CONSTRUCT is a software tool designed to identify functional and structurally important sites in proteins by searching amino acid sites evolving under strong purifying selection that cluster together in 3D structure.
- Linux Ubuntu 20.04 LTS (or higher)
- Python 3.10.12 (or higher)
- R 4.1.2 (or higher)
sudo apt install r-base-core
sudo apt install python3-pip
sudo apt install git
To make the program easier to use and install, once you have downloaded all the files from the repository, you will need to run the install_packages.sh script. It will check and, if necessary, install the various packages/software the program needs to function correctly.
You can easily download CONSTRUCT and install all dependencies with the following commands: Via HTTPS link :
git clone https://github.com/Rcoppee/CONSTRUCT
cd CONSTRUCT/
bash install_packages.sh
Once installed, you can easily run the program with the following command:
python CONSTRUCT.py
A graphical interface will open (see the figure below), where you only need to fill in the required information and start the execution.
CONSTRUCT generates three result files:
- spatial_rates.txt: a file containing the spatially correlated site-specific substitution rates of amino acid sites, ranked by their level of conservation.
- log_files.txt: indicates whether a patch of conserved amino acid sites was detected in the protein structure (with the best window size and corresponding correlation strength).
- color_conserved.pml: a file highlighting the top 10% of conserved amino acid sites (for use with PyMOL).
To analyze the KEAP1 propeller domain, two files must be submitted:
- A fasta file: This file should contain an alignment of orthologous sequences with the reference sequence listed first.
- A PDB file: This file should contain the Cartesian coordinates of the protein structure (in this example we hase used the PDB ID: 2FLU).
Once you have submitted these files, you can proceed by running the post-processing tool. When the process is complete, you'll see a score representing the strength of the correlation in site-specific substitution rates (a value > 8 indicates the presence of a patch of conserved amino acid sites). In this example, using the side-chain orientation option as Cartesian coordinates, you might observe a log score of 74.63, which is > 8, indicating the presence of a patch of conserved amino acid sites (corresponding to the surface interface with Nrf2, the substrate of KEAP1).
To visualize this patch, you can use PyMOL:
- Open PyMOL.
- Go to "File" and select "Open."
- Load the generated
color_conserved.pmlfile.
/!\ If you move the PDB file after running CONSTRUCT, you'll have to change the first line of color_conserved.pml, because the first line is: load {pdb_file_path}/my_pdb.pdb (where my_pdb.pdb is your PDB file). You can also manually open the PDB file in PyMOL then open color_conserved.pml.
Let’s take DHPS as an example.
In the initial analysis, no specific boundaries were set, and the following patch was identified:
This patch is located on the DHPS domain of the protein.
If you want to focus on a specific part of the protein, such as the PPPK domain, you can define the boundaries for that domain, which in this case would be from position 1 to 386.
After specifying these boundaries, a patch of conserved amino acid sites was specifically detected in the PPPK domain:
A video tutorial has been created for easy installation and execution of CONSTRUCT: https://www.youtube.com/watch?v=bf-VYReZIeM&t=10s
CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure
Lucas Chivot, Noé Mathieux, Anna Cosson, Antoine Bridier-Nahmias, Loic Favennec, Jean-Christophe Gelly, Jérôme Clain, Romain Coppée