 topoisomerases 93 topological bond 90 topological domain 86 103 toroidal superhelix 90 99 torsion angle 14 29 74 248 253 337 339 364 371 418 14 330 361 368 481 505 518 xxxvi 55 57 60 86 90 96 108 120 128 133 153 186 193 204 564 573 590 592 596 602 615 724 738 xxxvi 186 193 529 531 564 574 579 586 593 596 598 600 604 29 57 110 113 116 119 127 138 149 153 186 189 205 208 614 617 620 656 691 701 325 533 transition metals xxxvi 84 532 transition state xxxvi 76 84 152 175 246 250 377 455 506 515 628 630 638 663 668 691 679 685 688 696 699 701 702 719 669 675 680 696 xxxvi 108 120 127 186 189 301 327 564 618 torsional persistence length 72 tower helices 730 tramtrack 588 trans conformation transcription transcription factors 726 transfer RNA (tRNA) transferrin transition state analogs translation This page has been reformatted by Knovel to provide easier navigation Index Terms Links translational diffusion xxviii 21 73 75 89 117 158 170 337 413 434 441 460 521 552 556 566 579 593 631 634 686 688 697 709 383 410 427 503 723 transmembrane polypeptides transposable element transverse relaxation time (T2) trefoil 64 453 89 β-trefoil 384 trehalose 456 trialkyloxonium salts 241 tributyl phosphine 249 trichloroacetic acid (TCA) 217 224 497 triethylamine 225 279 281 triethyloxonium tetrafluoroborate 241 trifluoroacetic acid (TFA) 232 274 279 281 297 trifluoroethanol 353 trifluoromethanesulfonic acid 172 trihydrofluoride 225 trimethylamine-N-oxide 496 trimethylsilanolate 298 (trimethylsilyl)ethanol 275 trinitrobenzene sulfonate (TNBS) 235 triose phosphate isomerase (TIM) 373 405 422 629 670 689 496 triostine 57 triple helices (triplexes) 57 80 145 154 172 305 359 tRNA synthetases 129 560 614 620 656 665 691 tropomyosin 355 405 439 539 troponin 371 405 537 trp repressor 395 517 574 579 582 595 605 trypsin inhibitors 284 293 364 367 387 391 439 448 457 247 286 293 300 319 325 382 417 422 439 441 452 457 511 535 738 tryptophan 595 695 tryptophan biosynthesis 326 690 trypsin, trypsinogen This page has been reformatted by Knovel to provide easier navigation Index Terms Links tryptophan (Trp) residues tumbling, DNA 229 231 255 257 260 262 264 282 286 289 292 302 311 318 347 355 376 390 410 419 440 443 455 458 470 531 615 718 661 666 684 73 tungstate 268 tunneling, intermediates 690 turnover, enzyme 633 635 637 698 701 708 343 358 375 385 43 53 71 88 90 119 584 twist, β-sheet 342 358 372 374 378 406 729 two-component system 724 tyrosinase 652 tyrosine kinases 723 95 229 256 260 262 264 282 286 302 304 311 317 347 355 390 410 419 440 454 459 470 476 525 531 533 615 663 697 715 721 736 560 665 691 375 377 459 685 β-turns twist (Tw), DNA tyrosine (Tyr) residues tyrosyl-tRNA synthetase U U1 spliceosomal protein 614 UBF 588 ubiquitin UDP-glucose 733 ultrabithorax 581 uncompetitive enzyme inhibition 646 648 650 underwound superhelix 90 93 101 585 unfolded proteins 19 21 227 282 332 334 345 353 360 389 434 453 531 534 582 741 108 127 139 203 14 140 254 345 349 353 360 424 435 437 440 445 447 462 741 unfolding, nucleic acids unfolding, proteins unperturbed random coil, state 19 This page has been reformatted by Knovel to provide easier navigation Index Terms Links upstream 188 193 598 UpU 44 uracil, uridine 26 31 35 42 75 81 112 139 208 223 225 613 144 150 203 239 284 448 463 468 473 481 488 497 499 503 517 582 712 urethane 272 274 276 uridine turn 125 130 uridylyl transferase 737 uridylylation 737 urokinase 309 uteroglobin 403 uranyl acetate 108 99 urea UV absorbance 33 37 80 140 144 153 157 168 245 253 255 258 267 282 459 463 481 566 V V-8 proteinase 286 V-system 707 valine (Val) residues 229 231 260 262 265 273 281 287 302 306 311 317 333 340 347 354 371 390 392 411 419 44 270 338 389 462 491 501 538 547 572 577 582 587 591 25 69 106 179 189 366 370 389 412 438 520 601 Van der Waals surface 103 367 416 616 Van der Waals volume 231 260 389 423 438 440 548 van't Hoff plot 468 506 vanadate 671 Varkud satellite ribozyme 698 701 vectors, cloning 188 191 199 203 218 vectors, expression 192 327 615 valyl tRNA synthetase Van der Waals interactions 695 615 Van der Waals radius This page has been reformatted by Knovel to provide easier navigation Index Terms Links vicinal hydroxyl groups xxxvii 108 vinyl pyridine 285 vinylglycine 684 virtual bond 19 334 367 xxxvii 24 39 101 108 113 125 131 141 185 189 195 199 205 207 280 304 382 397 399 407 424 531 609 613 617 620 651 337 456 463 477 482 viruses 698 viscosity 140 vitamin K 540 volume fluctuations 439 458 12 35 44 49 56 64 68 75 79 113 117 126 144 244 261 269 273 286 333 336 338 343 346 352 358 372 388 407 409 427 436 444 447 456 462 464 469 479 482 490 519 521 525 537 548 552 572 578 587 595 599 615 631 638 669 677 697 701 25 41 46 52 56 61 66 88 112 115 123 133 147 171 178 572 621 625 701 W water Watson-Crick winged helix fold 588 worm-like chain 72 writhe (Wr), topological 96 wyosine (Wyo) 107 110 X X-ray crystallography 24 46 53 57 74 106 364 370 409 428 451 453 471 585 618 625 654 685 727 X-ray scattering 484 X-ray absorption spectroscopy 525 xanthine 82 This page has been reformatted by Knovel to provide easier navigation Index Terms Links xylulose kinase 680 Y yeast 327 yeast artificial chromosomes 191 Young modulus 615 690 716 723 46 54 69 72 93 72 Z Z-form DNA 30 Zif268 600 Zimm-Bragg model 150 349 zinc fingers 572 588 599 610 614 625 zinc ions 240 247 286 520 526 534 599 712 742 zinc proteinases 286 742 zipper, leucine 354 358 578 590 604 625 zipper, ribose 124 zippering 158 160 345 361 zwitterions xxxvi 228 498 669 zymogens 540 738 This page has been reformatted by Knovel to provide easier navigation 99 588 ... between proteins and nucleic acids (Chapter 13) The most impressive and important property of proteins and nucleic acids is their ability of catalyze the rates of chemical reactions by many orders of. .. in the case of DNA and RNA, and 20 amino acids in the case of proteins In each of these cases, each residue, i, of the chain consists of two parts: group X comprises the backbone and is the constant,... Calcium-binding proteins 12.3.A EF-hand calcium-binding proteins Calmodulin and troponin C 12.3.B Carboxylation and hydroxylation of Asp, Asn and Glu residues 12.4 NAD- and nucleotide-binding proteins