FIG 7.
Elucidation of the hydrophobic patches for molecular interactions of HIV-1NL4-3 immature CA protein. An HIV-1NL4-3 CA protein model was constructed by the homology modeling method from the reported immature CA structure (PDB code 4USN) (25). Distribution of the hydrophobic-interaction-prone patches (a minimal patch area of 50 Å2) on the surface of the CA model was assessed and visualized using the Protein Patch Analyzer tool in MOE (44–47). (A) Hydrophobic patches on the CA-CA interface. Patches that participate in the direct CA-CA interactions in an immature CA lattice (25) are shown in pink. (B) Hydrophobic patches outside the CA-CA interface. Patches that are not involved in the direct CA-CA interactions in an immature CA lattice (25) are shown in green. (C) Amino acid residues involved in forming the hydrophobic patches and their variations. Residues involved in the formation of hydrophobic patches are marked with colored circles: pink circles, residues for patches involved in direct CA-CA interactions; green circles, residues for patches that are not involved in direct CA-CA interactions. Shannon entropy scores calculated with the CA amino acid sequences of HIV-1 subtype B (n = 14,120) are shown above the corresponding residues.