Background

Previous work

Proteins are critical biological components that take part in all cellular processes. When we look at protein structures we can identify parts that form separated folding units, termed domains. To put an example, we find the same domain in white in this figure:

The same domains appear frequently in different contexts.

The TIM-barrel or (βα)8-barrel appears both in the pyruvate kinase and Imidazol glycerol phosphate synthase proteins. It is commonly understood that proteins evolved through the recruitment of domains and for this reason domains have been for long been defined as the basic evolutionary unit.

When we look at the domains themselves, we can distinguish smaller fragments from which the domains are formed. For example, in this figure we can see that the TIM-barrel and the flavodoxin domains, two ancient and highly populated superfolds, share a fragment:

The TIM-barrel and flavodoxin folds present a structural fragment in common (in blue and green, respectively). It was later found that the two folds are evolutionary related

By using this structural evidence, a chimeric protein made from CheY and HisF was built from smaller fragments. The resulting protein formed a barrel-like structure [1, 2], like in the above figure. In a follow-up study it was investigated whether these two proteins that had been chosen based on structural evidence were in fact evolutionary related. To do so, a search using profile hidden markov model (HMM) comparisons, able to find remote sequence homology, revealed strong evidence of homology between proteins of these two ancient and highly populated folds. Furthermore, a family of sequences that show intermediate features between both folds was detected, enabling the first crystallization of one of its members [3]:

Structure-based sequence alignment of the N-terminal domain of TM0182 (orange) with the flavodoxin-like cobalamin-binding protein from D. hafniense (PDB code 4JGI; green) and the (βα) 8 -barrel class I KDPG aldolase from T. maritima (PDB code 1WA3, blue). The (βα) 2 fragment with the higher identity and similarity is colored in the alignment as well as in the structural models (depicted as a cartoon), whereas the rest is in gray. Capital letters denote structurally aligned residues, | highlights identical residues, and + highlights similar residues. Figure and caption taken from reference [2]

These results support the vision that protein folds share a common ancestry and that sequence similarity searches such as the one in this work are useful tools to identify sub-domain sized fragments that, mimicking Nature, can serve as building blocks. We extended the previous search between the TIM-barrel and flavodoxin folds to a global search of the protein sequence space and stored here in FUZZLE. You can get detailed information on how the database was built here.

References

[1] TAM Bharat, S Eisenbeis, K Zeth, B Höcker A βα-barrel built by the combination of fragments from different folds. Proceedings of the National Academy of Sciences

[2] Simone Eisenbeis, William Proffitt, Murray Coles, Vincent Truffault, Sooruban Shanmugaratnam, Jens Meiler, Birte Höcker. Potential of fragment recombination for rational design of proteins. Journal of the American Chemical Society 134 (9), 4019-4022

[3] JA Farías-Rico, S Schmidt, B Höcker. Evolutionary relationship of two ancient protein superfolds. Nature chemical biology 10 (9), 710