There has recently been some interest in
There has recently been some interest in Uba6, which is most similar to slime mold, with BLAST identities of 59% and positives 73% in the 400–600 ADD range. The 400–600 ADD correlation of the two profiles is a striking 87%, so functional differences probably arise outside the ADD binding domain. Human Uba6 and Uba1 have distinct preferences for E2 charging in vitro, and their specificity depends in part on their C-terminal ubiquitin-fold domains, which recruit E2s . Comparison of Uba1 of yeast and slime mold with Uba6 shows that for the most part, where Uba6 differs from one of the two, it is similar to the other. The exceptional region is UFD, the ubiquitin fold domain (Fig. 5), where Uba6 has a strong hydrophobic peak. Similar differences are obvious in the human and GSK2578215A fly profiles. This “only” confirms the main conclusion of , but note that it does so through a simple one-dimensional analysis that also includes many species’ versions of Uba1.
Conclusions At present the most sophisticated structural studies involving MDS simulations with explicit water  can reveal short-range interspecies differences in Uba-E1 — Ub binding, but long-range interactions are not identified. Proteins are near thermodynamic critical points in amino acid configuration space, and near such points (especially transition states), long-range and short-range interactions are balanced. In many proteins the short-range interactions evolve in subtle ways inaccessible to experiment, while here we have shown that the long-range interactions change in ways that can be easily recognized in . Evolutionary trends are easily recognized by thermodynamic scaling theory.