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Fig. 5 | BMC Molecular and Cell Biology

Fig. 5

From: Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease

Fig. 5

Protocol used to compare the structural asymmetry of the wild-type and mutant structures of PR2. Step 1: Modeling of the 3D structure of PR2 mutants. First, the mutation is introduced into the wild-type structure of PR2 (PDB code: 3EBZ) using FoldX software [39] with five replications. Then, an energetic minimization step is applied to the wild-type and modeled mutant structures using Gromacs software [52]. Wild-type and mutant structures are presented in cartoon mode and colored according to their two chains: chain A is colored magenta, and chain B is colored cyan. Mutated residues are presented in stick mode and are indicated with black arrows. Step 2: Detection of structural asymmetry in the wild-type and mutant structures of PR2 using a protocol based on the HMM-SA structural alphabet. The HMM-SA structural alphabet [56] is a library of 27 protein prototypes of 4 residues classified according to their geometry. First, HMM-SA is used to simplify each PR2 chain of 99 residues into a sequence of 96 structural letters, in which each structural letter corresponds to the geometry of a 4-Cα fragment (i.e., representing the local conformation of each residue). Then, the structural letter for each position in the two sequences is compared to localize (i) symmetric positions that correspond to positions exhibiting the same local conformation (=structural letter) in the two chains of the dimer and (ii) asymmetric positions that correspond to positions exhibiting different local conformations (=structural letters) in the two chains of the dimer. To quantify the structural asymmetry in PR2 structures, the number of asymmetric positions in the dimer is finally counted

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