  Molecular dynamics studies within a coarse-grained structure based model were
used on two similar proteins belonging to the transcarbamylase family to probe
the effects in the native structure of a knot. The first protein,
N-acetylornithine transcarbamylase, contains no knot whereas human ormithine
transcarbamylase contains a trefoil knot located deep within the sequence. In
addition, we also analyzed a modified transferase with the knot removed by the
appropriate change of a knot-making crossing of the protein chain. The studies
of thermally- and mechanically-induced unfolding processes suggest a larger
intrinsic stability of the protein with the knot.
