FIG 10.
Effects of the linker and MHR mutations on the structural dynamics of HIV-1NL4-3 mature CA protein. Gag-CA protein models of HIV-1NL4-3 and its mutants were constructed from the reported structure of HIV-1 mature capsid (PDB code 3J34) (55). MD simulations were carried out under the same conditions as described for Fig. 8. RMSF values were calculated using 15,000 snapshots in the equilibrium states during MD simulations. Distribution of RMSF in the Gag-CA immature and mature proteins of NL4-3 (A) and those in the CA mature proteins of NL4-3 and mutants (B) are shown. Numbers on the horizontal axes indicate amino acid positions in the HIV-1NL4-3 Gag-CA protein. Arrows indicate the positions of mutated residues. #, positions of CypA binding loop; orange asterisks, sites upstream of WM184/185 residues in H9.