PyRosetta RosettaSurface

KEYWORDS: CORE_CONCEPTS GENERAL

Authors

Written by Emily Koo and Michael Pacella (Graylab), mpacella88@gmail.com

General Description

This demo will describe how to run the PyRosetta version of the RosettaSurface algorithm. The test case shown here will analyze the adsorption of the biomineralization protein osteocalcin to the 100 surface of the mineral hydroxyapatite

Algorithm

Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.

Commands

cd rosetta_inputs/Osteocalcin demo
surface_docking.py@flags

Input Files

1Q8H100.pdb = input pdb file, extended osteocalcin positioned above HAp 100
1Q8H_disulf = disulfide bond specification file
1Q8H_native.pdb = native crystal structure of osteocalcin
aa1Q8H_03_05.200_v1_3 = 3mer fragments for osteocalcin
aa1Q8H_09_05.200_v1_3 = 9mer fragments for osteocalcin
flags = arguments for rosetta surface

PyRosetta RosettaSurface Setup and Pre-processing

Before running the scripts for the first time, make sure that all the following details are addressed.

When PyRosetta is installed, the install directory may be different from user to user, so adding the scripts directories to the PATH environment variable in .bashrc file will allow the scripts to be run from any directory, independent from the actual location of the scripts. The following instructions show how the directories are added:
1. Create/open .bashrc in home directory
```
vi ~/.bashrc
```
2. If file exists, skip to 3. Else, add the following lines to the file:
```
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

export PATH=$PATH
```
3. Add all directories containing scripts to end of PATH statement, delimited by a colon
```
export PATH=$PATH:/path/to/scripts:/path/to/scripts/pdb_objects/
```
  where /path/to/scripts and /path/to/more/scripts should be modified to the correct directories.
4. Make sure that the SetPyRosettaEnvironment.sh is sourced every session. Add
```
source /path/to/PyRosetta/SetPyRosettaEnvironment.sh
```
5. Save and close file, then source it.
```
:wq
source ~/.bashrc
```
Make sure the python and bash scripts are given the permission to be executed. Run the following command in the directory containing the scripts
```
  chmod +x *.py *.sh ./pdb_objects/*
```
Gnuplot is the plotting program used to generate the plots, so the program path has to be modified in each Plot* file for the plots to be generated automatically. The version used is 4.2.
To generate plots, simply run:
```
  PostProcessRS.sh
```
Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs.

Post-processing

(in the directory with output decoys)

GetTop.sh Ads 4
cd TOP4.Ads
PostProcessRS.sh

These commands will extract the top 4 adsorbed-state decoys for analysis and generate secondary structure, protein-protein contact maps, and protein-surface contact maps

Example output:

Ads_SecStruct.png = adsorbed state secondary structure
Sol_SecStruct.png = solution state secondary struccture
Ads_ContactMap = adsorbed state contact map
Sol_ContactMap = solution state contact map
Surface_ContactMap.png = protein-surface contact map
Diff_ContactMap.png = difference map between contacts in the ads/sol state

Limitations

This app requires a single protein positioned above a solid surface whose parameters are present in Rosetta. The protein needs to appear before the surface in the pdb file and the two need to be separate chains