ENGLISH

Protein Supersecondary Structures: Methods and Protocols

By Alexander E. Kister

Book information

Publisher
Springer New York; Humana
Year
2019
ISBN
978-1-4939-9160-0;978-1-4939-9161-7
Language
english
Format
PDF
Filesize
15 MB (15325664 bytes)
Series
Methods in Molecular Biology 1958
Edition
2nd ed.
Pages
XVIII, 438\443
Time added
2019-09-18 12:16:59
Life Sciences; Protein Structure; Bioinformatics

Description

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 of the 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. Front Matter ....Pages i-xviii 55 Years of the Rossmann Fold (Woong-Hee Shin, Daisuke Kihara)....Pages 1-13 Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction (Elijah MacCarthy, Derrick Perry, Dukka B. KC)....Pages 15-45 Automated Family-Wide Annotation of Secondary Structure Elements (Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Taraka Ramji Moturu, Veronika Navrátilová, Jaroslav Koča et al.)....Pages 47-71 Computational Prediction of Secondary and Supersecondary Structures from Protein Sequences (Christopher J. Oldfield, Ke Chen, Lukasz Kurgan)....Pages 73-100 StackSSSPred: A Stacking-Based Prediction of Supersecondary Structure from Sequence (Michael Flot, Avdesh Mishra, Aditi Sharma Kuchi, Md Tamjidul Hoque)....Pages 101-122 Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures (Arun S. Konagurthu, Ramanan Subramanian, Lloyd Allison, David Abramson, Maria Garcia de la Banda, Peter J. Stuckey et al.)....Pages 123-131 Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope (Adam Liwo, Adam K. Sieradzan, Cezary Czaplewski)....Pages 133-146 Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction (Nasrin Akhter, Liban Hassan, Zahra Rajabi, Daniel Barbará, Amarda Shehu)....Pages 147-171 Exploring Protein Supersecondary Structure Through Changes in Protein Folding, Stability, and Flexibility (Douglas E. V. Pires, Carlos H. M. Rodrigues, Amanda T. S. Albanaz, Malancha Karmakar, Yoochan Myung, Joicymara Xavier et al.)....Pages 173-185 Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity (Philippe Youkharibache)....Pages 187-219 βαβ Super-Secondary Motifs: Sequence, Structural Overview, and Pursuit of Potential Autonomously Folding βαβ Sequences from (β/α)8/TIM Barrels (Rajasekhar Varma Kadamuri, Shivkumar Sharma Irukuvajjula, Ramakrishna Vadrevu)....Pages 221-236 Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for Their Prediction and Characterization (M. Rosario Fernández, Irantzu Pallarès, Valentín Iglesias, Jaime Santos, Salvador Ventura)....Pages 237-261 Stable Substructures in Proteins and How to Find Them Using Single-Molecule Force Spectroscopy (Katarzyna Tych, Gabriel Žoldák)....Pages 263-282 Supersecondary Structures and Fragment Libraries (Raphael Trevizani, Fábio Lima Custódio)....Pages 283-295 Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins (Bernard S. Gerstman, Prem P. Chapagain, Jeevan GC, Timothy Steckmann)....Pages 297-311 Sequence Pattern for Supersecondary Structure of Sandwich-Like Proteins (Alexander E. Kister)....Pages 313-327 Homology Searches Using Supersecondary Structure Code (Hiroshi Izumi)....Pages 329-340 Beyond Supersecondary Structure: Physics-Based Sequence Alignment (S. Rackovsky)....Pages 341-346 Secondary and Supersecondary Structure of Proteins in Light of the Structure of Hydrophobic Cores (Mateusz Banach, Leszek Konieczny, Irena Roterman)....Pages 347-378 Hands On: Using Tryptophan Fluorescence Spectroscopy to Study Protein Structure (Nadja Hellmann, Dirk Schneider)....Pages 379-401 Structural Characterization of Membrane Protein Dimers (António J. Preto, Pedro Matos-Filipe, Panagiotis I. Koukos, Pedro Renault, Sérgio F. Sousa, Irina S. Moreira)....Pages 403-436 Back Matter ....Pages 437-438

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