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Allostery

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Luisa Di Paola

    1. Unit of Chemical-Physics Fundamentals in Chemical Engineering Department of Engineering, Universitá Campus Bio-Medico di Rome, Rome, Italy

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  2. Alessandro Giuliani

    1. Environment and Health Department, Instituto Superiore di Sanità, Rome, Italy

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2253)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-xii
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  2. Allostery: The Rebound of Proteins

    • Alessandro Finazzi Agrò, Giampiero Mei
    Pages 1-6

  3. Disclosing Allostery Through Protein Contact Networks

    • Luisa Di Paola, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani
    Pages 7-20

  4. Identification of Allosteric Effects in Proteins by Elastic Network Models

    • Guang Hu
    Pages 21-35

  5. Locating and Navigating Energy Transport Networks in Proteins

    • Korey M. Reid, David M. Leitner
    Pages 37-59

  6. Probing Allosteric Mechanism with Long-Range Rigidity Transmission Across Protein Networks

    • Adnan Sljoka
    Pages 61-75

  7. Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments

    • Giampiero Mei, Almerinda Di Venere, Luisa Di Paola, Alessandro Finazzi Agrò
    Pages 77-88

  8. Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach

    • Vasundhara Gadiyaram, Anasuya Dighe, Sambit Ghosh, Saraswathi Vishveshwara
    Pages 89-112

  9. Topology Results on Adjacent Amino Acid Networks of Oligomeric Proteins

    • Claire Lesieur, Laurent Vuillon
    Pages 113-135

  10. Community Network Analysis of Allosteric Proteins

    • Ivan Rivalta, Victor S. Batista
    Pages 137-151

  11. The PyInteraph Workflow for the Study of Interaction Networks From Protein Structural Ensembles

    • Matteo Lambrughi, Valentina Sora, Matteo Tiberti
    Pages 153-174

  12. The Allosteric Effect in Antibody-Antigen Recognition

    • Jun Zhao, Ruth Nussinov, Buyong Ma
    Pages 175-183

  13. Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions

    • Melanie Goldstein, Nina M. Goodey
    Pages 185-219

  14. Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations

    • Elena Papaleo
    Pages 221-244

  15. Molecular Dynamics Simulation Techniques as Tools in Drug Discovery and Pharmacology : A Focus on Allosteric Drugs

    • Chiara Bianca Maria Platania, Claudio Bucolo
    Pages 245-254

  16. Cooperativity and Allostery in RNA Systems

    • Alla Peselis, Alexander Serganov
    Pages 255-271

  17. Back Matter

    Pages 273-274
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Keywords

About this book

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. 


Editors and Affiliations

  • Unit of Chemical-Physics Fundamentals in Chemical Engineering Department of Engineering, Universitá Campus Bio-Medico di Rome, Rome, Italy

    Luisa Di Paola

  • Environment and Health Department, Instituto Superiore di Sanità, Rome, Italy

    Alessandro Giuliani

Bibliographic Information

  • Book Title: Allostery

  • Book Subtitle: Methods and Protocols

  • Editors: Luisa Di Paola, Alessandro Giuliani

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1154-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1153-1Published: 15 December 2020

  • Softcover ISBN: 978-1-0716-1156-2Published: 16 December 2021

  • eBook ISBN: 978-1-0716-1154-8Published: 14 December 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 274

  • Number of Illustrations: 8 b/w illustrations, 91 illustrations in colour

  • Topics: Protein Science

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