Computational Design of Membrane Proteins

PART I: INTRODUCTION

1 Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View

N獳ia Ros嫫io-Ferreira, Catarina Marques-Pereira, Raquel P. Gouveia, Joana Mour緌, and Irina S. Moreira

PART II METHODS IN SYNTHETIC BIOLOGY

2 Integrating Membrane Transporter Proteins into Droplet Interface Bilayers

Heather E. Findlay, Nicola J. Harris, and Paula J. Booth

3 Membrane Protein Engineering with Rosetta

Rebecca F. Alford and Jeffrey J. Gray

4 Engineering of Biological Pathways: Complex Formation and Signal Transduction

Philipp Junk and Christina Kiel

5 Homology Modeling of Class a G-protein-coupled Receptors in the Age of the Structure Boom

Asma Tiss, Rym Ben Boubaker, Daniel Henrion, Hajer Guissouma, and Marie Chabbert

6 Interface Prediction for GPCR Oligomerization between Transmembrane Helices

Wataru Nemoto and Akira Saito

7 Memdock: An α-Helical Membrane Protein Docking Algorithm

Naama Hurwitz and Haim J. Wolfson

PART IV COARSE-GRAINED AND ATOMISTIC MD SIMULATIONS

8 Identification and Characterization of specific Protein-Lipid Interactions using Molecular Simulation

Robin A. Corey, Mark S. P. Sansom, and Phillip J. Stansfeld

9 Molecular Dynamics Simulation of Lipid-modified Signaling Proteins

Vinay Nair and Alemayehu A. Gorfe

10 In silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides

Nicolas Frazee, Violeta Burns, Chitrak Gupta, and Blake Mertz

PART V PH AND POLARIZATION EFFECTS

11 pKa Calculations in Membrane Proteins from Molecular Dynamics Simulations

Nuno F. B. Oliveira, Tom嫳 F. D. Silva, Pedro B. P. S. Reis, and Miguel Machuqueiro

12 Poor person's pH Simulation of Membrane Proteins

Chitrak Gupta, Umesh Khaniya, John W. Vant, Mrinal Shekhar, Junjun Mao, M. R. Gunner, and Abhishek Singharoy

13 Preparing and Analyzing Polarizable Molecular Dynami