Protein Folding Protocols presents protocols for studying and characterizing protein folding from the unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. These approaches have tremendous implications, ranging from drug design, functional assignment, comprehension of the nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular pathways and their dynamics. The protocols follow the successful Methods in Molecular BiologyT series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
Infrared Temperature-Jump Study of the Folding Dynamics of a-Helices and b-Hairpins; Feng Gai, Deguo Du, and Yao Xu; The Use of High-Pressure Nuclear Magnetic Resonance to Study Protein Folding; Michael W. Lassalle and Kazuyuki Akasaka; Characterization of Denatured Proteins Using Residual Dipolar Couplings; Erika B. Gebel and David Shortle; Characterizing Residual Structure in Disordered Protein States Using Nuclear Magnetic Resonance; David Eliezer; Population and Structure Determination of Hidden Folding, Intermediates by Native-State Hydrogen Exchange-Directed Protein Engineering and Nuclear Magnetic Resonance; Yawen Bai, Hanqiao Feng, and Zheng Zhou; Characterizing Protein Folding Transition States Using Y-Analysis; Adarsh D. Pandit, Bryan A. Krantz, Robin S. Dothager, and Tobin R. Sosnick; Advances in the Analysis of Conformational Transitions in Peptides Using Differential Scanning Calorimetry; Werner W. Streicher and George I. Makhatadze; Application of Single Molecule Forster Resonance Energy Transfer to Protein Folding; Benjamin Schuler; Single Molecule Studies of Protein Folding Using Atomic Force Microscopy; Sean P. Ng, Lucy G. Randles, and Jane Clarke; Using Triplet-Triplet Energy Transfer to Measure Conformational Dynamics in Polypeptide Chains; Beat Fierz, Karin Joder, Florian Krieger, and Thomas Kiefhaber; A Hierarchical Protein Folding Scheme Based on the Building Block Folding Model; Nurit Haspel, Gilad Wainreb, Yuval Inbar, Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Haim J. Wolfson, and Ruth Nussinov; Replica Exchange Molecular Dynamics Method for Protein Folding Simulation; Ruhong Zhou; Estimation of Folding Probabilities and F Values From Molecular Dynamics Simulations of Reversible Peptide Folding; Francesco Rao, Giovanni Settanni, and Amedeo Caflisch; Packing Regularities in Biological Structures Relate to Their Dynamics; Robert L. Jernigan and Andrzej Kloczkowski; Intermediates and Transition States in Protein Folding; D. Thirumalai and Dmitri K. Klimov; Thinking the Impossible: How to Solve the Protein Folding Problem With and Without Homologous Structures and Morem; Rita Casadio, Piero Fariselli, Pier Luigi Martelli, and Gianluca Tasco; Index