Protease diversity of HIV-1 subtype G

(1) Sequence diversity of HIV-1 subtype G in the portuguese outbreak group (PTO)

In this movie, we demonstrate the protease dimer structure (PDB: 2Q5K), and mapped amino acid diversity in surface representations. Protease inhibitor lopinavir is shown in the drug binding pocket. Amino acid diversity was mapped to the protein structures by colors scaled from blue (diversity score: 0) to red (diversity score ≥0.3).

(2) Sequence diversity of HIV-1 subtype G outside the portuguese outbreak group (non-PTO)

In this movie, we demonstrate the protease dimer structure (PDB: 2Q5K), and mapped amino acid diversity in surface representations. Protease inhibitor lopinavir is shown in the drug binding pocket. Amino acid diversity was mapped to the protein structures by colors scaled from blue (diversity score: 0) to red (diversity score ≥0.3).

RT diversity of HIV-1 subtype G

(1) Sequence diversity of HIV-1 subtype G in the portuguese outbreak group (PTO)

In this movie, we demonstrate the RT heterodimer structure (PDB: 3V4I), and mapped amino acid diversity in surface representations. Amino acid diversity of positions 1 to 241 was mapped to the p66 region of RT structure, where the reverse transcription takes place. Two natural polymorphisms R43 and I173 are highlighted in the HIV-1 RT structure. The RT structures crystalized with AZT (PDB: 3V4I) and NVP (PDB: 4PUO) are superimposed to show the drug binding pockets of NRTI and NNRTI, both of which are far from two point mutations. Note that in the movie, AZTTP molecular is located close to dsDNA, while NVP is below dsDNA (see 20s - 40s in the movie).

Amino acid diversity was mapped to the protein structures by colors scaled from blue (diversity score: 0) to red (diversity score ≥0.3).

(2) Sequence diversity of HIV-1 subtype G outside the portuguese outbreak group (non-PTO)

In this movie, we demonstrate the RT heterodimer structure (PDB: 3V4I), and mapped amino acid diversity in surface representations. Amino acid diversity of positions 1 to 241 was mapped to the p66 region of RT structure, where the reverse transcription takes place. Two natural polymorphisms R43 and I173 are highlighted in the HIV-1 RT structure. The RT structures crystalized with AZT (PDB: 3V4I) and NVP (PDB: 4PUO) are superimposed to show the drug binding pockets of NRTI and NNRTI, both of which are far from two point mutations. Note that in the movie, AZTTP molecular is located close to dsDNA, while NVP is below dsDNA (see 20s - 40s in the movie).

Amino acid diversity was mapped to the protein structures by colors scaled from blue (diversity score: 0) to red (diversity score ≥0.3).