Protein Folding, 1st ed. 2022 Methods and Protocols Methods in Molecular Biology Series, Vol. 2376

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.

Luis Alberto Campos

2. Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis

Michael Baxa, Tobin R. Sosnick

3. Site-Specific Interrogation of Protein Structure and Stability

4. Purification and Handling of the Chaperonin GroEL

Xiang Ye

5. ­Folding free energy surfaces from Differential Scanning Calorimetry

Jose M. Sanchez-Ruiz and Beatriz Ibarra-Molero

6. Fast Folding Kinetics using Nanosecond Laser-Induced Temperature Jump Methods

Michele Cerminara

7. Measurement of Submillisecond Protein Folding using Trp Fluorescence and Photochemical Oxidation

David Witalka and Lisa J. Lapidus

8. Native State Hydrogen Exchange-Mass Spectrometry Methods to Probe Protein Folding and Unfolding

Pooja Malhotra and Jayant B. Udgaonkar

9. Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes

Ginka S. Kubelka and Jan Kubelka

10. Nmr Analysis Of Protein Folding Interaction Networks

Eva de Alba

 V. N. Sivanandam, Nicola D’Amelio, and Victor Muñoz

Pooja Malhotra and Jayant B. Udgaonkar

13. Single-Molecule Fluorescence Spectroscopy Approaches for Probing Fast Biomolecular Dynamics and Interactions

Zifan Wang, Nivin Mothi, and Victor Muñoz

14. Theory and Analysis of Single-Molecule FRET experiments

Irina V. Gopich and Hoi Sung Chung

15. Mechanochemical Evolution Of Disulfide Bonds In Proteins

Jörg Schönfelder, Alvaro Alonso-Caballero, and Raul Perez-Jimenez

16. Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments

17. Analysis of Molecular Dynamics Simulations of Protein Folding

18. Atomistic Simulations of Thermal Unfolding

Angel E Garcia

19. Molecular Simulations of Intrinsically Disordered Proteins and their Binding Mechanisms

Xiakun Chu, Suhani Nagpal, and Victor Muñoz

20. Prediction of Folding and Unfolding Rates of Proteins with Simple Models

 David De Sancho and Victor Munoz

21. Predicting and Simulating Mutational Effects on Protein Folding Kinetics

Athi N. Naganathan

A. Brenda Guzovsky, Nicholas P. Schafer, Peter G. Wolynes, and Diego U. Ferreiro

23. Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES  Force Field

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible result

Contains key notes and implementation advice from the experts