Protein Folding Protocols

Protein Folding Protocols presents protocols for studying and characterizing steps and conformational ensembles populating pathways in protein folding from the unfolded to the folded state. It further presents a sample of approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. Protein folding is a crucial step in the transfer of genetic information from the DNA to the protein. The Genome Project has led to a huge number of available DNA sequences and, therefore, protein sequences. The Structural Genomics initiative largely aims to obtain new folds not currently present in the Protein Data Bank. Yet, the number of available structures inevitably lags behind the number of sequences. At the same time, an equally important problem is to find out the types and scope of dissimilar (nonhomologous) protein sequences that adopt a similar fold. Assembling data and comprehension of the sequence space of protein folds should be very useful in computational protein structure prediction. This would enhance the scope of homology modeling, which currently is the method of choice. Thus, experimental and theoretical studies on the relationship between sequence and structure are critical. Figuring out the relationship between sequence and structure would further assist in the prediction of fibril structures observed in protein misfolding diseases, and in figuring out the conformational changes and dynamics resulting from mutations. Protein folding is one of the most important and challenging problems in current molecular and chemical biology.

Includes supplementary material: sn.pub/extras

Klappentext
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.

Inhalt
Infrared Temperature-Jump Study of the Folding Dynamics of ?-Helices and ?-Hairpins.- The Use of High-Pressure Nuclear Magnetic Resonance to Study Protein Folding.- Characterization of Denatured Proteins Using Residual Dipolar Couplings.- Characterizing Residual Structure in Disordered Protein States Using Nuclear Magnetic Resonance.- Population and Structure Determination of Hidden Folding Intermediates by Native-State Hydrogen Exchange-Directed Protein Engineering and Nuclear Magnetic Resonance.- Characterizing Protein Folding Transition States Using ?-Analysis.- Advances in the Analysis of Conformational Transitions in Peptides Using Differential Scanning Calorimetry.- Application of Single Molecule Förster Resonance Energy Transfer to Protein Folding.- Single Molecule Studies of Protein Folding Using Atomic Force Microscopy.- Using Triplet-Triplet Energy Transfer to Measure Conformational Dynamics in Polypeptide Chains.- A Hierarchical Protein Folding Scheme Based on the Building Block Folding Model.- Replica Exchange Molecular Dynamics Method for Protein Folding Simulation.- Estimation of Folding Probabilities and ? Values From Molecular Dynamics Simulations of Reversible Peptide Folding.- Packing Regularities in Biological Structures Relate to Their Dynamics.- Intermediates and Transition States in Protein Folding.- Thinking the Impossible.