Conformations Apl_AvBD2 and its mutants during the MD simulation experiments for 1000 ps. The initial and final conformations are shown. Apl_AvBD2 form a stable dimer in the simulation system. The amino acids in the wild peptide are shown as sticks in different colours. The positions of amino acids in the mature peptide region selected for arginine substitution are represented as follows; red: 7th position (Phenylalanine to Arginine), yellow: 11th position (Isoleucine to Arginine), Magenta: 24th position (Valine to Arginine), Orange: 38th position (Serine to Arginine). The C-terminal residues form a distinct 'claw region (indicated by arrows) of the wild type Apl_AvBD2. In all the mutants, the shape and orientation of this claw region became less distinct during simulation.
Soman et al. BMC Bioinformatics 2010 11(Suppl 1):S7 doi:10.1186/1471-2105-11-S1-S7