CoCoPOD

Coiled-Coil Protein Origami Design platform

CoCoPOD is capable of designing amino-acid sequences and building 3D models for arbitrary polyhedral meshes constructed from a single polypeptide chain. The edges of the polyhedron are realized as coiled-coil dimer building modules. The design strategy consists of several steps:

1. Specifying the polyhedral geometry
2. Routing the chain
3. Selecting the optimal topology and circular permutation
4. Selecting the building modules from the CC toolkit
5. Building the 3D model
6. Refining/validating the models via folding simulations

CoCoPOD performs the first five steps of the design process. Scripts are provided for automatic execution of all the steps, for maximum flexibility the package functionality is also available from python code.

• Quick Start
• Video Tutorials
• Installation
• Dependencies
• Tests

Citing CoCoPOD

When using this platform in publications please cite:

A. Ljubetič, F. Lapenta ... R. Jerala; Design of coiled-coil protein origami cages that self-assemble in vitro and in vivo; Nature Biotechnology, 2017, http://dx.doi.org/10.1038/nbt.3994

Quick Start

Two full examples are provided in the examples subfolder.

APHsh

APHsh is centered on building models and also serves as an integration test. An antiparallel APH segment is built The second To run the program user needs to provide an input file (make_config.py) containing information on the sequence of the protein origami design. The input consists of four sections:

• model_name, specifying the name of the protein origami design
• annotated_sequence, where the sequence is broke down into individual CC segments and linkers, for every CC segment a name should be provided
• pairs_info, in this section segment pairing is specified. For every pair the orientation (A for antiparallel and P for parallel) of the CC dimer should be provided, along with the name of CC dimer structure template file and name of the chains in the model structure.

An example of the input file can be found under examples/APHsh/make_config.py. Two APH segments are connected by a linker forming a covalently linked CC dimer. The models can be built and viewed by by typing in the terminal

cd cocopod/examples/APHsh	
doit N_fold=1 N_homology=3
chimera */03-*.pdb

Where N_fold is the number of independent folding simulations and N_homology the number of independent homology refinements of each folding simulation. The final number of models built thus equals N_fold*N_homology.

TET

The TET example contains a complete tutorial on designing protein origami polyhedral. The tutorial is presented in the from of a python notebook. The demonstrated steps include loading a geometry (ply) file, enumerating all the typologies and circular permutations, choosing the best topology and constructing and evaluating 3D models. The notebook can be opened by:

cd cocopod/examples/TET	
jupyter notebook TET.ipynb
	 

Video Tutorials

Several video tutorials (screen casts) demonstrate how to effectively use CoCoPOD:

Part 1: installation

Part 2: APHsh model building

Part 3: de novo tetrahedron design

Installation

Using the Anaconda python distribution is recommended as it simplifies installing further dependencies. Miniconda also works nicely. Git for windows is also recommended. Dependencies can be installed by running:

conda install numpy scipy pandas ipython ipython-notebook ipywidgets pyyaml xlrd biopython
#set the modeller liscence key
export KEY_MODELLER=XXXX
conda install -c salilab modeller
conda install -c omnia mdtraj 
pip install plyfile doit #not available in conda

respectively. Chimera has to be installed separately. Chimera must be available on the system path. Note: Currently there are some problems installing Modeller via conda on windows. In case of problems use the standalone installer.

CoCoPOD is available on github. The files can be cloned to any location. To install the package run:

git clone https://github.com/NIC-SBI/protein_origami.git cocopod	
cd cocopod
python setup.py develop

Alternatively a zip file can be download, extracted and installed with python setup.py develop.

##Dependencies The package requires Python 2.7 or Python 3.3+ with numpy and pandas and works on Windows and Linux. On Windows a bash enviorment is recommended and can be obtained by installing git for windows.

Other dependencies:

• Modeller
• Chimera
• Snakemake (only python 3+)
• MdTraj
• plyfile
• Numpy, Scipy, pandas, ipython, ipywidgets

Testing:

• py.test
• pytest-xdist (optional)

Tests

Installation can be tested by executing py.test, which checks if core modules of the software are working appropriately and all dependencies have been installed.

conda install pytest
cd cocopod	
py.test