  Approximately 1% of the known protein structures display knotted
configurations in their native fold but their function is not understood. It
has been speculated that the entanglement may inhibit mechanical protein
unfolding or transport, e.g., as in cellular threading or translocation
processes through narrow biological pores. Here we investigate tigh peptide
knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted
peptides using all-atom molecular dynamics computer simulations. We find that
the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm,
respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore
diameter of ~2 nm below which a translocated knotted protein might get stuck.
The 4_1-knot length is in agreement with recent AFM pulling experiments.
Detailed TPK characteristics however, may be sequence-specific: we find a
different size and structural behavior in polyglycines, and, strikingly, a
strong hydrogen bonding and water molecule trapping capability of hydrophobic
TPKs due to side chain shielding of the polar TPK core. Water capturing and
release is found to be controlla ble by the tightening force in a few cases.
These mechanisms result into a sequence-specific 'locking' and metastability of
TPKs what might lead to a blocking of knotted peptide transport at designated
sequence-positions. Intriguingly, macroscopic tight 4_1-knot structures are
reproduced microscopically ('figure-of-eight' vs. the 'pretzel') and can be
tuned by sequence in contrast to mathematical predictions. Our findings may
explain a function of knots in native proteins, challenge previous studies on
macromolecular knots, and may find use in bio- and nanotechnology.
