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Computational Design of Membrane Proteins

  • Book
  • © 2021

Overview

Editors:
  1. Irina S. Moreira

    1. Department of Life Sciences, University of Coimbra, Coimbra, Portugal

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    You can also search for this editor in PubMed   Google Scholar

  2. Miguel Machuqueiro

    1. BioISI, University of Lisboa, Lisboa, Portugal

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    You can also search for this editor in PubMed   Google Scholar

  3. Joana MourĂ£o

    1. Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal

    View editor publications

    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 2315)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View

      • NĂ­cia RosĂ¡rio-Ferreira, Catarina Marques-Pereira, Raquel P. Gouveia, Joana MourĂ£o, Irina S. Moreira
      Pages 3-28

  3. Methods in Synthetic Biology

    1. Front Matter

      Pages 29-29
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    2. Integrating Membrane Transporter Proteins into Droplet Interface Bilayers

      • Heather E. Findlay, Nicola J. Harris, Paula J. Booth
      Pages 31-41

    3. Membrane Protein Engineering with Rosetta

      • Rebecca F. Alford, Jeffrey J. Gray
      Pages 43-57

    4. Engineering of Biological Pathways: Complex Formation and Signal Transduction

      • Philipp Junk, Christina Kiel
      Pages 59-70Open Access

  4. Structure Prediction and Oligomerization

    1. Front Matter

      Pages 71-71
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    2. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom

      • Asma Tiss, Rym Ben Boubaker, Daniel Henrion, Hajer Guissouma, Marie Chabbert
      Pages 73-97

    3. Interface Prediction for GPCR Oligomerization Between Transmembrane Helices

      • Wataru Nemoto, Akira Saito
      Pages 99-110

    4. Memdock: An α-Helical Membrane Protein Docking Algorithm

      • Naama Hurwitz, Haim J. Wolfson
      Pages 111-117

  5. Coarse-Grained and Atomistic MD Simulations

    1. Front Matter

      Pages 119-119
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    2. Identification and Characterization of Specific Protein–Lipid Interactions Using Molecular Simulation

      • Robin A. Corey, Mark S. P. Sansom, Phillip J. Stansfeld
      Pages 121-139

    3. Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins

      • Vinay V. Nair, Alemayehu A. Gorfe
      Pages 141-159

    4. In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides

      • Nicolas Frazee, Violeta Burns, Chitrak Gupta, Blake Mertz
      Pages 161-182

  6. pH and Polarization Effects

    1. Front Matter

      Pages 183-183
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    2. pK a Calculations in Membrane Proteins from Molecular Dynamics Simulations

      • Nuno F. B. Oliveira, TomĂ¡s F. D. Silva, Pedro B. P. S. Reis, Miguel Machuqueiro
      Pages 185-195

    3. Poor Person’s pH Simulation of Membrane Proteins

      • Chitrak Gupta, Umesh Khaniya, John W. Vant, Mrinal Shekhar, Junjun Mao, M. R. Gunner et al.
      Pages 197-217

    4. Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model

      • Justin A. Lemkul
      Pages 219-240

  7. Membrane Permeability and Transport

    1. Front Matter

      Pages 241-241
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Keywords

About this book

This volume provides an overview of the current successes as well as pitfalls and caveats that are hindering the design of membrane proteins. Divided into six parts, chapters detail membrane transporter, FoldX force field, protein stability, G-Protein Coupled Receptors (GPCR) structures, transmembrane helices, membrane molecular dynamics (MD) simulations, pH-dependent protonation states, membrane permeability, and passive transport. 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.

 

Authoritative and cutting-edge,  Computational Design of Membrane Proteins aims to ensure successful results in the further study of this vital field.

Chapter 4 is available open access under a Creative CommonsAttribution 4.0 International License via link.springer.com.





Editors and Affiliations

  • Department of Life Sciences, University of Coimbra, Coimbra, Portugal

    Irina S. Moreira

  • BioISI, University of Lisboa, Lisboa, Portugal

    Miguel Machuqueiro

  • Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal

    Joana MourĂ£o

Bibliographic Information

  • Book Title: Computational Design of Membrane Proteins

  • Editors: Irina S. Moreira, Miguel Machuqueiro, Joana MourĂ£o

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1468-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-0716-1467-9Published: 25 July 2021

  • Softcover ISBN: 978-1-0716-1470-9Published: 26 July 2022

  • eBook ISBN: 978-1-0716-1468-6Published: 24 July 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 290

  • Number of Illustrations: 4 b/w illustrations, 53 illustrations in colour

  • Topics: Protein Science

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