Side-Chain Optimization and Mutation Using Many-Body Dead-End Elimination
Discrete rotamer libraries of optimal side-chain conformations have been developed to find the global minimum energy conformation of a protein. However, implementation of rotamer libraries using brute force is computationally expensive, as there exists large number of permutations. Through rigorous inequalities eliminating high-energy rotamers, rotamer pairs, and rotamer trimers, the Dead-End Elimination (DEE) algorithm eliminates many permutations, finding optimal side-chain positions in a reasonable amount of time.
Application to Mutation A3L in F5H7E5
The following example demonstrates global optimization with mutation A3L in F5H7E5 (PDB F5H7E5). The general protocol is as follows:
- Refine/optimize the wild-type model using all-versus-all global optimization. If the protein is large, use the sliding window method.
- Perform the mutation.
- Perform a local optimization around the mutated region using a distance cutoff.
Using DEE to Globally Optimize the Wild-Type PDB File
To perform an all-versus-all global optimization using DEE for all residues, use the following command:
ffxc ManyBody -a 2 -c A -l 2 -x 1 -dee F5H7E5.pdb
The resulting PDB file is automatically saved as F5H7E5.pdb_2. Rename the PDB file F5H7E5_rotOpt.pdb to remove the "_2" from the extension.
Mutating Residue 3 from Alanine to Leucine
To mutate residue 3 in chain A from alanine to leucine, use the following command:
ffxc MutatePDB -c A -n LEU -r 3 F5H7E5_rotOpt.pdb
The PDB file with the mutation is saved as F5H7E5_rotOpt.pdb_2. Rename the pdb file F5H7E5_rotOpt_A3L.pdb to remove the "_2" from the extension.
| Command | Description |
|---|---|
| -c A | Chain 'A' |
| -n LEU | Three-letter abbreviation of mutated amino acid |
| -r 3 | Residue 3 is mutated |
Using DEE to Optimize the Mutated Region
To perform an all-versus-all global optimization using DEE for all residues, use the following command:
ffxc ManyBody -a 2 -c A -l 2 -x 1 -dee F5H7E5_rotOpt_A3L.pdb
To perform a global optimization using DEE within the residue range 1-5, use the following command:
ffxc ManyBody -a 2 -c A -l 2 -s 1 -f 5 -dee F5H7E5_rotOpt_A3L.pdb
To perform a global optimization using DEE within a distance cutoff of 5 Angstroms from residue 3, use the following command:
ffxc ManyBody -a 4 -c A -l 2 -s 3 -f 3 -w 1 -r 5.0 -dee F5H7E5_rotOpt_A3L.pdb
A description of all of the flags used in the optimization commands is found below:
| Command | Description |
|---|---|
| -a 2 | Algorithm using Goldstein elimination |
| -a 4 | Algorithm using sliding window method |
| -c A | Chain 'A' |
| -f 5 | Final residue 5 |
| -dee | Goldstein criteria not used |
| -l 2 | Richardson rotamer library |
| -r 5.0 | Distance cutoff of 5.0 Angstroms |
| -s 1 | Starting residue 1 |
| -t | Turn on three-body interactions |
| -w 1 | Sliding window size of 1 residue |
| -x 1 | Optimization of all residues |