Membrane Protein Structure and Dynamics: Methods and Protocols (Paperback)

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 Spectroscopy Victor 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 Models Christofer 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 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 Spectroscopy Victor 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 Ch