Multiscale Modeling of Virus Structure, Assembly, and Dynamics - Computational Modeling of Biological Systems - page 172

Fig. 3 Canonical capsids as a model. The basic subunit prototile-the bisected trapezoid (shaded
in ( a ))-predicted from the analysis of the simplistic canonical capsid model [ 40 ] bears a
strong resemblance to the subunit design ubiquitously found in virus capsids ( b ), indicating a
mathematically motivated pressure in maintaining a trapezoidal subunit shape in nature. Apart
from explaining the importance of the capsid subunit shape, the strong resemblance between these
geometric entities and their real counterparts (exampled in ( c )), allows for a number of studies in
capsid design criteria [ 36 , 37 ]

3.3 Hexamer Complexity as a Predictor of Capsid Properties

Analysis of the virus structural data collected over the last half century indicates
that a very large array of capsid sizes ranging from tens to many thousands of
subunits are known to exist in nature (Fig. 1 ). However, some capsid sizes are
rarer than others (such as T D 12; 19; and 27), an observation that has puzzled
structural virologists as early as 1961 [ 25 , 26 ]. The cause for this apparent bias in the
distribution of the observed capsid sizes is still not clearly understood. To explore if
there is an evolutionary pressure that discriminates against certain capsid shapes, we
further investigated intrasubunit interactions within virus capsids using a canonical
capsid model. Specifically, we explored how subunits interact and how the angles
between subunits can impose constraints on the capsid shape.