internal_documentation/membrane

Metadata

The Rosetta Membrane Framework was developed by Julia Koehler Leman and Rebecca Alford at the Gray Lab at JHU. Last updated: 12/12/14.

For questions please contact:

Julia Koehler Leman (julia.koehler1982@gmail.com)
Rebecca Alford (rfalford12@gmail.com)
Corresponding PI: Jeffrey J. Gray (jgray@jhu.edu)

Description

A lips file describes the lipophilicity (i.e. lipid environment preference) of a residue in a helix. This information can be used to orient the helices in the membrane and distinguish lipid-facing vs. protein-facing residues. The Rosetta implementation uses the LIPS server from Adamian & Liang on the back-end. Updates are coming soon.

Generate .lips4 file.

BRD4.lips4 - lipophilicity prediction file created using run_lips.pl script as follows (note that blastpgp and nr database are necessary to run run_lips.pl script

run_lips.pl <fasta file> <span file> <path to blastpgp> <path to nr database> <path to alignblast.pl script>

Example command:

<path to mini>/mini/src/apps/public/membrane_abinitio/run_lips.pl BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/alignblast.pl

Sample lips4 file:

Lipid exposed data: resnum mean-lipo lipophil entropy
      6  -1.000   3.004   1.211
      9  -1.000   2.268   2.137
     10  -1.000   4.862   1.095
     13  -1.000   1.304   1.552
     16  -1.000   3.328   2.025
  ...

Code and documentation

core/conformation/membrane contains the LipidAccInfo class that stores the information from the lips file.

Flags

-mp:setup:lipsfile 1afo.lips4

NOTE: The flag for the original RosettaMembrane is -in:file:lipofile 1afo.lips4 but this option will be deprecated. Please use the new flag!

Example

An example of how the original RosettaMembrane used lips files can be found in Rosetta/main/tests/integration/tests/membrane_abinitio. This functionality has not yet been tested in the membrane framework.

References

Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley D, Elazar A, Gray JJ. (2015) An integrated framework enabling computational modeling and design of Membrane Proteins. PlosOne - in preparation

References for original RosettaMembrane

Yarov-Yarovoy V, Schonbrun J, Baker D. (2006 Mar 1) Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4):1010-25.
Barth P, Schonbrun J, Baker D. (2007 Oct 2) Toward high-resolution prediction and design of transmembrane helical protein structures. Proc Natl Acad Sci U S A. 104(40):15682-7.
Barth P, Wallner B, Baker D. (2009 Feb 3) Prediction of membrane protein structures with complex topologies using limited constraints. Proc Natl Acad Sci U S A. 106(5):1409-14.

internal_documentation/membrane_proteins/Lipsfile