Protein Supersecondary Structures: Methods and Protocols(1958 Methods in Molecular Biology)

This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of ‘transformer proteins’; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists ofthe necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about  the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.

Table of Contents:
55 Years of the Rossmann Fold.- Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction.- Automated Family-Wide Annotation of Secondary Structure Elements.- Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences.- StackSSSPred: A Stacking Based Prediction of Supersecondary Structure from Sequence.- Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures.- Secondary and Supersecondary Structure of Proteins as Coupling between Local and Local and Backbone-Electrostatic Interactions: A View through Cluster-Cumulant Scope.- Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction.- Exploring Protein Supersecondary Structure through Changes in Protein Folding, Stability, and Flexibility.- Protodomains: Symmetry Related Supersecondary Structures in Proteins and Self-Complementarity.- bab Super Secondary Motifs: Sequence, Structural Overview and Pursuit of Potential Autonomously Folding bab Sequences from (b/a)8/TIM Barrels.- Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for their Prediction and Characterization.- Stable Sub-Structures in Proteins and How to Find Them using Single-Molecule Force Spectroscopy.- Supersecondary Structures and Fragment Libraries.- Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins.- Sequence Pattern for Supersecondary Structure of Sandwich-Like Proteins.- Homology Searches using Supersecondary Structure Code.- Beyond Supersecondary Structure: Physics-Based Sequence Alignment.- Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores.- Hands On: Using Tryptophan Fluorescence Spectroscopy to Study Protein Structure.- Structural Characterization of Membrane Protein Dimers.