Muñoz Victor (ed.) Protein Folding: Methods and Protocols

Humana Press, 2022. — 415 p. — (Methods in Molecular Biology 2376). — ISBN 978-1-0716-1715-1.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.Protein Engineering and Protein Chemistry Methods
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
Kinetic and Thermodynamic Analysis of Protein Folding
Folding Free Energy Surfaces from Differential Scanning Calorimetry
Fast-Folding Kinetics Using Nanosecond Laser-Induced Temperature-Jump Methods
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 Substates
Single-Molecule Spectroscopy Techniques
Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy
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
Molecular Simulations
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 Methods
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