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TADOSS - TAndem DOmain Swap Stability predictor

DOI License: MIT

TADOSS estimates the stability of tandem domain swap conformations using an alchemical approximation based on coarse-grained (Go-like) simulation models from the three-dimensional structure of a protein domain.

The stability is defined as the relative free energy difference (ΔΔG) between the native and swap conformations of a pair of tandem identical domains. More information about the energetic model can be found here and all the details in the following publication:

Aleix Lafita, Pengfei Tian, Robert B Best, Alex Bateman. TADOSS: computational estimation of tandem domain swap stability, Bioinformatics (2018) https://doi.org/10.1093/bioinformatics/bty974

Requirements

A Conda environment.yaml is provided to facilitate installation.

conda env create --name tadoss --file environment.yaml
conda activate tadoss

Installation

Simply clone this repository to your desired location

git clone git@github.com:lafita/tadoss.git ~/tadoss

Optionally add ~/tadoss to your PATH (symlinks do not currently work).

Usage

The input to the method is a PDB file of a protein domain structure. We demonstrate the usage with an SH3 domain (ECOD:e1shgA1).

Bundle script

A BASH script that bundles all the steps in the calculation is provided with a simple command line interface

~/tadoss/tadoss -d sh3 -f e1shgA1.pdb -m

Step by step calculation

Each of the steps can also be run separately to allow more flexibility and control to advanced users.

  1. Download and prepare the domain structure (ECOD domain e1shgA1 as example):
# Under the example folder in this repository
cd example
mkdir tmp # temporary intermediate files will be stored here

# Select only protein residues from the structure
python2.7 ~/tadoss/trim_nonprotein.py e1shgA1.pdb tmp/sh3_protein.pdb
  1. Add missing hydrogens to the structure:
# Using Reduce (use the path to the "reduce" script)
reduce tmp/sh3_protein.pdb > tmp/sh3_hadded.pdb
  1. Generate native contact energy (Go model) from the structure:
python2 ~/tadoss/go_builder/go_builder.py -k sh3 --gmx tmp/sh3_hadded.pdb

The generated native contact energies are listed in file go_sh3/go_sh3_gomodel_golist.dat. Other files are not needed for domain swap stability estimation.

The first two columns of the file contain the pair of residues forming the contact (i,j), the third column contains their distance in Amstrongs and the last column is the absolute Go energy of the interaction in kcal/mol.

  1. Alchemical domain swap stability estimation from the Go model contact energies:
python2 ~/tadoss/tadoss.py sh3 tmp/sh3_hadded.pdb

Use the -h (help) option to see all the available options, including linker and hinge lengths.

  1. Modelling tandem domain swap conformations:
Rscript ~/tadoss/modelling/model_tswap.R -s tmp/sh3_hadded.pdb -b ~/tadoss/modelling/calpha_bounds.tsv -o sh3_tswap33.pdb -i 33 -g 1 -f 1

Use the -h (help) option to see all the available parameters, including linker and hinge lengths.

Output

The output results are split into the following files in table format:

  • sh3-dG_cut.tsv: with the length of hinge loops (Lhinge), the residue position, and the alchemical cut free energy (dGcut) representing the penalty of creating a hinge loop centered at the position.
  • sh3-dG_join.tsv: with the free residues (without contacts) at the N and C termini (free_N and free_C), the distance (dist_NC) and angle (angle_NC) between the N and C termini, the length of the inter-domain linker as a parameter (Llinker), the M parameter and the alchemical free energy of connecting the termini (dGjoin).
  • sh3-ddG_tot.tsv: with the length of the domain, the free energy of joining and cutting the domain (dGjoin and max_dGc) and the total alchemical free energy: ddGtot = dGjoin + max_dGcut.

Visualization

Two R scripts are provided to plot the free energy profile of the domain as a barplot and the Go contacts as a matrix. Use the following commands:

Rscript ~/tadoss/dGc_profile.R -i sh3-dG_cut.tsv -o sh3-dG_cut.pdf


Rscript ~/tadoss/go_contacts.R -i go_sh3/go_sh3_gomodel_golist.dat -o sh3_go-contacts.pdf

In order to visualize the mapping of the alchemical free energy onto the native domain structure, a new PDB file sh3-dG_cut.pdb is generated with the ΔGc values in the B-factor column. To take a look at it in PyMOL, open the structure and select Action > preset > b factor putty to obtain a representation like the one below:

Finally, open the model of the most stable tandem domain swap conformation to inspect the hinge loop and the domain orientations:

Census

Alchemical free energy estimations by TADOSS for 129 manual representative domains from the topologies of the ECOD database can be found here.

Citation

If you find this method useful, please consider citing the following publication:

Aleix Lafita, Pengfei Tian, Robert B Best, Alex Bateman. TADOSS: computational estimation of tandem domain swap stability, Bioinformatics (2018) https://doi.org/10.1093/bioinformatics/bty974

FAQs

What does a positive total alchemical free energy (ΔΔG) mean?

As defined by our model ΔΔG = ΔG(native) - ΔG(swap), therefore a positive ΔΔG means that the domain swap conformation of the tandem domains is more stable than the native domains in tandem (non-swapped). Analogously, the more negative the ΔΔG, the more stable the native conformation is relative to the domain swap.

Why are Go contact energies positive?

The file go_sh3/go_sh3_gomodel_golist.dat contains the absolute value of the contact energies, in kcal/mol. The value of the Go energy is the negative of that.

How are the residue indices in the output files generated?

The residue positions in the output file sh3-dG_cut.tsv are the indices of the residues in the input structure. This indices are different from the residue numbers in the input PDB file and independent to the original amino acid sequence of the protein, i.e. they are only relating to the amino acids in the input structure and their sequential order.