Mutational Energy Landscape Trap (MELT) is a computational tool designed to control protein dynamics by combining Normal Mode Analysis (NMA) and in silico mutagenesis. It offers a novel approach for manipulating protein structures, focusing on their dynamic behaviors rather than static conformations. By displacing protein structures along low-frequency normal modes and introducing mutations, MELT can either lock proteins into specific conformations or enhance dynamic behaviors along chosen normal modes.
- Utilizes Normal Mode Analysis (NMA) to explore protein flexibility and dynamics.
- Introduces mutations that trap or favor dynamics, altering the protein's energy landscape.
Prerequisites:
R for executing the normal mode analysis (NMA). PyRosetta for structural relaxation and mutagenesis design. Make sure to have the required libraries installed:
# R installation
install.packages("bio3d")
# PyRosetta (follow PyRosetta installation instructions)
pip install pyrosetta
pdb: Input PDB structure (e.g., 2LZT). mode: Normal mode used for displacement (e.g., mode 7). direction: Displacement direction ("plus" or "minus"). scale: Scale of displacement (default is 10).
Displaced PDB files: desloc__.pdb
The displacement will generate altered conformations of the protein based on the selected normal mode, such as:
desloc_7_minus.pdb desloc_7_plus.pdb
Once the protein structure is displaced, you can apply in silico mutagenesis using PyRosetta by running the Step2_DesignPyrosetta.py script.
Example Usage:
python Step2_DesignPyrosetta.py
Relaxation: After displacement, the structure is relaxed using the FastRelax protocol to minimize energy.
Mutagenesis: Selected regions of the protein are mutated to introduce the desired dynamics while maintaining structural integrity.
pose: Displaced protein structure loaded into PyRosetta. scorefxn: PyRosetta score function for energy calculations (e.g., ref2015_cart.wts). chain: Chain of the protein to design (e.g., "A"). Outputs: Relaxed and mutated PDB files:
desloc_7_relaxed.pdb
desloc_7_relaxed_designed.pdb
The mutated designs aim to either lock the protein into the displaced conformation or enhance the dynamics observed along the chosen normal mode.
Displace protein structures along low-frequency normal modes using Step1_NormalModes.R.
Output: Displaced PDB files.
In Silico Mutagenesis and Relaxation:
Use PyRosetta to apply mutagenesis and relax the displaced structures.
Output: Mutated, relaxed PDB files with desired dynamic properties.
Validate the protein dynamics using molecular dynamics, and if possible confirm the structures using AlphaFold