Table of Contents

1. Expression and Purification of Human Mitochondrial Intramembrane Protease PARL

Elena Arutyunova, Laine Lysyk, Melissa Morrison, Cory Brooks, and M. Joanne Lemieux

2. Reconstitution of Detergent-Solubilized Membrane Proteins into Proteoliposomes and Nanodiscs for Functional and Structural Studies

Kerry M. Strickland, Kasahun Neselu, Arshay J. Grant, Carolann L. Espy, Nael A. McCarty, and Ingeborg Schmidt-Krey

3. Biochemical Characterization of GPCR-G Protein Complex Formation

Filip Pamula and Ching-Ju Tsai

4. Electrophysiological Approaches for the Study of Ion Channel Function

Guiying Cui, Kirsten A. Cottrill, and Nael A. McCarty

5. Isothermal Titration Calorimetry of Membrane Proteins

Han N. Vu, Alan J. Situ, and Tobias S. Ulmer

6. Atomic Force Microscopy Reveals Membrane Protein Activity at the Single Molecule Level

Kanokporn Chattrakun, Katherine G. Schaefer, Lucas S. Chandler, Brendan P. Marsh, and Gavin M. King

7. Structure Determination of Membrane Proteins Using X-Ray Crystallography

Evan Billings, Karl Lundquist, Claire Overly, Karthik Srinivasan, and Nicholas Noinaj

8. Studying Membrane Protein Structures by MicroED

Michael W. Martynowycz and Tamir Gonen

9. Single-Particle Cryo-EM of Membrane Proteins

Dovile Januliene and Arne Moeller

10. Helical Membrane Protein Crystallization in the New Era of Electron Cryo-Microscopy

Mary D. Hernando, Joseph O. Primeau, and Howard S. Young

11. NMR Spectroscopic Studies of Ion Channels in Lipid Bilayers: Sample Preparation Strategies Exemplified by the Voltage Dependent Anion Channel

Robert Silvers and Matthew Eddy

12. Preparation of a Deuterated Membrane Protein for Small-Angle Neutron Scattering

Yuqi Wu, Kevin L. Weiss, and Raquel L. Lieberman

13. Preparing Membrane Proteins for Simulation Using CHARMM-GUI

Yupeng Li, Jinchan Liu, and James C. Gumbart

14. Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide

William Glass, Jonathan W. Essex, Franca Fraternali, James Gebbie-Rayet, Irene Marzuoli, Marley L. Samways, Philip C. Biggin, and Syma Khalid

15. Continuous Constant pH Molecular Dynamics Simulations of Transmembrane Proteins

Yandong Huang, Jack A. Henderson, and Jana Shen

16. Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions Dylan Ogden and Mahmoud Moradi 17. Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations

Wesley M. Botello-Smith and Yun Lyna Luo

18. Large Scale Molecular Dynamics Simulations of Cellular Compartments Eric Wilson, John Vant, Jacob Layton, Ryan Boyd, Hyungro Lee, Matteo Turilli, Benjamin Hernandez, Sean Wilkinson, Shantenu Jha, Chitrak Gupta, Daipayan Sarkar, and Abhishek Singharoy