Computational protocol: Improving the Anti-Toxin Abilities of the CMG2-Fc Fusion Protein with the Aid of Computational Design

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Protocol publication

[…] To investigate the relationship between the affinity of CMG2-Fc for PA and its ability to neutralize anthrax toxin, a model of CMG2-PA complex was required. The X-ray crystal structures of CMG2 in complex with PA have been solved at a resolution of 2.5 Å and 4.3 Å , respectively. These structural models provide valuable information about the interaction between CMG2 and PA.Because it is not easy to decide which mutations will improve the affinity between subunits in a complex, one possible approach is to ask the FoldX protein design algorithm – to scan all the positions along the interface between the two molecules. In this study, the computational design of high-affinity CMG2 mutants was performed using FoldX. First, the residues comprising the PA-binding interface of CMG2 were identified by using the AnalyseComplex option of FoldX. Next, the residues in the PA-binding interface of CMG2 were scanned by PositionScan to all other 19 naturally occurring amino acids. The effect on the binding energy between CMG2 and PA was calculated as the difference between the binding energy of the mutant and the wild-type amino acid (ΔΔG; in kcal/mol). The amino acid substitutions that caused a decrease in the binding energy toward the PA molecule were selected. PositionScan mutates one amino acid to the other ones and repairs the neighboring residues. This command first mutates the selected position to Ala and annotates all the neighboring residues, then restores the WT residue, and then restores the neighbors to the original amino acids –. A detailed description of the protein design algorithm FoldX (version 3.0) is available elsewhere at http://foldx.crg.es.Protein structure analysis was performed in Discovery Studio 2.5 (Accelrys, USA). Molecular structure illustrations were generated with PyMOL Molecular Graphics Software (www.pymol.org). The coordinates (PDB ID: 1t6b ) for the CMG2-PA complex structure were taken from the protein data bank. […]

Pipeline specifications

Software tools FoldX, PyMOL
Application Protein structure analysis
Organisms Bacillus anthracis, Homo sapiens