Use case: OmpLA

[nathanmlim]

Attachment

Input: 1qd5_omp.pdb
Output: step5_assembly[.pdb/.psf]

1qd5.zip

Setup description

The preparation protocol closely follows the setup as reported by Gumbart and Roux.¹ First, the structure of Outer membrane phospholipase A (OmpLA) was taken from the Orientations of Proteins in Membranes OPM database so that the membrane normal is aligned with the Z-axis and the origin is centered to the middle of the membrane.² Protein protonation states were determined through PROPKA via the PDB2PQR webserver using pH 3.8 and the CHARMM27 forcefields.³ Following, the protein-membrane system was assembled and prepared through the CHARMM-GUI webserver. Patches were added to the terminal groups and to the proper residues as determined by PROPKA. A DLPC bilayer was constructed using approximately a 1:1 ratio of lipids in the upper and lower leaflets. Then, the system was solvated with TIP3P waters with 0.308M Na+/Cl- ions.⁴

References:

1 Gumbart, J., & Roux, B. (2012). Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations. Biophysical Journal, 102(4), 795–801.
2 Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625.
3 Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32 W665-W667 (2004).
4 Sunhwan Jo, Joseph B. Lim, Jeffery B. Klauda, Wonpil Im, CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes, Biophysical Journal, Volume 97, Issue 1, 8 July 2009, Pages 50-58, ISSN 0006-3495