Membrane Proteins Tutorial

University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology
Theoretical and Computational Biophysics Group
Computational Biophysics Workshop
Membrane Proteins
Tutorial
Alek Aksimentiev
Marcos Sotomayor
David Wells
August 2009
A current version of this tutorial is available at
http://www.ks.uiuc.edu/Training/Tutorials/
Join the tutorial-l@ks.uiuc.edu mailing list for additional help.CONTENTS 2
Contents
1 Building a Structural Model of KcsA 5
1.1 Downloading and Viewing the Protein . . . . . . . . . . . . . . . 5
1.2 Examining the PDB File . . . . . . . . . . . . . . . . . . . . . . . 7
1.3 Building the KcsA Tetramer . . . . . . . . . . . . . . . . . . . . . 8
1.4 Generating PSF and PDB Files for KcsA . . . . . . . . . . . . . 11
1.5 Solvating the Protein (Optional) . . . . . . . . . . . . . . . . . . 17
2 Placing KcsA in a Membrane 23
2.1 Building a Membrane Patch . . . . . . . . . . . . . . . . . . . . . 23
2.2 Alignment of Membrane and Protein . . . . . . . . . . . . . . . . 24
2.3 Combination of Membrane and Protein . . . . . . . . . . . . . . 25
2.4 Solvation and Ionization . . . . . . . . . . . . . . . . . . . . . . . 28
3 Running a Simulation of KcsA 33
3.1 Melting of Lipid Tails . . . . . . . . . . . . . . . . . . . . . . . . 33
3.2 Minimization and Equilibration with Protein Constrained . . . . 38
3.3 Equilibration with Protein Released . . . . . . . . . . . . . . . . 40
3.4 Production Runs . . . . . . . . . . . . . . . . . . ...