Introduction to Protein Science: Architecture, Function, and Genomics / Edition 3

by Arthur Lesk

Overview

Over the last century, the centrality of proteins to life on earth has become increasingly clear - from forming crucial molecules such as antibodies in the immune system to acting as catalysts for specific reactions, and as signalling molecules between cells. In fact, the more they are studied, the more proteins continue to reveal new and exciting functions. Indeed, by studying amino acid sequences it is even possible to unravel some of the mysteries of evolution itself.

Introduction to Protein Science, 3rd edition, provides a rich and broad introduction to this fascinating field by covering not only the structure and function of proteins, but also the methods and experimental techniques used to study them. The practical applications of our knowledge to diverse fields such as biotechnology and medicine are emphasized throughout, to help students appreciate the relevance of the subject to the real world.

Product Details

ISBN-13:	9780198716846
Publisher:	Oxford University Press
Publication date:	03/14/2016
Edition description:	New Edition
Pages:	488
Product dimensions:	10.40(w) x 7.60(h) x 0.90(d)

About the Author

Arthur Lesk, The Pennsylvania State University

Arthur M. Lesk is Professor of Biochemistry and Molecular Biology at The Pennsylvania State University. He is the author of the highly successful Introduction to Bioinformatics, and Introduction to Genomics, both published by Oxford University Press.

Table of Contents

Preface to the first edition xvii

Preface to the second edition xx

Preface to the third edition xxi

1 Introduction 1

Proteins in their biological context 2

The amino acids 4

Dogmas-central and peripheral 5

The relationship between ammo acid sequence and protein stricture is robust 6

Disorder in proteins 7

Regulation 10

The genetic code 11

With life so dependent on proteins, there is ample opportunity for things to go wrong 12

Genome sequences 15

Gene sequence determines amino acid sequence 16

Protein synthesis: the ribosome is the point of contact between genes and proteins-it is the fulcrum of genomics 17

Ribosomes were implicated in protein synthesis very early on 18

Structural studies of ribosomes by X-ray crystallography and electron microscopy 18

Protein stability, denaturation, aggregation, and turnover 19

Protein turnover 19

Description of protein structures 20

Primary structure 21

Secondary structure: helices and sheets are favourable conformations of the chain that recur in many proteins 21

Tertiary and quaternary structure 23

Folding patterns in native proteins-themes and variations 23

Modular proteins, and 'mixing and matching' as a mechanism of evolution 25

How do proteins develop new functions? 27

The study of proteins: in the laboratory, in the cell, in the computer 29

Spectroscopic methods of characterizing proteins in solution 30

Absorbance and fluorescence of proteins 32

Fluorescence is sensitive to the environment and dynamics of the chromophore 34

Fluorescence resonance energy transfer (FRET) 34

Circular dichroism 34

Protein expression patterns in space and time: Proteomics 35

Subcellular localization 35

The transcriptome 36

DNA microaaays 37

Mass spectrometry 38

Computing in protein science 38

Computer-instrument partnerships in the laboratory 38

Simulations, including molecular dynamics 39

Bioinformatics 40

Introduction to databanks for protein science 40

Information-retrieval tools 41

Web access to the scientific literature 41

Useful websites 42

Recommended reading 42

Exercises and Problems 43

2 Protein structure 46

Introduction 47

Structures of the amino acids 47

Protein conformation 50

Conformational angles and the Sasisekharan-Ramakrishnan-Ramachandran plot 51

Sidechain conformation 53

Rotamer libraries 53

Stabilization of the naïve state 54

Conformational change 59

Protein folding patterns 60

Supersecondary structures 60

An album of small structures 62

Comparison of the folding patterns of acylphosphatase and a fungal toxin 64

Classification of protein structures 67

Databanks of protein structure classifications 68

SCOP 68

SCOP2 70

CATH 71

The DALI Database 72

A survey of protein structures and functions 73

Fibrous proteins 73

Enzymes-proteins that catalyse chemical reactions 76

Antibodies 77

Inhibitors 77

Carrier proteins 77

Membrane proteins 78

Receptors 80

Regulatory proteins 81

Motor proteins 81

Control of protein activity 81

Regulation of tyrosine hydroxylase illustrates several control mechanisms common to many proteins 84

Control cascades 84

Recommended reading 85

Exercises and Problems 85

3 Protein structure determination 92

Introduction 93

X-ray crystallography 94

X-ray structure determination 95

X-ray crystallography of proteins 96

Interpretation of the electron density: model building and improvement 100

The endgame-refinement 102

How accurate are the structures? 102

X-ray crystallography-the theoretical background 104

Nuclear magnetic resonance spectroscopy in structural biology 110

NMR spectra of proteins 111

Measurement of NMR spectra 113

Protein structure determination by NMR 113

Assignment of the spectrum 114

Transverse relaxation optimized spectroscopy 117

From the data to the structure 117

Solid-state NMR: magic angle spinning 118

Near atomic-resolution low-temperature electron microscopy (cryo-EM) 119

Octameric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hildenborough 120

Conformational change in activation of human integrin αVβ3 120

Trajectories of conformational change 124

The elastic network model accounts for conformational change in Mycobacterium tuberculosis thioredoxin reductase 125

The relationship between structure determinations of Isolated proteins, and protein structure and function in vivo 127

Protein structure prediction and modeling 127

A priori methods of protein structure prediction 128

Empirical, or 'knowledge-based', methods of protein structure prediction 129

Secondary structure prediction 131

Homology modelling 133

Fold recognition 135

Antibody modeling 137

Prediction of special categories of structures 139

Conformational energy calculations and molecular dynamics 140

ROSETTA 142

Protein structure prediction from contact maps derived from correlated mutations in multiple sequence alignments 144

Critical Assessment of Structure Prediction (CASP) 146

CAPRI 153

Recommended reading 153

Exercises and Problems 154

4 Bioinformatics of protein sequence and structure 160

Introduction 160

Databases and information retrieval 161

Amino acid sequence databases 162

Protein databases at the U.S. National Center for Biotechnology Information 163

Specialized, or 'boutique', databases 164

Nucleic acid sequence databases 165

Genome databases and genome browsers 166

Ensembl 166

Expression and proteomics databases 166

Debases of macromolecular structure 168

Organization of wwPDB entries 169

Retrieval of sequences and structures 170

Retrieval of amino acid sequences by keyword 171

The Protein Information Resource (PIR) and associated databases 171

Retrieval of structures by keyword 172

Probing databanks with sequence information 173

Sequence alignment 174

The dotplot 175

Dotplots and alignments 176

BLAST and PSI-BLAST 177

Significance of alignments 179

Multiple sequence alignment 181

A multiple sequence alignment of thioredoxins shows the importance of conservation patterns 182

Analysis of structures 184

Superposition of structures 184

Structural alignment 185

Multiple structure alignment 187

Database searching for structures or fragments 187

Databases of protein families 188

Classifications of protein structures 189

Classification and assignment of protein function 189

The Enzyme Commission 189

The Gene Ontology™ Consortium protein function classification 190

The ENZYME database and PROSITE 192

Databases of metabolic networks 193

Recommended reading 194

Exercises and Problems 195

5 Proteins as catalysts: enzyme structure, kinetics, and mechanism 197

Introduction 197

What are the crucial features of enzymes? 198

Reaction rates and transition states 201

The activated complex 203

Measurement of reaction rates 204

Slow the reaction down 205

Fast methods of data collection 205

Active sites 206

Cofactors 206

Protein-ligand binding equilibria 207

The Scatchard plot 207

Catalysis by enzymes 208

Enzyme kinetics 209

Derivation of K_M and V_max from rate data 210

Measures of effectiveness of enzymes 211

Inhibitors 212

Irreversible inhibitor binding 212

Multisubstrate reactions 213

Enzyme mechanisms 214

The mechanism of action of thymidylate synthase 216

Computational approaches to enzyme mechanisms 218

The mechanism of action of chymotrypsin 220

The evidence from kinetics 221

The evidence from crystallography 221

Blood coagulation 222

Thrombosis 222

Serpins: serine proteinase inhibitors-conformational disease 226

Several conformational states of serpins are known 227

Mechanism of proteinase inhibition by serpins 228

Evolutionary divergence of enzymes 229

The mechanism of action of malate and lactate dehydrogenases 229

Enolase, mandelate racemase, and muconate lactonizing enzyme catalyse different reactions but have related mechanisms 230

The structure and mechanism of E. coli topoisomerase III 231

Motor proteins 233

The sliding filament mechanism of muscle contraction 233

ATP synthase 234

Membrane transport 238

Specificity of the potassium channel from Streptomyces lividans-room to swing a cation? 238

Allosteric regulation of protein activity 239

The allosteric structural change of haemoglobin 242

Recommended reading 246

Exercises and Problems 246

6 Proteins with partners 252

Introduction 252

General properties of protein-protein interfaces 254

Burial of protein surface 254

The composition of the interface 254

Complementarity 254

Specific interactions at protein-protein interfaces 255

Phage M13 gene III protein and E. coli TolA 255

Multisubunit proteins 256

Diseases of protein aggregation 257

Amyloidoses 258

Alzheimer's disease 258

Prion diseases-spongiform encephalopathies 259

The immune system 260

Antibody structure 261

Antibody maturation 266

Catalytic antibodies-'abzymes' 267

Proteins of the major histocompatibility complex 268

T-cell receptors 273

Virus structures 274

Tomato bushy stunt virus 278

Bacteriophage HK97: protein chain-mail 278

Photosynthetic reaction centres 279

Protein-DNA interactions 280

Structural themes in protein-DNA binding and sequence recognition 281

Bacteriophage T7 DNA polymerase 282

Some protein-DNA complexes that regulate gene transcription 283

Recommended reading 287

Exercises and Problems 288

7 Evolution of protein structure and function 291

Introduction 291

Protein structure classification 294

A case study: superpositions and alignments of pairs of proteins with increasingly more-distant relationships 296

Structural relationships among homologous domains 298

Changes in proteins during evolution give clues to the roles of residues at different positions 302

To what constraint are pathways of protein evolution subject? 302

Closed β-barrel structures 303

The TIM barrel 303

Evolution of the globins 307

Mammalian globins 308

What determines the globin folding pattern? 310

Truncated globins 312

Expansion of the globin family 313

Classification of the globins 313

Globin functions 316

Phycocyanins and the globins 316

Evolution of NAD-binding domains of dehydrogenases 318

Comparison of NAD-binding domains of dehydrogenases 320

The sequence motif G*G**G 323

Structure and evolution of serine proteinases of the chymotrypsin family 324

Structures of individual domains 324

The domain/domain interface 326

The specificity pocket 327

The β-barrels in serine proteinase domains and the packing of residues in their interiors 328

Evolution of visual pigments and related molecules 331

Selection has tuned vertebrate opsins so that the absorption maximum varies with the light environment 335

How do proteins evolve new functions? 338

Pathways and limits in the divergence of sequence, structure and function 339

Evolution of functional change in the enolase superfamily 342

Protein evolution at the level of domain assembly 345

Domain swapping is a general mechanism for forming an oligomer from a multidomain protein 345

Directed evolution 346

Directed evolution of subtilisin E 347

Enhancement of thermal stability 347

Activity in organic solvents 348

Affinity selectivity by phage display 349

Recommended reading 350

Exercises and Problems 350

8 Protein folding and design 356

Introduction 356

Why is protein folding so fast? 357

Thermodynamics-key concepts 358

Entropy 359

Spontaneity and equilibrium 359

Kinetics 360

Thermodynamics, protein folding 360

Thermodynamics of mutated proteins 361

Experimental character nation of events in protein folding 362

The molten globule 363

Folding funnels 364

The effect of denaturants on rates of folding and unfolding: chevron plots 365

The kinetics of folding of mutated proteins gives clues to the structure of the transition state for folding 365

Comparison of folding pathways of a natural protein and a circular permutant 366

Relationship between native structure and folding 369

The hierarchical model of protein folding 371

How fast could a protein fold? 372

Protein misfolding and the GroEL-GroES chaperone protein 373

The GroEL-GroES conformational change 375

Protein design 376

Protein design 376

ab initio design of a hyperstable variant of Streptococcal protein G, β1 domain 376

Expanding and contracting the genetic code 378

Expansion of the genetic code 378

Contraction of the genetic code 381

Understanding the contents and layout of the common genetic code 382

Recommended reading 382

Exercises and Problems 383

9 Proteomics and systems biology 387

Introduction 388

Separation and analysis of proteins 389

Polyacrylamide gel electrophoresis 389

Two-dimensional polyacrylamide gel electrophoresis 390

Difference gel electrophoresis 390

Mass spectrometry 393

Identification of components of a complex mixture 393

Protein sequencing by mass spectrometry 395

Quantitative analysis of relative abundance 395

Measuring deuterium exchange in proteins 398

'Ome, 'ome, on the range-environmental genomics and proteomics 398

Metagenomics 398

Metaproteomics 398

Dynamic proteomics of the response to cadmium challenge 399

Microarrays 401

Microarray data are semiquantitative 401

Applications of DNA microarrays 403

Analysis of microarray data 404

Expression patterns in different physiological states 406

Expression pattern changes in development: the life cycle of Drosophila melanogaster 406

RNAseq 408

RNAseq v. microarrays 409

Systems biology 411

Two parallel networks: physical and logical 411

Networks and graphs 412

Robustness and redundancy 413

Connectivity in networks 414

Dynamics, stability, and robustness 416

Protein complexes and aggregates 417

Protein interaction networks 417

Regulatory networks 421

Structures of regulatory networks 422

Structural biology of regulatory networks 423

Gene regulation 424

The transcriptional regulatory network of E. coli 424

Regulation of the lactose operon in E. coli 427

The genetic regulatory network of Saccharomyces cerevisiae 429

Adaptability of the yeast regulatory network 430

Recommended reading 433

Exercises and Problems 434

Epilogue 437

List of Abbreviations 438

Glossary 440

Index 453