Handbook of Proteins: Structure, Function and Methods, 2 Volume Set

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 A Orengo).

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

Hydrophobic Effect (Judith Herzfeld and Donald J Olbris).

Hydrophobic Interactions in Proteins (Brian W Matthews).

Immunoglobulin Fold: Structures of Proteins in the Immunoglobulin Superfamily (IsraelMGelfand, Cyrus Chothia and Alexander 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 (Amram Mor).

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

Proline Residues in Proteins (Charles M Deber and Barbara Brodsky).

Protein Databases (Gerritsen Vivienne Baillie and Bairoch Amos).

Protein Denaturation and the Denatured State (Per Hammarstro and 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 TJ Delbaere).

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

Protein Motifs: the Helix-Loop-Helix Motif (Fred Sablitzky).

Protein Motifs: the Helix-Turn-Helix Motif (BrianW Matthews).

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

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

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

Protein Quaternary Structure: Symmetry Patterns (Ronald E Stenkamp).

Protein Secondary Structures: Prediction (John-Marc Chandonia).

Protein Sequence Databases (Winona C Barker).

Protein Stability (C Nick Pace and Gerald R Grimsley).

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

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

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

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

Protein Unfolding and Denaturants (Lars Konermann).

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

Proteins: Fundamental Chemical Properties (Alain J Cozzone).

Structural Databases of Biological Macromolecules (Helen M Berman).

Unstructured Proteins (A Keith Dunker).

Protein Synthesis.

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

Chaperonins (Valerio Consalvi and Roberta Chiaraluce).

Codon Usage in Molecular Evolution (Richard L Grantham).

Protein Folding In Vivo (Sarah Teter and F Ulrich Hartl).

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

Protein Synthesis Initiation in Bacteria (Marianne Grunberg-Manago).

Proteins: Postsynthetic Modification – Function and Physical Analysis (Brigitte Wittmann-Liebold and Theodora Choli-Papadopoulou).

Protein Degradation.

Amino Acid Degradation (Gary Sawers).

Lysosomal Degradation of Proteins (J Fred Dice).

Protease Complexes (Marion Schmidt and Daniel Finley).

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 J Winzor).

Engineered Enzymes (Ben M Dunn).

Enzymatic Rate Enhancements (Daniel M Quinn and R Steven Sikorski).

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

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

Enzyme Kinetics: Steady State (W Wallace Cleland).

Enzyme Kinetics: Transient Phase (Kenneth A Johnson).

Enzyme Specificity and Selectivity (Lizbeth Hedstrom).

Enzymes: General Properties (Timothy DH Bugg).

Enzymes: Purification (Jerome Salem).

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

Radical Enzymes (Britt-Marie Sjoerg and Margareta Sahlin).

Substrate Binding to Enzymes (Vladimir K Pliska).

Enzyme Activity.

Acid–Base Catalysis by Enzymes (Anthony John Kirby).

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 (Thomas Traut).

Enzyme Activity: Reversible Inhibition (John F Morrison).

Enzymes: Irreversible Inhibition (Keith F Tipton).

Ground State Destabilization (Vernon E Anderson).

Metalloenzymes and Electrophilic Catalysis (Jason Eames and Michael Watkinson).

Regulation by Covalent Modification (Bruce L Martin).

Thermodynamics in Biochemistry (Robert A Alberty).

Transition State Stabilization (Shahriar Mobashery and Lakshmi P Kotra).

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

Enzyme Cofactors.

Cobalamin Coenzymes and Vitamin B12 (Wolfgang Buckel).

Coenzymes and Cofactors (Joan B Broderick).

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

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

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

Flavin Coenzymes (Sandro Ghisla and Dale E Edmondson).

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

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

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

Protein-derived Cofactors (Victor L Davidson).

Quinone Cofactors (Benjamin Schwartz and Judith P Klinman).

Thiamin Diphosphate and Vitamin B1 (Susana K Schowen, K Barbara 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, Haim Wolfson, Neeti Sinha and Ruth Nussinov).

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

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

Protein–Ligand Interactions: Molecular Basis (Harvey F Fisher).

Protein–Nucleic Acid Interactions.

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

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

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

Protein–DNA Complexes: Nonspecific (Ruth M Saecker).

Protein–DNA Complexes: Specific (Mark A Strauch).

Protein–DNA Interactions (Marianne Rooman and Rene Wintjens).

Protein–DNA Interactions: Energetics (Tom K Kerppola).

Protein–DNA Interactions: Polyelectrolyte Effects (Ruth M Saecker).

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

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

Protein–Protein Interactions.

Interaction Networks of Proteins (Shailesh V Date and Guang Chen).

Protein–Protein Interactions (Jeremy H Lakey and Isa Gokce).

Membrane Proteins.

ATPases: Ion-motive (Florent Guillain and Elisabeth Mintz).

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

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

Membrane Proteins (Reinhart AF Reithmeier).

Protein Translocation Across Membranes (Michael T Ryan and Nikolaus Pfanner).

Sodium, Calcium and Potassium Channels (Stefan H Heinemann).

Water Channels (Landon S King and Peter Agre).

Techniques: Production, Isolation and Purification Autoradiography and Fluorography (Pavel S Gromov and Julio E Celis).

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

Capillary Electrophoresis (Pier Giorgio Righetti).

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

Chromatographic Techniques (Alastair C Lewis).

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

Expression Tags for Protein Production (Su-Ming Hu, Andrew H-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 (Andreas Chrambach).

Gel Filtration (Lars Hagel).

Gel Staining Techniques (Carl R Merril).

Gene Expression in Yeast (Georgios Scheiner-Bobis).

Gene Synthesis for Protein Production (Lance Stewart).

Hydrophobic Interaction Chromatography (Herbert P Jennissen).

Immunoglobulin Purification (Mark Page).

Ion Exchange Chromatography (David Sheehan and Siobhan O'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 Gromov and 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 and Florian 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 van Noort).

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

Calorimetry (Kenneth P Murphy).

Centrifugation Techniques (David Rickwood).

Circular Dichroism: Studies of Proteins (Nicholas C Price).

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

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

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

Electron Cryomicroscopy (Jacques Dubochet and Henning Stahlberg).

Electron Cryomicroscopy and Three-dimensional Computer Reconstruction of Biological Molecules (Steven J Ludtke and Wah Chiu).

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 and Cristobal G dos Remedios).

Fluorescence Spectrophotometry (Peter TC So and Chen Y Dong).

Fluorescent Analogues in Biological Research (Joseph R Lakowicz).

Fourier Transform Infrared (Johannes Orphal).

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

Hydrophobicity Plots (Mark SP Sansom).

Immuno-electron Microscopy (Heinz Schwarz and Heinz Hohenberg).

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

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

Macromolecular Structure Determination: Comparison of Crystallography and NMR (J Mitchell Guss and Glenn F King).

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

Mass Spectrometry Instrumentation in Proteomics (Peter Roepstorff).

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

Mass Spectrometry: Peptide Sequencing (J Throck Watson).

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 Miyashita and Florence Tama).

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

Nuclear Magnetic Resonance (NMR) Spectroscopy: Structural Analysis of Proteins and Nucleic Acids (Milton H Werner).

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

Optical Tweezers (Karl Otto Greulich).

Peptide Sequencing by Edman Degradation (John Bryan Smith).

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

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

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

Protein Structure Design and Engineering (Yi Lu and Steven M Berry).

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 and Volker Uhl).

Spectroscopic Techniques (H Jane Dyson).

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

Time-resolved X-ray Crystallography (Barry L Stoddard).

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

Two-dimensional Electron Crystallography (Thomas Braun and Andreas Engel).

Two-photon Fluorescence Light Microscopy (Peter TC So).

Ultracentrifugation (Alfred Vokl).

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

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

X-ray Diffraction: Principles (Jan Drenth).

Techniques: Interactions.

Array-based Proteomics (Gerald Walter, Konrad Busow, Zoltan Konthur, Angelika Lueking, Jon Gloler and Ulrich Schneider).

Immunoprecipitation Techniques (Karl-Heinz Scheidtmann).

Molecular Entry Point: Strategies in Proteomics (Eric T Fung).

Protein–DNA Interactions: Techniques Used (Mark A Strauch).

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

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

Protein–Protein Interactions: Prediction (Julie C Mitchell).

Proteins: Affinity Tags (Shaorong Chong).

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