Notably the
molecular system, which was subjected to a five nanosecond molecular
dynamics simulation never reached equilibrium. On the contrary, the
homology model of the same protein bearing the bacterial insert structures
that end in α-helical conformation, quickly reached equilibrium
(±150 ps) and remained there for the rest of the simulation time. Judging
on structural features, the bacterial α-helical insert as well as the 21
amino acid α-helical fragment fit nicely to its environment by joining in
a multiple α-helix bundle conformation, next to the pack of α-helices
already present in the core of the protein. The smaller 21 amino acid
long insert wasmodeled in α-helical upon the application of secondary
structure prediction algorithms that pointed this way.