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Membrane Protein Structure and Dynamics

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Nagarajan Vaidehi

    1. , Division of Immunology, Beckman Research Institute of the City o, Duarte, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Judith Klein-Seetharaman

    1. , Department of Structural Biology, University of Pittsburgh School of Medic, Pittsburgh, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Lists the necessary materials and provides the needed background information for all experiments
  • Provides step-by-step detail essential fro reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 914)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
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  2. Experimental Techniques for Membrane Protein Structure Determination

    1. Front Matter

      Pages 1-1
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    2. Crystallization of Membrane Proteins in Bicelles

      • Sayeh Agah, Salem Faham
      Pages 3-16

    3. Vapor Diffusion-Controlled Meso Crystallization of Membrane Proteins

      • J. Labahn, J. Kubicek, F. Schäfer
      Pages 17-24

    4. Solution NMR Studies of Integral Polytopic α-Helical Membrane Proteins: The Structure Determination of the Seven-Helix Transmembrane Receptor Sensory Rhodopsin II, pSRII

      • Antoine Gautier, Daniel Nietlispach
      Pages 25-45

    5. Use of NMR Saturation Transfer Difference Spectroscopy to Study Ligand Binding to Membrane Proteins

      • Rani Parvathy Venkitakrishnan, Outhiriaradjou Benard, Marianna Max, John L. Markley, Fariba M. Assadi-Porter
      Pages 47-63

    6. How to Investigate Interactions Between Membrane Proteins and Ligands by Solid-State NMR

      • Andrea Lakatos, Karsten Mörs, Clemens Glaubitz
      Pages 65-86

    7. Identifying and Measuring Transmembrane Helix–Helix Interactions by FRET

      • Damien Thévenin, Tzvetana Lazarova
      Pages 87-106

    8. Studying Substrate Binding to Reconstituted Secondary Transporters by Attenuated Total Reflection Infrared Difference Spectroscopy

      • Víctor A. Lórenz-Fonfría, Xavier León, Esteve Padrós
      Pages 107-126

    9. UV–Visible and Infrared Methods for Investigating Lipid–Rhodopsin Membrane Interactions

      • Michael F. Brown
      Pages 127-153

    10. Proteomic Characterization of Integral Membrane Proteins Using Thermostatted Liquid Chromatography Coupled with Tandem Mass Spectrometry

      • Sarah M. Moore, Christine C. Wu
      Pages 155-164

  3. Computational Methods for Prediction of Membrane Protein Structure and Dynamics

    1. Front Matter

      Pages 165-165
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    2. LITiCon: A Discrete Conformational Sampling Computational Method for Mapping Various Functionally Selective Conformational States of Transmembrane Helical Proteins

      • Supriyo Bhattacharya, Nagarajan Vaidehi
      Pages 167-178

    3. Homology Model-Assisted Elucidation of Binding Sites in GPCRs

      • Anat Levit, Dov Barak, Maik Behrens, Wolfgang Meyerhof, Masha Y. Niv
      Pages 179-205

    4. Comparative Modeling of Lipid Receptors

      • Abby L. Parrill
      Pages 207-218

    5. Quantification of Structural Distortions in the Transmembrane Helices of GPCRs

      • Xavier Deupi
      Pages 219-235

    6. Structure Prediction of G Protein-Coupled Receptors and Their Ensemble of Functionally Important Conformations

      • Ravinder Abrol, Adam R. Griffith, Jenelle K. Bray, William A. Goddard III
      Pages 237-254

    7. Target Based Virtual Screening by Docking into Automatically Generated GPCR Models

      • Christofer S. Tautermann
      Pages 255-270

    8. Predicting the Biological Activities Through QSAR Analysis and Docking-Based Scoring

      • Santiago Vilar, Stefano Costanzi
      Pages 271-284

    9. Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation

      • Basak Isin, Kalyan C. Tirupula, Zoltán N. Oltvai, Judith Klein-Seetharaman, Ivet Bahar
      Pages 285-317
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Keywords

About this book

Membrane proteins play key roles in numerous cellular processes, in particular mediating cell-to-cell communication and signaling events that lead to a multitude of biological effects. Membrane proteins have also been implicated in many critical diseases such as atherosclerosis, hypertension, diabetes and cancer. In Membrane Protein Structure Predictions Methods: Methods and Protocols, expert researcher in the field detail the advances in both experimental and computational approaches of the structure, dynamics and interactions of membrane proteins dividing the volume into two sections. The first section details the procedures used for measurements of structure and dynamics of membrane proteins. While the second section contains a survey of the computational methods that have played a critical role in membrane protein structure prediction as well as in providing atomic level insight into the mechanism of the dynamics of membrane receptors. Written in the highly successful Methods in Molecular Biologyâ„¢ series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Thorough and intuitive, Membrane Protein Structure Predicitons: Methods and Protocols seeks to aid scientists in the further study of membrane protein structure and function.

Editors and Affiliations

  • , Division of Immunology, Beckman Research Institute of the City o, Duarte, USA

    Nagarajan Vaidehi

  • , Department of Structural Biology, University of Pittsburgh School of Medic, Pittsburgh, USA

    Judith Klein-Seetharaman

Bibliographic Information

  • Book Title: Membrane Protein Structure and Dynamics

  • Book Subtitle: Methods and Protocols

  • Editors: Nagarajan Vaidehi, Judith Klein-Seetharaman

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-023-6

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2012

  • Hardcover ISBN: 978-1-62703-022-9Published: 12 September 2012

  • Softcover ISBN: 978-1-4939-6233-4Published: 23 August 2016

  • eBook ISBN: 978-1-62703-023-6Published: 14 September 2012

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 357

  • Topics: Protein Science, Membrane Biology

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