Fig 1.
Diagram of structural mapping of the bioactive peptides on structural superfamilies.
Once a BP was detected in a given protein after sequence exact searches, we identified putative folds for that sequence using fold-assignment techniques. Templates in this fold identification were those domains deposited in CATH database. We then structurally aligned the sequence putative CATH template with the corresponding representative protein of the structural superfamily again accordingly with CATH database. We finally mapped the BP occurrence to the representative template of each structural superfamily.
Fig 2.
Flowchart of main procedure followed to mapping the structural occurrence of biopeptides.
Fig 3.
Distribution of protein folds that contains biopeptides extracted from BIOPEP database.
Table 1.
Description of the top ten most abundant superfamilies found in the assignation of structure of the sequences with at least one peptide.
Fig 4.
Distribution of number of GO terms associated with folds with more and less than 5 biopeptides.
Distributions of different GO terms per each class (Molecular function, Cellular components and Biological process) for proteins showing less than 5 and 5 or more BP (panels a, b, and c). Panel d, shows the same distribution but now using FunTree clusters information. In all the cases it is possible to observe that proteins with more than 5 BPs are functionally more diverse than those proteins with less than 5 BPs.
Fig 5.
Number of different structural and sequential clusters derived from CATH database.
Blue dots represent proteins with less than 5 BPs and the orange ones those with 5 or more BPs. It is possible to see that proteins with more than 5 BPs are more diverse structurally and sequentially.
Fig 6.
Structure of dethiobiotin synthase (PDB ID 1byi) represented in cartoon representation showing mapped BPs.
Red indicates ACE inhibitor BP activity (14), blue antibacterial (4), yellow inmunomodulating (3), green antioxidative (3), magenta neuropeptide (1), light grey chemotactic (1) and dark grey stimulating activities (1) (as derived from BIOPEP database). It is possible to see that different activities have similar location. BPs found in different proteins of the same superfamily have been mapped on a representative structure (1byi) accordingly to CATH (see Materials and methods).
Table 2.
Detail of the sequence and activity of biopeptides of the first four superfamilies with the highest number of biopeptides.
The activity corresponds to the classification in BIOPEP.