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 transcarb
amylase, 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.
A simple model of Laplacian growth is considered, in which the growth takes place only at the tips of long, thin fingers. In a recent paper, Carleson and Makarov used the deterministic Loewner equation to describe the evolution of such a system. We e
xtend their approach to a channel geometry and show that the presence of the side walls has a significant influence on the evolution of the fingers and the dynamics of the screening process, in which longer fingers suppress the growth of the shorter ones.
