Note: Intro -- Preface -- Editor -- List of contributing authors -- Abbreviations -- Acknowledgements -- 1 Three-phase partitioning -- 1.1 Method -- 1.2 The mechanism of TPP -- 1.3 A practical example - the isolation of cathepsin L from liver tissue -- 1.4 Other applications -- 2 Folding and degradation functions of molecular chaperones -- 2.1 Introduction -- 2.2 The domain structure of Hsc/Hsp70 -- 2.3 The Hsc/Hsp70 reaction cycle -- 2.4 Cochaperones determine the function of Hsc/Hsp70 -- 2.5 In vitro reconstitution and functional analysis of the Hsc/Hsp70 chaperone system -- 2.6 Measuring the ATPase activity of Hsc/Hsp70 -- 2.7 Determining chaperone activity -- 2.8 In vitro reconstitution of chaperone-assisted ubiquitylation -- 2.9 Concluding remarks -- 3 Membrane protein folding in detergents -- 3.1 Introduction -- 3.2 Interactions of membrane proteins with detergents -- 3.3 Techniques to characterize TM proteins in detergents -- 3.4 Applications of TM protein-detergent complexes -- 3.5 Conclusions -- 4 Glycoprotein-folding quality control in the endoplasmic reticulum -- 4.1 Introduction -- 4.2 Glycoprotein-folding quality control (QC) -- 4.3 The UGGT -- 4.4 GII -- 4.5 CNX and CRT -- 4.6 ERp57 -- 4.7 Methods to study glycoprotein folding QC -- 5 Conformational dynamics in peptides and proteins studied by triplet-triplet energy transfer -- 5.1 Introduction -- 5.2 Concept of TTET experiments to study intrachain loop formation in polypeptide chains -- 5.3 Diffusion-controlled loop formation in unstructured polypeptide chains -- 5.4 Detection of fast conformational fluctuations in folded peptides and proteins by TTET -- 5.5 Conclusions -- 6 Protein import into the intermembrane space of mitochondria -- 6.1 Introduction -- 6.2 The mitochondrial IMS -- 6.3 The mitochondrial disulfide relay -- 6.4 The sulfhydryl oxidase Erv1 -- 6.5 The oxidoreductase Mia40. , 6.6 Substrates of the mitochondrial disulfide relay -- 6.7 Methods to study mitochondrial protein translocation -- 6.8 General comments to the analysis of thiol-disulfide redox states -- 6.9 Outlook -- 7 On-membrane identification of gel-resolved proteins by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) -- 7.1 Introduction -- 7.2 Methods for identifying proteins electroblotted onto the PVDF membrane -- 7.3 General comments to the analysis of proteins on membranes -- 7.4 PVDF membranes or diamond-like carbon-coated (DLC) stainless steel plates? -- 7.5 Concluding remarks -- 8 Analysis of protein complexes using chemical cross-linking and mass spectrometry -- 8.1 Introduction -- 8.2 Reagents for chemical cross-linking -- 8.3 The chemical cross-linking workflow -- 8.4 MS and data analysis -- 8.5 Practical examples -- 8.6 The use of spatial constraints for modeling -- 8.7 Conclusion and outlook -- 9 Single-crystal spectroscopy correlated with X-ray crystallography provides complementary perspectives on macromolecular function -- 9.1 Introduction -- 9.2 Ionizing radiation: essential for crystal structures -- a problem and a reagent -- 9.3 Cofactors in biology provide spectroscopic access to reaction cycles -- 9.4 Single-crystal spectroscopy correlated with X-ray diffraction -- 9.5 Correlated studies at beamline X26-C of the NSLS -- 9.6 Future prospects -- 10 Wide-angle X-ray solution scattering (WAXS) -- 10.1 Introduction -- 10.2 Sample preparation -- 10.3 Sample-handling robot -- 10.4 Data collection -- 10.5 Data processing -- 10.6 Structural information -- 10.7 Size and shape -- 10.8 Secondary and tertiary structure -- 10.9 Quaternary structure -- 10.10 Structural changes -- 10.11 Unfolding -- 10.12 Molecular modeling -- 10.13 Modeling of structural fluctuations -- 10.14 Outlook. , 11 Where purity matters: recombinant versus synthetic peptides in beta amyloid formation -- 11.1 Amyloid fibrils possess a defined quaternary structure -- 11.2 The importance of purity for reproducible kinetics of amyloid fibril formation in vitro: the Aß as an example -- 11.3 Future challenges for the characterization of fibrillar structures -- 12 Chemical modification of proteins in living cells -- 12.1 Introduction -- 12.2 Site-specific labeling of proteins with chemical probes -- 12.3 Selecting an appropriate labeling technique -- 12.4 Live cell applications -- 12.5 Technical Protocols for SNAP- tag labeling -- 13 Proteomics of human bronchoalveolar lavage fluid: discovery of biomarkers of chronic obstructive pulmonary disease (COPD) with difference gel electrophoresis (DIGE) and mass spectrometry (MS) -- 13.1 Introduction -- 13.2 Application of DIGE platform to COPD biomarker discovery -- 13.3 Outlook -- 14 Proteomic analysis of Duchenne muscular dystrophy (DMD) -- 14.1 Introduction -- 14.2 Materials -- 14.3 Methods -- 14.4 Results and Discussion -- 14.5 Conclusion -- 15 Target-oriented peptide arrays in a palliative approach to cystic fibrosis (CF) -- 15.1 Introduction -- 15.2 PDZ domains -- 15.3 CF -- 15.4 Role of PDZ domains in CFTR trafficking -- 15.5 Target-oriented peptide arrays -- 15.6 An engineered peptide inhibitor of CAL extends the half-life of AF508-CFTR -- 15.7 Methods -- 15.8 Outlook -- 16 Probing protein dynamics in vivo using backbone cyclization: bacterial acyl carrier protein as a case study -- 16.1 Introduction -- 16.2 In vivo protein cyclization, biophysical analyses and functional assays -- 16.3 Outlook -- 17 The protein epitope mimetic approach to protein-protein interaction inhibitors -- 17.1 Introduction -- 17.2 Mechanisms of protein-protein interactions -- 17.3 Small-molecule screening approaches. , 17.4 Protein epitope mimetic approaches -- 18 The structural biology of α1-antitrypsin deficiency and the serpinopathies -- 18.1 Clinical phenotypes of the serpinopathies -- 18.2 The serpin mechanism of protease inhibition -- 18.3 Folding, misfolding and polymerization -- 18.4 Serpin folding -- 18.5 Dissecting the pathways of polymerization -- 18.6 Cellular processing of polymers -- 18.7 Stem cell technology to generate models of disease -- 18.8 Conclusions -- Index.