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G Protein-Coupled Receptors - Modeling and Simulation

  • Book
  • © 2014

Overview

Editors:
  1. Marta Filizola

    1. Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York,, USA

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  • This book is unique in its sort
  • The GPCR field is fast evolving, and computational techniques such as those described in this book, are becoming more and more utilized
  • Includes state-of-the-art views on modeling and simulation by recognized experts with an established reputation in the development and/or application of computational methods to GPCRs

Part of the book series: Advances in Experimental Medicine and Biology (AEMB, volume 796)

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Table of contents (10 chapters)

  1. Front Matter

    Pages i-viii
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  2. Progress in Structural Modeling of GPCRs

    1. Front Matter

      Pages 1-1
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    2. The GPCR Crystallography Boom: Providing an Invaluable Source of Structural Information and Expanding the Scope of Homology Modeling

      • Stefano Costanzi, Keyun Wang
      Pages 3-13

    3. Modeling of G Protein-Coupled Receptors Using Crystal Structures: From Monomers to Signaling Complexes

      • Angel Gonzalez, Arnau Cordomí, Minos Matsoukas, Julian Zachmann, Leonardo Pardo
      Pages 15-33

  3. GPCRs in Motion: Insights from Simulations

    1. Front Matter

      Pages 35-35
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    2. Structure and Dynamics of G-Protein Coupled Receptors

      • Nagarajan Vaidehi, Supriyo Bhattacharya, Adrien B. Larsen
      Pages 37-54

    3. How the Dynamic Properties and Functional Mechanisms of GPCRs Are Modulated by Their Coupling to the Membrane Environment

      • Sayan Mondal, George Khelashvili, Niklaus Johner, Harel Weinstein
      Pages 55-74

    4. Coarse-Grained Molecular Dynamics Provides Insight into the Interactions of Lipids and Cholesterol with Rhodopsin

      • Joshua N. Horn, Ta-Chun Kao, Alan Grossfield
      Pages 75-94

    5. Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods

      • Jennifer M. Johnston, Marta Filizola
      Pages 95-125

  4. GPCR-Focused Rational Design and Mathematical Modeling

    1. Front Matter

      Pages 127-127
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    2. From Three-Dimensional GPCR Structure to Rational Ligand Discovery

      • Albert J. Kooistra, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf
      Pages 129-157

    3. Mathematical Modeling of G Protein-Coupled Receptor Function: What Can We Learn from Empirical and Mechanistic Models?

      • David Roche, Debora Gil, Jesús Giraldo
      Pages 159-181

  5. Bioinformatics Tools and Resources for GPCRs

    1. Front Matter

      Pages 183-183
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    2. GPCR & Company: Databases and Servers for GPCRs and Interacting Partners

      • Noga Kowalsman, Masha Y. Niv
      Pages 185-204

    3. Bioinformatics Tools for Predicting GPCR Gene Functions

      • Makiko Suwa
      Pages 205-224

  6. Back Matter

    Pages 225-228
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Keywords

About this book

G protein-coupled receptors (GPCRs) are heptahelical transmembrane receptors that convert extra-cellular stimuli into intra-cellular signaling, and ultimately into biological responses. Since GPCRs are natural targets for approximately 40% of all modern medicines, it is not surprising that they have been the subject of intense research. Notwithstanding the amount of data generated over the years, discovering ligands of these receptors with optimal therapeutic properties is not straightforward and has certainly been hampered for years by the lack of high-resolution structural information about these receptors. Luckily, there has been a steady increase of high-resolution crystal structures of these receptors since 2007, and this information, integrated with dynamic inferences from computational and experimental methods, holds great potential for the discovery of new, improved drugs. This book, which provides, for the first time, state-of-the-art views on modeling and simulation of GPCRs, is divided into 4 parts. In the first part, the impact of currently available GPCR crystal structures on structural modeling is discussed extensively as are critical insights from simulations in the second part of the book. The third part reports recent progress in rational ligand discovery and mathematical modeling, whereas the fourth part provides an overview of bioinformatics tools and resources that are available for GPCRs.

Editors and Affiliations

  • Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York,, USA

    Marta Filizola

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