Handbook of Proteins: Structure, Function and Methods / Edition 1

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Overview

The Handbook of Proteins provides scientists and studentswith a focused and accessible resource covering all aspects ofprotein biochemistry. It describes traditional and state-of-the-arttechniques for elucidating protein function and structure. 

  • Derived from the acclaimed Encyclopedia of LifeSciences
  • Presented in full-colour throughout
  • Assembles more than 200 peer-reviewed articles, written by topscientists in each field
  • The articles are reliable, self-contained and cross-referencedthroughout
  • Almost all aspects of protein structure, function, andchemistry are illuminated by one or more articles
  • Numerous articles also provide an introduction to methods forpurifying proteins, determining their structures and properties,and cataloguing them in databases
  • Dozens of additional articles detail important aspects ofenzymatic catalysis and protein-ligand interactions

The Handbook of Proteins is a comprehensive andauthoritative resource for teachers, students and researchers inthe molecular life sciences. The easy layout encourages frequentretrieval.

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Editorial Reviews

From the Publisher
“A useful reference for instructors who teach related topics, as well as students and postdoctoral researchers working with proteins.” (The Quarterly Review of Biology, March 2009)

"The writing is clear in either type. Illustrations and diagrams are excellent and the coverage is broad. The index is good. The Handbook of Proteins is recommended for all academic libraries." (American Reference Books Annual, March 2009)

"A comprehensive guide to modern protein science and at the same time provides an enjoyable read … .[It] will be invaluable to all researchers." (ChemBioChem, August 2008)

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Product Details

  • ISBN-13: 9780470060988
  • Publisher: Wiley
  • Publication date: 2/25/2008
  • Edition number: 1
  • Pages: 1378
  • Product dimensions: 8.88 (w) x 11.32 (h) x 3.87 (d)

Table of Contents

Volume 1.

Contributors.

Preface.

How to Use This Book.

Introduction.

History of Protein Chemistry (Graeme K Hunter).

Protein Structure.

Amino Acid Side Chain Hydrophobicity (Hue Sun Chan).

Amino Acid Substitutions: Effects on Protein Stability(Zhiping Weng and Charles DeLisi).

Evolution of Protein Domains (Corin A Yeats and Christine AOrengo).

Hydrogen Bonds in Proteins: Role and Strength (Roderick EHubbard).

Hydrophobic Effect (Judith Herzfeld and Donald JOlbris).

Hydrophobic Interactions in Proteins (Brian WMatthews).

Immunoglobulin Fold: Structures of Proteins in theImmunoglobulin Superfamily (IsraelMGelfand, Cyrus Chothia andAlexander E Kister).

Mining Biological Databases (Jaime Prilusky).

Molten Globule (Anthony L Fink).

Peptide Bonds, Disulfide Bonds and Properties of Small Peptides(Hiram F Gilbert).

Peptides: Biological Activities of Small Peptides (AmramMor).

Primary Protein and Nucleic Acid Three-dimensional StructureDatabases (Philip E Bourne).

Proline Residues in Proteins (Charles M Deber and BarbaraBrodsky).

Protein Databases (Gerritsen Vivienne Baillie and BairochAmos).

Protein Denaturation and the Denatured State (Per Hammarstroand Bengt-Harald Jonsson).

Protein Design (Emmanuel Lacroix and Luis Serrano).

Protein Family Databases (Nicola J Mulder).

Protein Motifs: ATP-binding Motifs (Allan Matte and Louis TJDelbaere).

Protein Motifs: GTP-binding Loop (Guangpu Li).

Protein Motifs: the Helix-Loop-Helix Motif (FredSablitzky).

Protein Motifs: the Helix-Turn-Helix Motif (BrianWMatthews).

Protein Motifs: the Leucine Zipper (Dmitry Krylov and CharlesR Vinson).

Protein Motifs: Zinc-fingers (David Gell, Merlin Crossley andJoel Mackay).

Protein Quaternary Structure: Subunit–Subunit Interactions(Susan Jones and Janet M Thornton).

Protein Quaternary Structure: Symmetry Patterns (Ronald EStenkamp).

Protein Secondary Structures: Prediction (John-MarcChandonia).

Protein Sequence Databases (Winona C Barker).

Protein Stability (C Nick Pace and Gerald RGrimsley).

Protein Structural Flexibility: Molecular Motions (Richard HHenchman and J Andrew McCammon).

Protein Structure Classification (Frances MG Pearl, ChristineA Orengo and Janet M Thornton).

Protein Structure: Unusual Covalent Bonds (Nancy L Scott andJuliette T J Lecomte).

Protein Tertiary Structures: Prediction from Amino AcidSequences (Hongyu Zhang).

Protein Unfolding and Denaturants (Lars Konermann).

Protein: Cotranslational and Posttranslational Modification inOrganelles (Doug A Brooks).

Proteins: Fundamental Chemical Properties (Alain JCozzone).

Structural Databases of Biological Macromolecules (Helen MBerman).

Unstructured Proteins (A Keith Dunker).

Protein Synthesis.

Chaperones, Chaperonin and Heat-Shock Proteins (ValerioConsalvi and Roberta Chiaraluce).

Chaperonins (Valerio Consalvi and RobertaChiaraluce).

Codon Usage in Molecular Evolution (Richard LGrantham).

Protein Folding In Vivo (Sarah Teter and F UlrichHartl).

Protein Synthesis Inhibitors (D N Wilson, U Stelzl and Knud HNierhaus).

Protein Synthesis Initiation in Bacteria (MarianneGrunberg-Manago).

Proteins: Postsynthetic Modification – Function andPhysical Analysis (Brigitte Wittmann-Liebold and TheodoraCholi-Papadopoulou).

Protein Degradation.

Amino Acid Degradation (Gary Sawers).

Lysosomal Degradation of Proteins (J Fred Dice).

Protease Complexes (Marion Schmidt and DanielFinley).

Proteases (Alan J Barrett and Neil D Rawlings).

Ubiquitin Pathway (Y Amy Lam and Cecile M Pickart).

Enzymes.

Binding Constants: Measurement and Biological Range (Donald JWinzor).

Engineered Enzymes (Ben M Dunn).

Enzymatic Rate Enhancements (Daniel M Quinn and R StevenSikorski).

Enzyme Activity: Control (Shorena Nadaraia, George J YohrlingIV, George C-T Jiang, John M Flanagan and Kent E Vrana).

Enzyme Classification and Nomenclature (Sinead Boyce andKeith F Tipton).

Enzyme Kinetics: Steady State (W Wallace Cleland).

Enzyme Kinetics: Transient Phase (Kenneth A Johnson).

Enzyme Specificity and Selectivity (LizbethHedstrom).

Enzymes: General Properties (Timothy DH Bugg).

Enzymes: Purification (Jerome Salem).

Enzymes: The Active Site (Eman Ghanem and Frank MRaushel).

Radical Enzymes (Britt-Marie Sjoerg and MargaretaSahlin).

Substrate Binding to Enzymes (Vladimir K Pliska).

Enzyme Activity.

Acid–Base Catalysis by Enzymes (Anthony JohnKirby).

Binding and Catalysis (Michael D Toney).

Covalent Nucleophilic Catalysis (George L Kenyon).

Enzymatic Free Radical Reactions (Squire J Booker).

Enzyme Activity and Assays (Robert K Scopes).

Enzyme Activity: Allosteric Regulation (ThomasTraut).

Enzyme Activity: Reversible Inhibition (John FMorrison).

Enzymes: Irreversible Inhibition (Keith F Tipton).

Ground State Destabilization (Vernon E Anderson).

Metalloenzymes and Electrophilic Catalysis (Jason Eames andMichael Watkinson).

Regulation by Covalent Modification (Bruce L Martin).

Thermodynamics in Biochemistry (Robert A Alberty).

Transition State Stabilization (Shahriar Mobashery andLakshmi P Kotra).

Transition States: Substrate-induced Conformational Transitions(Carol B Post).

Enzyme Cofactors.

Cobalamin Coenzymes and Vitamin B12 (WolfgangBuckel).

Coenzymes and Cofactors (Joan B Broderick).

Coenzymes: Haem (Jennifer Cheek and John H Dawson).

Enzymes: Coenzyme A Dependent (Peter M Shoolingin-Jordan andMatthew P Crump).

Enzymes: Phosphopantetheine Dependent (Matthew P Crump andPeter M Shoolingin-Jordan).

Flavin Coenzymes (Sandro Ghisla and Dale EEdmondson).

Iron Cofactors: Non-haem (Brian G Fox).

NAD+ and NADP+ as Prosthetic Groups for Enzymes (Norman JOppenheimer).

NADP+ Binding to Dehydrogenases (Henry Weiner and Thomas DHurley).

Protein-derived Cofactors (Victor L Davidson).

Quinone Cofactors (Benjamin Schwartz and Judith PKlinman).

Thiamin Diphosphate and Vitamin B1 (Susana K Schowen, KBarbara Schowen and Richard L Schowen).

Volume 2.

Protein–Ligand Interactions.

Haemoglobin: Cooperativity in Protein–Ligand Interactions(Chien Ho and Jonathan A Lukin).

Induced Fit (Buyong Ma, Sandeep Kumar, Chung-Jung Tsai, HaimWolfson, Neeti Sinha and Ruth Nussinov).

Protein–Ligand Interactions: Energetic Contributions andShape Complementarity (Chung-Jung Tsai, Raquel Norel, Haim JWolfson, Jacob V Maizel and Ruth Nussinov).

Protein–Ligand Interactions: General Description(Michael F Dunn).

Protein–Ligand Interactions: Molecular Basis (Harvey FFisher).

Protein–Nucleic Acid Interactions.

DNA Structure Changes Coupled to Protein Binding (MensurDlakic and Tom K Kerppola).

DNA-binding Enzymes: Structural Themes (Charles W Knopf andWaldemar Waldeck).

Protein Motifs for DNA Binding (Hang Xu and Scott WMorrical).

Protein–DNA Complexes: Nonspecific (Ruth MSaecker).

Protein–DNA Complexes: Specific (Mark AStrauch).

Protein–DNA Interactions (Marianne Rooman and ReneWintjens).

Protein–DNA Interactions: Energetics (Tom KKerppola).

Protein–DNA Interactions: Polyelectrolyte Effects (RuthM Saecker).

Protein–Nucleic Acid Interaction: Major Groove RecognitionDeterminants (Yong Xiong and Muttaiya Sundaralingam).

Protein–RNA Interactions (Felicia Houser-Scott andDavid R Engelke).

Protein–Protein Interactions.

Interaction Networks of Proteins (Shailesh V Date and GuangChen).

Protein–Protein Interactions (Jeremy H Lakey and IsaGokce).

Membrane Proteins.

ATPases: Ion-motive (Florent Guillain and ElisabethMintz).

Clathrin-coated Vesicles and Receptor-mediated Endocytosis(Mark Marsh).

Ion Motive ATPases: V- and P-type ATPases (George Sachs andDavid Keeling).

Membrane Proteins (Reinhart AF Reithmeier).

Protein Translocation Across Membranes (Michael T Ryan andNikolaus Pfanner).

Sodium, Calcium and Potassium Channels (Stefan HHeinemann).

Water Channels (Landon S King and Peter Agre).

Techniques: Production, Isolation and PurificationAutoradiography and Fluorography (Pavel S Gromov and Julio ECelis).

Baculovirus Expression System (Monique M van Oers and Just MVlak).

Capillary Electrophoresis (Pier Giorgio Righetti).

Chromatofocusing (Douglas D Frey, Chittoor R Narahari andRonald C Bates).

Chromatographic Techniques (Alastair C Lewis).

Electroelution of Proteins from Polyacrylamide Gels (Pavel SGromov and Julio E Celis).

Expression Tags for Protein Production (Su-Ming Hu, AndrewH-J Wang and Ting-Fang Wang).

Gel Electrophoresis of Proteins: High-resolution Two-dimensional(Julio E Celis and Pavel S Gromov).

Gel Electrophoresis: One-dimensional (AndreasChrambach).

Gel Filtration (Lars Hagel).

Gel Staining Techniques (Carl R Merril).

Gene Expression in Yeast (Georgios Scheiner-Bobis).

Gene Synthesis for Protein Production (LanceStewart).

Hydrophobic Interaction Chromatography (Herbert PJennissen).

Immunoglobulin Purification (Mark Page).

Ion Exchange Chromatography (David Sheehan and SiobhanO'Sullivan).

Liquid Chromatography (Mohammad Azam Mansoor).

Peptide Mapping (Ralph C Judd).

Permeabilized Mammalian Cell Systems for Protein Synthesis(Neil J Bulleid).

Protein Determination (Martin Guttenberger).

Protein Identification: Overlay Procedures (Pavel S Gromovand Julio E Celis).

Protein Production for Biotechnology (Sarah E Giuliani,Elizabeth V Landorf and Frank R Collart).

Protein Production in Mammalian Cells (David L Hacker andFlorian M Wurn).

Protein Synthesis: Measuring Errors (Gregg Bogosian).

Solid-phase Peptide Synthesis: Fmoc (Chi C Yang).

Techniques: Characterization.

Alignment: Statistical Significance (Richard Mott).

Atomic Force Microscopy (Martijn de Jager and John vanNoort).

Biological Macromolecules: UV-visible Spectrophotometry(Franz-Xaver Schmid).

Calorimetry (Kenneth P Murphy).

Centrifugation Techniques (David Rickwood).

Circular Dichroism: Studies of Proteins (Nicholas CPrice).

Crystallization of Protein–DNA Complexes (Adrian HBatchelor, Derek E Piper and Cynthia Wolberger).

Crystallization of Proteins and Protein–Ligand Complexes(Alexander McPherson).

Crystallization of Proteins: Two-dimensional (Bing K Jap andPeter J Walian).

Electron Cryomicroscopy (Jacques Dubochet and HenningStahlberg).

Electron Cryomicroscopy and Three-dimensional ComputerReconstruction of Biological Molecules (Steven J Ludtke and WahChiu).

Electron Paramagnetic Resonance (EPR) and Spin-labelling(Peter G Fajer).

Enzymology Methods (Robert A Copeland).

Flow Cytometers (John A Steinkamp).

Fluorescence Resonance Energy Transfer (Deepak Chhabra andCristobal G dos Remedios).

Fluorescence Spectrophotometry (Peter TC So and Chen YDong).

Fluorescent Analogues in Biological Research (Joseph RLakowicz).

Fourier Transform Infrared (Johannes Orphal).

Green Fluorescent Protein (GFP) (Leila D Hebshi, Brigitte MAngres, Xianqiang L Li and Steven R Kain).

Hydrophobicity Plots (Mark SP Sansom).

Immuno-electron Microscopy (Heinz Schwarz and HeinzHohenberg).

Low Angle Scattering of Neutrons and X-rays (JillTrewhella).

Macromolecular Structure Determination by X-ray Crystallography(Joachim Jaeger).

Macromolecular Structure Determination: Comparison ofCrystallography and NMR (J Mitchell Guss and Glenn FKing).

Mass Measurements by Scanning Transmission Electron Microscopy(David AD Parry).

Mass Spectrometry Instrumentation in Proteomics (PeterRoepstorff).

Mass Spectrometry: Analysis of Two-dimensional Protein Gels(Hanjo Lim and John R Yates III).

Mass Spectrometry: Peptide Sequencing (J ThrockWatson).

Molecular Dynamics (Jarosaw Meller).

Mutagenesis: Site-specific (M Raafat El-Gewely, Chris Fenton,Elisabeth Kjeldsen and Hao Xu).

Normal Mode Analysis in Structural Biology (Osamu Miyashitaand Florence Tama).

Nuclear Magnetic Resonance (NMR) Spectroscopy of Proteins(Kurt Wuhrich).

Nuclear Magnetic Resonance (NMR) Spectroscopy: StructuralAnalysis of Proteins and Nucleic Acids (Milton HWerner).

Nuclear Magnetic Resonance (NMR): Solid State (Stanley JOpella and Francesca M Marassi).

Optical Tweezers (Karl Otto Greulich).

Peptide Sequencing by Edman Degradation (John BryanSmith).

Phase Problem in X-ray Crystallography, and its Solution(Kevin Cowtan).

Phosphorimager (Daniel J Robertson, Willard M Freeman andKent E Vrana).

Protein Characterization: Analytical Approaches and Applicationsto Proteomics (Kris Gevaert and Joe Vandekerckhove).

Protein Structure Design and Engineering (Yi Lu and Steven MBerry).

Proteomics: A Shotgun Approach without Two-dimensional Gels(Claire Delahunty and John R Yates III).

Pulse-field Gel Electrophoresis (John C Maule).

Resonance Raman Spectroscopy (Ishita Mukerji).

Sedimentation (Thomas Maxon Laue).

Single-molecule Light Microscopy (Karl Otto Greulich andVolker Uhl).

Spectroscopic Techniques (H Jane Dyson).

Structural Genomics (John Norvell, Jiayin Li, KirstieSaltsman and Jeremy Berg).

Time-resolved X-ray Crystallography (Barry LStoddard).

Transmission Electron Microscopy: Preparation of Specimens(Henry S Slayter).

Two-dimensional Electron Crystallography (Thomas Braun andAndreas Engel).

Two-photon Fluorescence Light Microscopy (Peter TCSo).

Ultracentrifugation (Alfred Vokl).

X-ray Absorption Spectroscopy (James E Penner-Hahn).

X-ray Diffraction at Synchroron Light Sources (Jhon RHelliwell).

X-ray Diffraction: Principles (Jan Drenth).

Techniques: Interactions.

Array-based Proteomics (Gerald Walter, Konrad Busow, ZoltanKonthur, Angelika Lueking, Jon Gloler and UlrichSchneider).

Immunoprecipitation Techniques (Karl-HeinzScheidtmann).

Molecular Entry Point: Strategies in Proteomics (Eric TFung).

Protein–DNA Interactions: Techniques Used (Mark AStrauch).

Protein–Ligand Interactions: Computational Docking(David Schwarz and Lydia E Kavraki).

Protein–Protein Interactions: Identification (Matthew ELopper and James L Keck).

Protein–Protein Interactions: Prediction (Julie CMitchell).

Proteins: Affinity Tags (Shaorong Chong).

Tandem-affinity Purification (TAP) Tags (Cynthia Maria BorgesDamasceno and Jocelyn Kenneth Campbell Rose)

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