Computational Design of Membrane Proteins, 1st ed. 2021 Methods in Molecular Biology Series, Vol. 2315

This volume provides an overview of the current successes as well as pitfalls and caveats that are hindering the design of membrane proteins. Divided into six parts, chapters detail membrane transporter, FoldX force field, protein stability, G-Protein Coupled Receptors (GPCR) structures, transmembrane helices, membrane molecular dynamics (MD) simulations, pH-dependent protonation states, membrane permeability, and passive transport. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge,  Computational Design of Membrane Proteins aims to ensure successful results in the further study of this vital field.

Chapter 4 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

PART I: INTRODUCTION

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

            Nícia Rosário-Ferreira, Catarina Marques-Pereira, Raquel P. Gouveia, Joana Mourão, 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, Tomás 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 Dynamics Simulations with the Classical Drude Oscillator Model

            Justin Lemkul

PART VI        MEMBRANE PERMEABILITY AND TRANSPORT

14        In silico Prediction of Permeability Coefficients

Ricardo J. Ferreira

15        Identification of Pan Assay INterference compoundS (PAINS) using an MD-Based Protocol

Pedro R. Magalhães, Pedro B. P. S. Reis, Diogo Vila-Viçosa, Miguel Machuqueiro, and Bruno Victor

16        Transmembrane Anion Transport Mediated by Halogen Bonds: using Off-Center Charges

            Paulo J. Costa

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts