Protein Supersecondary Structures Methods and Protocols

About this book

Super Secondary Structure (SSS) helps to understand the relationship between primary and tertiary structure of proteins. In Protein Supersecondary Structure: Methods and Protocols expert researchers in the field detail the usefulness of the study of super secondary structure in different areas of protein research. This is done through four main studies SSS representation, SSS prediction, SSS and protein folding, and other application of SSS concept to protein biology.

Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Supersecondary Structure: Methods and Protocols highlight some of the major advances in the many fast-growing areas of supersecondary structure research.

Contents

1. Super-secondary Structure: A Historical Perspective Michael G. Rossmann

Part I: Representation of Supersecondary Structure
2. Hierarchical Representation of Super-secondary Structures Using a Graph-theoretical Approach Ina Koch and Annika Kreuchwig and Patrick May
3. Up, Down and Around: Identifying Recurrent Interactions Within and Between Super Secondary Structures in b-Propellers Soren Thirup, Vikas Gupta and Esben M. Quistgaard
4. Structure Description and Identification using the Tableau Representation of Protein Folding Patterns Arun S. Konagurthu and Arthur M. Lesk

Part II: Super-secondary Structure Prediction
5. Computational Prediction of Secondary and Supersecondary Structures Ke Chen and Lukasz Kurgan
6. A Survey of Machine Learning Methods for Secondary and Supersecondary Protein Structure Prediction Hui Kian Ho, Lei Zhang, Kotagiri Ramamohanarao, and Shawn Martin
7. Beyond Supersecondary Structure: The Global Properties of Protein Sequences S. Rackovsky
8. Creating Supersecondary Structures with BuildBeta Silvia Crivelli and Nelson Max
9. A Modular Perspective of Protein Structures; Application to Fragment Based Loop Modeling Narcis Fernandez-Fuentes and Andras Fiser
10. Residue-residue Contacts: Application to Analysis of Secondary Structure Interactions Vladimir Potapov, Marvin Edelman, Vladimir Sobolev

Part III: Supersecondary Structure and Protein Folding
11. Super-secondary Structures and Modeling of Protein Folds Alexander V. Efimov
12. Computational Simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation Bernard S. Gerstman and Prem P. Chapagain
13. Protein Folding at Atomic Resolution: Analysis of Autonomously Folding Supersecondary Structure Motifs by Nuclear Magnetic Resonance Lorenzo Sborgi, Abhinav Verma, Mourad Sadqi, Eva de Alba, and Victor Munoz
14. Artificial Supersecondary Structures Based on Aromatic Oligoamides Hai-Yu Hu and Chuan-Feng Chen

Part IV: Other Applications of Supersecondary Structure to Protein Biology
15. Cross-b-sheet Super-secondary Structure in Amyloid Folds: Techniques for Detection and Characterization Raimon Sabate and Salvador Ventura
16. Analyzing Oligomerization of Individual Transmembrane Helices and of Entire Membrane Proteins in E. coli: A Hitchhiker's Guide to GALLEX Florian Cymer, Charles R. Sanders, and Dirk Schneider
17. Super-secondary Structure Prediction of Transmembrane Beta-Barrel Proteins Van Du T Tran, Philippe Chassignet and Jean-Marc Steyaert
18. Functional Structural Motifs for Protein-ligand, Protein-protein and Protein-nucleic Acid Interactions and their Connection to Supersecondary Structures Akira R. Kinjo and Haruki Nakamura

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