The membrane protein refinement application, MPrelax is implemented as a Rosetta Script and can be found in Rosetta/main/source/src/apps/public/membrane/mp_relax.xml which can be passed as input to the rosetta_scripts.cc executable
A demo for this application including detailed steps, command lines, and example inputs can be found in Rosetta/demos/protocol_captures/mp_relax
Rosetta Revision #58096
High-resolution refinement is key for advancing low resolution structures from x-ray crystallography to atomic level detail. For membrane proteins, this method can also reveal an ensemble of possible membrane embeddings: the position and orientation of the biomolecule with respect to the membrane bilayer.
The membrane relax application combines the Rosetta FastRelax algorithm with the all atom energy function for membrane proteins and a gradient-based technique for optimizing the membrane embedding. First, a series of small backbone moves, rotamer trials, and minimization are used to refine the protein structure. In addition, the membrane position is optimized by minimizing the "jump" or connecting relating the MEM residue to the biomolecule.
This protocol is currently designed for single chain refinement with an MEM jump. Be aware that this protocol is currently not extensively tested on multi-chain proteins!
Two inputs are required for the membrane relax application: (1) PDB for the protein structure of interest. (2) Span file describing the location of trans-membrane spans.
| Flag | Description | Type |
|---|---|---|
| -parser:protocol | Use the membrane relax protocol Rosetta script | XML Script |
| -mp:setup:spanfiles | Spanfile describing spanning topology of starting structure | String |
| -mp:scoring:hbond | Turn on depth-dependent hydrogen bonding term when using the membrane high resolution energy function | Boolean |
| -relax:fast | Use the FastRelax mode of Rosetta Relax (uses 5-8 repeat cycles) | Boolean |
| -relax:jump_move | Allow the MEM and other jumps to move during refinement | Boolean |
| -packing:prepack_missing_sidechains false | Wait to repack sidechains during pdb initialization until the membrane pose is fully initialized with the membrane framework | Boolean |
To run this application, use the following command line:
./rosetta_scripts.<exe> -database /path/to/my/rosettadb @flags
Alford RF, Koehler Leman J, Weitzner BD, Duran A, Tiley DC, Gray JJ (2015). An integrated framework advancing membrane protein modeling and design. PLoS Comput. Biol. - In Press
Tyka MD, Keedy DA, Andre I, DiMaio F, Song Y, et al. (2011) Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol.
Barth P, Schonbrun J, Baker D (2007) Toward high-resolution prediction and design of transmembrane helical protein structures. Proc Natl Acad Sci 104: 15682–15687.
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, et al. (2011) RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE 6: e20161.
Questions and comments to: