Protein Folding Methods and Protocols

This volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

 

Authoritative and cutting-edge, Protein Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

Mutational Analysis of Protein Folding Transition States: Phi-values.- Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.- Site-Specific Interrogation of Protein Structure and Stability.- Purification and Handling of the Chaperonin GroEL.- ­Folding free energy surfaces from Differential Scanning Calorimetry.- Fast Folding Kinetics using Nanosecond Laser-Induced Temperature Jump Methods7. Measurement of Submillisecond Protein Folding using Trp Fluorescence and Photochemical Oxidation.- Native State Hydrogen Exchange-Mass Spectrometry Methods to Probe Protein Folding and Unfolding.- Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes.- Nmr Analysis Of Protein Folding Interaction Networks.- NMR Relaxation Dispersion Methods for the Structural and Dynamic Analysis of Quickly Interconverting, Low-Populated Conformational Sub-States.-  Native State Hydrogen Exchange-Mass Spectrometry Methods to Probe Protein Folding and Unfolding.- Single-Molecule Fluorescence Spectroscopy Approaches for Probing Fast Biomolecular Dynamics and Interactions.- Theory and Analysis of Single-Molecule FRET experiments.- Mechanochemical Evolution Of Disulfide Bonds In Proteins.- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.- Analysis of Molecular Dynamics Simulations of Protein Folding.- Atomistic Simulations of Thermal Unfolding.- Molecular Simulations of Intrinsically Disordered Proteins and their Binding Mechanisms.- Prediction of Folding and Unfolding Rates of Proteins with Simple Models.- Predicting and Simulating Mutational Effects on Protein Folding Kinetics.- Localization of Energetic Frustration in Proteins.- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES  Force Field.