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Despite the fact that the three atypical ubiquitin linkage residues (K27, K29, and K33) are close in both sequence and configuration space, little is known about their functional roles.
Function
Among the four atypical linkages, K27, K29 and K33 have less well-established functional roles [6]. The three atypical linkage lysine residues are close in both sequence and configuration space. This makes it difficult to distinguish their functional roles using experimental tools like mass spectroscopy.
The structural studies of these atypical diUbs have suggested that they have different biological functions than their K48-diUb counterparts. We explored their functional landscape by simulating CGK63 (two Ub monomers linked by a CGK63 isopeptide bond) and CGM1 (two Ub monomers linked by CGK1-G76 isopeptide bond, also denoted as linear model). For more details please visit cgk 33
The free energy profiles show that both CGK63 and CGM1 have two functional states, which are similar to the compact state of K6-diUb with I36-I44 interface in PDB 2XK5 and the open state of K11-diUb with I36-I36 interface in PDB 3NOB. Furthermore, we found that both CGK63 and CGM1 are highly dependent on pH. Decreasing pH will increase the population of their open conformations, which is consistent with experimental data from Varadan and Hirano et al.