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Fig. 7.9.
Global mode shapes predicted for the intact STMV.
Results are based on ANM
(a) The
l
= 0 breathing mode, mode 22 in Fig. 7.8. (b) The
l
= 2 squeezing mode, 5-fold degenerate modes
1-5. (c) The
l
= 3 squeezing mode, modes 6-9. (d) The torsional mode (13-17). All panels are
colored according to their mobilities from small (blue) to large (red).
The collective eigenmodes can be divided into two distinctive types (Coccia
et al.
, 1998). The first type is torsional modes, in which the deformations have
no radial component. An example of this type of motion is modes13-17, shown
in Fig. 7.9d. The other type is spheroidal modes (e.g. modes 1-5, Fig. 7.9b),
in which the eigenvectors contain both tangential and radial components. Each
mode can be described by a wave number,
l
, that corresponds to the degree of the
spherical harmonic that best aligns with the mode. Qualitatively, the wave
number may be thought of as the degree of symmetry of a mode:
l
= 0 indicates
spherical symmetry,
l
= 2 indicates deformation along a single axis, and so on.
Figures 7.9a-c illustrates the spheroidal modes with wave numbers 0, 2 and 3,
respectively.
Figure 7.9a displays a typical
l
= 0 spheroidal mode, corresponding to
mode 22 of STMV (capsid + RNA) in the mode frequency distribution shown in
Fig. 7.8.
It is non-degenerate because it preserves icosahedral symmetry. Such
modes correspond to purely radial motions — shrinking or swelling (
breathing
)
of the entire structure. This type of deformation occurs in response to strong
