The edition details methods to study intrinsically disordered proteins (IDPs) including recent topics such as extremely high-affinity disordered complexes, kinetics that evade established concepts, liquid-liquid phase separation, and novel disorder-driven allosteric mechanisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and…mehr
The edition details methods to study intrinsically disordered proteins (IDPs) including recent topics such as extremely high-affinity disordered complexes, kinetics that evade established concepts, liquid-liquid phase separation, and novel disorder-driven allosteric mechanisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Intrinsically Disordered Proteins: Methods and Protocols aims to help scientists with different backgrounds to further their investigations into these fascinating and dynamic molecules.
Chapter 24 is available open access under a CC BY 4.0 license via link.springer.com.
Chapters "40 and 42 " are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Disorder for Dummies: Functional Mutagenesis of Transient Helical Segments in Disordered Proteins.- Computational Prediction of Intrinsic Disorder in Protein Sequences with the disCoP Meta-predictor.- Computational Prediction of Disordered Protein Motifs using SLiMSuite.- How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource.- Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER.- Exploring Protein Intrinsic Disorder with MobiDB.- An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.- Expression and Purification of an Intrinsically Disordered Protein.- Production of Intrinsically Disordered Proteins for Biophysical Studies; Tips and Tricks.- Recombinant Production of Monomeric Isotope-Enriched Aggregation-Prone Peptides: Polyglutamine Tracts and Beyond.- Cell-free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy.- Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-ray Scattering.- Determining Rg of IDPs from SAXS data.- Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements.- Quantitative Protein Disorder Assessment using NMR Chemical Shifts.- Determination of pKa Values in Intrinsically Disordered Proteins.- Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates.- Predicting Conformational Properties of Intrinsically Disordered Proteins from Sequence.- Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins.- Computational Protocol for Determining Conformational Ensembles of Intrinsically Disordered Proteins.- Computing, Analyzing and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins.- Binding Thermodynamics to Intrinsically Disordered Protein Domains.- Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements.- NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions.- Measuring Effective Concentrations Enforced by Intrinsically Disordered Linkers.- Determining the Protective Activity of IDPs under Partial Dehydration and Freeze-thaw Conditions.- Screening Intrinsically Disordered Regions for Short Linear Binding Motifs.- Probing IDP Interactions with Membranes by Fluorescence Spectroscopy.- Protocol for Investigating the Interactions between Intrinsically Disordered Proteins and Membranes by Neutron Reflectometry.- Interactions of IDPs with Membranes Using Dark State Exchange NMR Spectroscopy.- Determination of Binding Kinetics of Intrinsically Disordered Proteins by Surface Plasmon Resonance.- Measuring and Analysing Binding Kinetics of Coupled Folding and BindingReactions under Pseudo-first Order Conditions.- Understanding Binding Induced Folding by Temperature Jump.- Determining Binding Kinetics of Intrinsically Disordered Proteins by NMR spectroscopy.- Determination of Protein Phase Diagrams by Centrifugation.- In vitro Transition Temperature Measurement of Phase Separating Proteins by Microscopy.- Walking along a Protein Phase Diagram to Determine Coexistence Points by Static Light Scattering.- Expression and Purification of Intrinsically Disordered Abeta Peptide and Setup of Reproducible Aggregation Kinetics Experiment.- Measuring Interactions between Tau and Aggregation Inducers with Single Molecule Förster Resonance Energy Transfer.- Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins using Phos-tag SDS-PAGE.- Multiple Site-specific Phosphorylation of IDPs Monitored by NMR.- Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins usingQuantitative Mass-Spectrometry.- Targeting an Intrinsically Disordered Protein by Covalent Modification.- Recording in-cell NMR-spectra in Living Mammalian Cells.- In-cell NMR of Intrinsically Disordered Proteins in Mammalian Cells.- Analyzing IDPs in Interactomes.
Disorder for Dummies: Functional Mutagenesis of Transient Helical Segments in Disordered Proteins.- Computational Prediction of Intrinsic Disorder in Protein Sequences with the disCoP Meta-predictor.- Computational Prediction of Disordered Protein Motifs using SLiMSuite.- How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource.- Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER.- Exploring Protein Intrinsic Disorder with MobiDB.- An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.- Expression and Purification of an Intrinsically Disordered Protein.- Production of Intrinsically Disordered Proteins for Biophysical Studies; Tips and Tricks.- Recombinant Production of Monomeric Isotope-Enriched Aggregation-Prone Peptides: Polyglutamine Tracts and Beyond.- Cell-free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy.- Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-ray Scattering.- Determining Rg of IDPs from SAXS data.- Obtaining Hydrodynamic Radii of Intrinsically Disordered Protein Ensembles by Pulsed Field Gradient NMR Measurements.- Quantitative Protein Disorder Assessment using NMR Chemical Shifts.- Determination of pKa Values in Intrinsically Disordered Proteins.- Paris-DÉCOR: A Protocol for the Determination of Fast Protein Backbone Amide Hydrogen Exchange Rates.- Predicting Conformational Properties of Intrinsically Disordered Proteins from Sequence.- Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins.- Computational Protocol for Determining Conformational Ensembles of Intrinsically Disordered Proteins.- Computing, Analyzing and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins.- Binding Thermodynamics to Intrinsically Disordered Protein Domains.- Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements.- NMR Lineshape Analysis of Intrinsically Disordered Protein Interactions.- Measuring Effective Concentrations Enforced by Intrinsically Disordered Linkers.- Determining the Protective Activity of IDPs under Partial Dehydration and Freeze-thaw Conditions.- Screening Intrinsically Disordered Regions for Short Linear Binding Motifs.- Probing IDP Interactions with Membranes by Fluorescence Spectroscopy.- Protocol for Investigating the Interactions between Intrinsically Disordered Proteins and Membranes by Neutron Reflectometry.- Interactions of IDPs with Membranes Using Dark State Exchange NMR Spectroscopy.- Determination of Binding Kinetics of Intrinsically Disordered Proteins by Surface Plasmon Resonance.- Measuring and Analysing Binding Kinetics of Coupled Folding and BindingReactions under Pseudo-first Order Conditions.- Understanding Binding Induced Folding by Temperature Jump.- Determining Binding Kinetics of Intrinsically Disordered Proteins by NMR spectroscopy.- Determination of Protein Phase Diagrams by Centrifugation.- In vitro Transition Temperature Measurement of Phase Separating Proteins by Microscopy.- Walking along a Protein Phase Diagram to Determine Coexistence Points by Static Light Scattering.- Expression and Purification of Intrinsically Disordered Abeta Peptide and Setup of Reproducible Aggregation Kinetics Experiment.- Measuring Interactions between Tau and Aggregation Inducers with Single Molecule Förster Resonance Energy Transfer.- Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins using Phos-tag SDS-PAGE.- Multiple Site-specific Phosphorylation of IDPs Monitored by NMR.- Detection of Multisite Phosphorylation of Intrinsically Disordered Proteins usingQuantitative Mass-Spectrometry.- Targeting an Intrinsically Disordered Protein by Covalent Modification.- Recording in-cell NMR-spectra in Living Mammalian Cells.- In-cell NMR of Intrinsically Disordered Proteins in Mammalian Cells.- Analyzing IDPs in Interactomes.
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