These ubiquitin pathways evolved much in parallel to other familiar markup systems used in the cell, namely methylation of DNA, and phosphorylation of specific amino acids in proteins.
Now the ubiquitin E3 ligase itself is just one specific kind of ubiquitin ligase whose job it is to add some of these subunits together under specific cellular conditions.
Unfolding forces in different pulling directions have been measured for green fluorescent protein (GFP) (16), ubiquitin (17), and the lipoyl domain (E2lip3) of the acetyl transferase subunit E2p (17).
AFM studies measuring the mechanical stability of ubiquitin monomers under various stretching conditions demonstrated the existence of well defined stages in ubiquitin folding (19-21).
8 nm, the contour length increment that was consistent with the unfolding of a portion of one ubiquitin monomer from Lys 48 to the C-terminus.
In particular, Szymczak and Cieplak have used a Gotype model to examine the statistics of mechanical unfolding of ubiquitin and integrin (25).
Here we studied the unfolding of ubiquitin by force (Figure 1), using all atom MD simulations with an alternative, speed-independent simulation protocol, the "pull and wait" technique (PNW) (21, 28).