3. Iterative Optimizations
This simulation became accurate by the peptide collision with water
molecules, residues received larger torques, and planar amino acids to
rotate faster. The length of the side chain was estimated as the maximum
of bonds from the Cα atom. The order of calculation of the pair of bonds
of the residue from the sum of the priority from torsional property.
The 8 amino acids of 1n9v were arranged into
‘D(7)R(2)V(8)Y(1)I(5)H(4)P(6)F(3)’. The smaller number was calculated
first and received higher priority.
Consequently, the 4th peptide bond between Tyr(Y) and
Ile(I) was first calculated(1+5=6), and the bond between Tyr(Y) and
Val(V)(1+8=9). The order of priority is
‘D-(3)-R-(4)-V-(2)-Y-(1)-I-(6)-H-(7)-P-(5)-F’. The numbers in the round
brackets designate the order of the linkage among residues. The dihedral
angles flanking peptide bond are φ and ψ angles. Between these two
dihedral angles, we calculated the one close to the higher priority
first, and the other close to the lower priority later.
In this order, we iteratively optimized the initial structure from
cotranslational folding. This was performed until the convergence of
potential energy. The structure in which potential energy converged in
six times from the initial structure was taken.