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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:

  1. Refine/optimize the wild-type model using all-versus-all global optimization. If the protein is large, use the sliding window method.
  2. Perform the mutation.
  3. 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