Additional file 4: of A single-residue change in the HIV-1 V3 loop associated with maraviroc resistance impairs CCR5 binding affinity while increasing replicative capacity

Figure S3. Structure and dynamics of free V3 from the MVC-Sens (grey) or MVC-Res (black) isolates. (A) Time series of root mean square deviation (RMSD) values for all atoms of the V3 loops, using as reference the average coordinates computed from the five independent simulations. (B) The phi and psi angular fluctuations were calculated and averaged by residue for every 25 ps segment of the five molecular dynamics trajectories. Standard deviations are reported for phi (top) and psi (bottom) backbone torsion angles. (C) The average RMS fluctuations (RMSF) were calculated for the carbon alpha atoms of the V3 loop residues from the ensemble of structures after superimposition of residues 296 to 330 (complete V3 loop, plain lines) or superimposition of residues 308 to 315 (V3 tip, dotted lines).