Vaidehi N., Klein-Seetharaman J. (Eds.) Membrane Protein Structure and Dynamics: Methods and Protocols

Humana Press, 2012. - 362 p. - 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 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
Experimental Techniques for Membrane Protein Structure Determination
Crystallization of Membrane Proteins in Bicelles
Vapor Diffusion Controlled meso Crystallization of Membrane Proteins
Solution NMR Studies of Integral Polytopic a-helical Membrane Proteins: The Structure Determination of the Seven-helix Transmembrane Receptor Sensory Rhodopsin II, pSRII
Use of NMR Saturation Transfer Difference Spectroscopy to Study Ligand Binding to Membrane Proteins
How to Investigate Interactions Between Membrane Proteins and Ligands by Solid-state NMR
Identifying and Measuring Transmembrane Helix-helix Interactions by FRET
Studying Substrate Binding to Reconstituted Secondary Transporters by Attenuated Total Reflection Infrared Difference Spectroscopy
UV-Visible and Infrared Methods for Investigating Lipid-Rhodopsin Membrane Interactions Proteomic Characterization of Integral Membrane Proteins Using Thermostatted Liquid Chromatography Coupled with Tandem Mass Spectrometry
Computational Methods for Prediction of Membrane Protein Structure and Dynamics
LITiCon: A Discrete Conformational Sampling Computational Method for Mapping Various Functionally Selective Conformational States of Transmembrane Helical Proteins
Homology Model-assisted Elucidation of Binding Sites in GPCRs
Comparative Modeling of Lipid Receptors
Quantification of Structural Distortions in the Transmembrane Helices of GPCRs
Structure Prediction of G Protein-Coupled Receptors and Their Ensemble of Functionally Important Conformations
Target Based Virtual Screening by Docking into Automatically Generated GPCR Models
Predicting the Biological Activities through QSAR Analysis and Docking-based Scoring Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation
Modeling the Structural Communication in Supramolecular Complexes Involving GPCRs Exploring Substrate Diffusion in Channels using Biased Molecular Dynamics Simulations