1;Preface;6 2;Editor;8 3;Contents;12 4;List of contributing authors;8 5;Abbreviations;18 6;Acknowledgements;26 7;1 Three-phase partitioning;28 7.1;1.1 Method;29 7.2;1.2 The mechanism of TPP;30 7.3;1.3 A practical example - the isolation of cathepsin L from liver tissue;31 7.4;1.4 Other applications;32 8;2 Folding and degradation functions of molecular chaperones;40 8.1;2.1 Introduction;40 8.2;2.2 The domain structure of Hsc/Hsp70;40 8.3;2.3 The Hsc/Hsp70 reaction cycle;42 8.4;2.4 Cochaperones determine the function of Hsc/Hsp70;43 8.5;2.5 In vitro reconstitution and functional analysis of the Hsc/Hsp70 chaperone system;43 8.6;2.6 Measuring the ATPase activity of Hsc/Hsp70;45 8.7;2.7 Determining chaperone activity;45 8.8;2.8 In vitro reconstitution of chaperone-assisted ubiquitylation;46 8.9;2.9 Concluding remarks;48 9;3 Membrane protein folding in detergents;50 9.1;3.1 Introduction;50 9.2;3.2 Interactions of membrane proteins with detergents;51 9.3;3.3 Techniques to characterize TM proteins in detergents;56 9.4;3.4 Applications of TM protein-detergent complexes;62 9.5;3.5 Conclusions;68 10;4 Glycoprotein-folding quality control in the endoplasmic reticulum;74 10.1;4.1 Introduction;74 10.2;4.2 Glycoprotein-folding quality control (QC);74 10.3;4.3 The UGGT;76 10.4;4.4 GII;79 10.5;4.5 CNX and CRT;81 10.6;4.6 ERp57;84 10.7;4.7 Methods to study glycoprotein folding QC;85 11;5 Conformational dynamics in peptides and proteins studied by triplet-triplet energy transfer;100 11.1;5.1 Introduction;100 11.2;5.2 Concept of TTET experiments to study intrachain loop formation in polypeptide chains;100 11.3;5.3 Diffusion-controlled loop formation in unstructured polypeptide chains;106 11.4;5.4 Detection of fast conformational fluctuations in folded peptides and proteins by TTET;112 11.5;5.5 Conclusions;118 12;6 Protein import into the intermembrane space of mitochondria;122 12.1;6.1 Introduction;122 12.2;6.2 The mitochondrial IMS;122 12.3;6.3 The mitochondrial disulfide relay;123 12.4;6.4 The sulfhydryl oxidase Erv1;123 12.5;6.5 The oxidoreductase Mia40;125 12.6;6.6 Substrates of the mitochondrial disulfide relay;125 12.7;6.7 Methods to study mitochondrial protein translocation;126 12.8;6.8 General comments to the analysis of thiol-disulfide redox states;132 12.9;6.9 Outlook;134 13;7 On-membrane identification of gel-resolved proteins by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS);140 13.1;7.1 Introduction;140 13.2;7.2 Methods for identifying proteins electroblotted onto the PVDF membrane;143 13.3;7.3 General comments to the analysis of proteins on membranes;145 13.4;7.4 PVDF membranes or diamond-like carbon-coated (DLC) stainless steel plates?;151 13.5;7.5 Concluding remarks;151 14;8 Analysis of protein complexes using chemical cross-linking and mass spectrometry;154 14.1;8.1 Introduction;154 14.2;8.2 Reagents for chemical cross-linking;154 14.3;8.3 The chemical cross-linking workflow;158 14.4;8.4 MS and data analysis;160 14.5;8.5 Practical examples;163 14.6;8.6 The use of spatial constraints for modeling;164 14.7;8.7 Conclusion and outlook;165 15;9 Single-crystal spectroscopy correlated with X-ray crystallography provides complementary perspectives on macromolecular function;170 15.1;9.1 Introduction;170 15.2;9.2 Ionizing radiation: essential for crystal structures; a problem and a reagent173 15.3;9.3 Cofactors in biology provide spectroscopic access to reaction cycles;174 15.4;9.4 Single-crystal spectroscopy correlated with X-ray diffraction;177 15.5;9.5 Correlated studies at beamline X26-C of the NSLS;180 15.6;9.6 Future prospects;186 16;10 Wide-angle X-ray solution scattering (WAXS);192 16.1;10.1 Introduction;192 16.2;10.2 Sample preparation;193 16.3;10.3 Sample-handling robot;194 16.4;10.4 Data collection;195 16.5;10.5 Data processing;196 16.6;10.6 Structural information;198 16.7;10.7 Size and shape;198 16.8;10.8 Secondary and tertiary structure;199 16.9;10.9 Quaternary structure;200 16.10;10.10 Structural c