Translocation of Knotted Proteins into Mitochondria

Abstract

In recent years a surge of interest has arisen in properties and function of knotted proteins. As more and more knotted structures are discovered in the Protein Data Bank, it becomes increasingly important to understand how, if at all, the non-trivial topology affects the protein's function in the cell. In particular, it has been hypothesized that the presence of a knot in the polypeptide backbone may affect the ability of knotted proteins to be degraded in proteosome or translocated through the intercellular membranes, e.g. during import into mitochondria. In these processes, the translocating proteins typically have to pass through constrictions that are too narrow to accommodate folded structures, thus translocation must be coupled to protein unfolding. However, as shown in a number of theoretical and experimental studies the protein knots get tightened under the tension. The radius of gyration of the tight knot is about 7-8 Angstrom, whereas the diameters of the narrowest constriction of the mitochondrial pores are in the 12-15 Angstrom range, making it possible for the knots to get stuck during the translocation process. In this communication, we report the result of molecular dynamics simulations of knotted protein translocation which show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other ATPases transform chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. This research has been supported by the Polish NCN grant N N202 055440.