Membrane Protein Structure Methods and Protocols

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 researchers 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 Biology 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.

Contents

Part I. Experimental Techniques for Membrane Protein Structure Determination
1. Crystallization of Membrane Proteins in Bicelles Sayeh Agah and Salem Faham
2. Vapor Diffusion Controlled meso Crystallization of Membrane Proteins J. Labahn, J. Kubicek, F.Schafer
3. Solution NMR Studies of Integral Polytopic a-helical Membrane Proteins: The Structure Determination of the Seven-helix Transmembrane Receptor Sensory Rhodopsin II, pSRII Antoine Gautier and Daniel Nietlispach
4. Use of NMR Saturation Transfer Difference Spectroscopy to Study Ligand Binding to Membrane Proteins Rani Parvathy Venkitakrishnan, Outhiriaradjou Benard, Marianna Max, John L. Markley, and Fariba M. Assadi-Porter
5. How to Investigate Interactions Between Membrane Proteins and Ligands by Solid-state NMR Andrea Lakatos, Karsten Mors, Clemens Glaubitz
6. Identifying and Measuring Transmembrane Helix-helix Interactions by FRET Damien Thevenin, and Tzvetana Lazarova
7. Studying Substrate Binding to Reconstituted Secondary Transporters by Attenuated Total Reflection Infrared Difference SpectroscopyVictor A. Lorenz-Fonfria, Xavier Leon, and Esteve Padros
8. UV-Visible and Infrared Methods for Investigating Lipid-Rhodopsin Membrane Interactions Michael F. Brown
9. Proteomic Characterization of Integral Membrane Proteins Using Thermostatted Liquid Chromatography Coupled with Tandem Mass Spectrometry Sarah M. Moore and Christine C. Wu

Part II. Computational Methods for Prediction of Membrane Protein Structure and Dynamics
10. LITiCon: A Discrete Conformational Sampling Computational Method for Mapping Various Functionally Selective Conformational States of Transmembrane Helical Proteins Supriyo Bhattacharya and Nagarajan Vaidehi
11. Homology Model-assisted Elucidation of Binding Sites in GPCRs Anat Levit, Dov Barak, Maik Behrens, Wolfgang Meyerhof and Masha Y. Niv
12. Comparative Modeling of Lipid Receptors Abby L. Parrill
13. Quantification of Structural Distortions in the Transmembrane Helices of GPCRs Xavier Deupi
14. Structure Prediction of G Protein-Coupled Receptors and Their Ensemble of Functionally Important Conformations Ravinder Abrol , Adam R. Griffith, Jenelle K. Bray, and William A. Goddard III
15. Target Based Virtual Screening by Docking into Automatically Generated GPCR ModelsChristofer S. Tautermann
16. Predicting the Biological Activities through QSAR Analysis and Docking-based Scoring Santiago Vilar and Stefano Costanzi
17. Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation Basak Isin, Kalyan Tirupula, Zoltan N. Oltvai, Judith Klein-Seetharaman and Ivet Bahar
18. Modeling the Structural Communication in Supramolecular Complexes Involving GPCRs Francesca Fanelli
19. Exploring Substrate Diffusion in Channels using Biased Molecular Dynamics Simulations James Gumbart

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