This volume explores the basic issues of “allostery” and “network” that are fundamental to studying this field. Chapters in this book look at how the basic “machine-like” proteins, that are similar to “human machines,” need to be organized, architecturally, to relate to different organizational layers. Chapters cover topics such as methodological/computational factors focused on links between allostery and network formalism; the presence of oscillating modes transversing the structure and underlying network wiring of the allosteric process; the “action at distance” by transduction of signals across an organized network structure; and the P53 protein located at the cross-road of cell cycle regulation, genome integrity, and cancer development. 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.
Thorough and practical, Allostery: Methods and Protocols is a valuable resource for any scientists and researcher interested in learning more about this developing field.
Table of Contents...
1. Allostery: The Rebound of Proteins
Alessandro Finazzi Agrò and Giampiero Mei
2. Disclosing Allostery Through Protein Contact Networks
Luisa Di Paola, Giampiero Mei, Almerinda Di Venere, and Alessandro Giuliani
3. Identification of Allosteric Effects in Proteins by Elastic Network Models
4. Locating and Navigating Energy Transport Networks in Proteins
Korey M. Reid and David M. Leitner
5. Probing Allosteric Mechanism with Long-Range Rigidity Transmission across Protein Networks
6. Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments
Giampiero Mei, Almerinda Di Venere, Luisa Di Paola, and Alessandro Finazzi Agrò
7. Network Re-Wiring during Allostery and Protein-Protein Interactions: A Graph Spectral Approach
Vasundhara Gadiyaram, Anasuya Dighe, Sambit Ghosh, and Saraswathi Vishveshwara
8. Topology Results on Adjacent Amino Acid Networks of Oligomeric Proteins
Claire Lesieur and Laurent Vuillon
9. Community Network Analysis of Allosteric Proteins
Ivan Rivalta and Victor S. Batista
10. The PyInteraph Workflow for the Study of Interaction Networks Form Protein Structural Ensembles
Matteo Lambrughi, Valentina Sora, and Matteo Tiberti
11. The Allosteric Effect in Antibody-Antigen Recognition
Jun Zhao, Ruth Nussinov, and Buyong Ma
12. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions
Melanie Goldstein and Nina M. Goodey
13. Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations
14. Molecular Dynamics Simulation Techniques as a Tool in Drug Discovery and Pharmacology: A Focus on Allosteric Drugs
Chiara Bianca Maria Platania and Claudio Bucolo
15. Cooperativity and Allostery in RNA Systems
Alla Peselis and Alexander Serganov
Subject Index List…
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