Metadata

Author: P. Ben Stranges (stranges@unc.edu), PI is Brian Kuhlman: (bkuhlman@unc.edu)

Code and Demo

The code is at rosetta/main/source/src/apps/public/scenarios/beta_strand_homodimer/ ; there's an integration test at rosetta/main/tests/integration/tests/beta_strand_homodimer/ . However if you want to actually use the code you should look at the demo: rosetta/demos/public/beta_strand_homodimer_design/

References

Stranges PB, Machius M, Miley MJ, Tripathy A, and Kuhlman B. (2011) "Computational design of a symmetric homodimer using beta-strand assembly" PNAS in press.

Purpose

This code was written for a relatively singular application: finding proteins with surface exposed beta-strands, then trying to make and design a homodimer that will form via that beta-strand. It could be used for general homodimer design but has not been tested.

Algorithm

The below is coppied verbatim from the paper given above: We defined a beta-strand as surface-exposed if it met three criteria. 1) Five sequential residues had beta-strand secondary structure as judged by DSSP. 2) There were no backbone-backbone hydrogen bonds formed by every other residue in the strand. 3) Every other residue had fewer than 16 neighboring residues, or had 16 to 30 neighbors and a solvent-accessible surface area (SASA) per atom greater than 2.0 Å2. Residues are defined as neighbors if their Cbeta to Cbeta distance is < 10Å. An example command line used to find the exposed strands follows:

The output from the above is then used to put together the command line for the construction of the potential homodimers. The procedure is as follows: The axis of an exposed beta-strand was defined as a vector from the Calpha atom on the first residue of the strand to the Calpha atom on the final residue of the strand. Another vector is defined at the center residue of the strand from the carbonyl carbon to carbonyl oxygen. A final vector is drawn perpendicular to the two vectors described through the Calpha atom of the residue at center of the strand. The anti-parallel homodimer is constructed by copying the protein and rotating the copy 180° about this axis. The copied chain is then translated away from the original by 6.0 Å to create a starting point for evaluation. The copied chain was then translated along the axis of the exposed strand in steps of 7 Å to identify alternate conformations that have no clashing backbone atoms. As a final filter, we check to make sure there are no backbone-backbone clashes between the two chains. The identification of exposed beta-strands generated from the above protocol was used as input for the next step.

The homodimer model generated above was used to generate the symmetry definition and starting structure for interface design. First, the protein is symmetrically docked against itself to sample rigid body degrees of freedom. After the docking step, all residues within 8 Å of the other chain were symmetrically designed. Finally, the backbone and side chains of all interface residues were minimized.

Input Files

See the demo at: rosetta/main/demos/public/beta_strand_homodimer_design

Options

exposed_strand_finder options

General options:

-s or -l for input structure(s)
-ignore_unrecognized_res - bool - Good to have true for large numbers of input structures
-packing::pack_missing_sidechains
-out::nooutput -bool- this protocol manages its own output, prevent job distributor from helping
-struct_file -file- path to the file for the structure restrictor if needed

App specific options

-beta_length - integer - how long of an exposed strand do you look for
-sat_allow - integer - how many satisfied bb atoms do you allow in this range

Allow alignment of a found strand to some target protein (optional):

-check_rmsd false - bool - whether you should check the exposed strand against some tagret strand
-native - file - the target structure to check the rms of the exposed strand against
-strand_span - string vector - chain start end of the native to check the exposed strand against (example: B 10 15)

homodimer_maker options

-s input stucture to make into a homodimer
-run::chain - char - PDB chain letter for the chain you want to use to make the homodimer
-sheet_start - integer - PBD residue # of the first residue in the strand
-sheet_stop - integer - PBD residue # of the last residue in the strand
-window_size - integer - number of residues to consider within the exposed strand when calculating vectors. Cannot be larger than sheet_stop - sheet_start + 1.

homodimer_design options General options:

-s - *_INPUT.pdb from symmetery script
-symmetry:symmetry_definition -file- symmetry deffinition file from script
-nstruct -integer- try 5000 or so for production runs

Application specific:

-pack_min_runs - integer - number of cycles through design/minimization
-make_ala_interface - bool - make the interface all Ala before docking
-find_bb_hbond_E - bool - calculate the bb-bb H bonding energy for the output
-disallow_res CGP # prevents design up Gly, Cys, Pro

Other useful options

-favor_native_res 0.5
-run:min_type dfpmin
-pose_metrics:interface_cutoff 8.0
-use_input_sc
-ex1
-ex2
-overwrite
-docking::docking_local_refine true/false
-docking::sc_min true
-docking::dock_ppk false
symmetry:perturb_rigid_body_dofs 3 5
-out::file::fullatom

Tips

These protocols are specific for one method of finding exposed beta-strands and designing that protein to be a homodimer. We are not sure how easily it could be used for other purposes.

Expected Outputs

See the full description in rosetta/main/demos/public/beta_strand_homodimer_design/README

Post Processing

The demo located in rosetta/main/demos/public/beta_strand_homodimer_design/ has a full description of how to handle outputs.

Changes since last release

3.4 is the first release of this code. - stranges

beta_strand_homodimer_design suite of apps