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Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation

Figure 4

Rotation of the α2/β2 dimer with respect to the α1/β1 dimer during T→R transitions.

(A/B) Colored rods indicate the dimers and the spheres represent the center of mass (COM) of the four subunits as labeled in the panels A/B. Before analyzing the rotation of the α2/β2 dimer, the α1/β1 dimer of the structures were superimposed on the α1/β1 dimer of the T X-ray structure (red rods and transparent surface). The R, R2, and R3 X-ray structures are colored in light green, dark green, and lime green, respectively (compare legend). Representative structures of simulations that displayed TR transitions are presented as blue, violet, and orange rods. The colored arrows indicate the rotation axes that map the T α2/β2 dimer (red rod) onto the dimer of the respective X-ray or simulation structure. The colors of the arrows correspond to the colors of the dimer rods. (C) Rotation of the axis connecting the center of mass of the α2 and β2 subunits during simulations T.HC3-2 and T.HC3-3. The angle is computed with respect to the respective axis in the T X-ray structure. The angles between the T and the R, R2, and R3 X-ray structures are indicated by dotted lines. The simulation snapshots corresponding to the blue and violet rods in panels A/B are indicated by colored dots.

Figure 4

doi: https://doi.org/10.1371/journal.pcbi.1000774.g004