In-silico mutagenesis
To assess the consistency of the predicted CENP-HIKM organizational
pattern with experimental reports from previous studies [14, 37],in-silico mutants of the CENP-H and CENP-M were designed using
the Chimera-curated backbone-dependent Dunbrack rotamer library
[42]. The backbone-dependent rotamer library is composed of
variances, rotamer frequencies, and mean dihedral angles as a function
of the backbone dihedral angles. The prediction of structures and
methods of design that utilizes backbone flexibility benefit strongly
from smoothly varying angles and probabilities. A new backbone-dependent
rotamer library version was developed to use adaptive kernel
regression for variances and mean dihedral angle calculations and also
the adaptive kernel density calculations for the frequency of rotamers.
This design creates an avenue for the estimation of variances,
probabilities of rotamers, and mean angles as a continuous and smooth
function of psi and phi [42]. The estimation of continuous
probability density for the nonrotameric degrees of freedom of aromatic
side chains, amides, and carboxylates was modeled as a function of the
rotamers and backbone dihedrals of the residual degrees of freedom.