Membrane Protein Structure and Dynamics: Methods and Protocols

ISBN-13: 9781493962334 / Angielski / Miękka / 2016 / 357 str.

Nagarajan Vaidehi; Judith Klein-Seetharaman

Opis

This Methods in Molecular Biology (TM) book details approaches to the structure, dynamics and interactions of membrane proteins, including measurement procedures and computational methods for structure prediction and insight on the dynamics of membrane receptors.

Spis treści

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.Schäfer

 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 Mörs, Clemens Glaubitz

 6. Identifying and Measuring Transmembrane Helix-helix Interactions by FRET

Damien Thévenin, and Tzvetana Lazarova

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

Víctor A. Lórenz-Fonfría, Xavier León, and Esteve Padrós

 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,Zoltán 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 Mörs, Clemens Glaubitz

 6. Identifying and Measuring Transmembrane Helix-helix Interactions by FRET

Damien Thévenin, and Tzvetana Lazarova

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

Víctor A. Lórenz-Fonfría, Xavier León, and Esteve Padrós

 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,Zoltán 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

 

 6. Identifying and Measuring Transmembrane Helix-helix Interactions by FRET

Damien Thévenin, and Tzvetana Lazarova

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

Víctor A. Lórenz-Fonfría, Xavier León, and Esteve Padrós

 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,Zoltán 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

 

Víctor A. Lórenz-Fonfría, Xavier León, and Esteve Padrós

 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,Zoltán 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

 

 James Gumbart

 

Blurb

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.