Feature characterization of DPF: the dual personality fragments in proteins

The dynamics of protein structures are further obfuscated by the order and disorder paradigm. The disordered regions of a protein may become ordered under specific circumstances: such is the definition of Intrinsically Disordered Protein. However, there exists a structural state that lies amidst the regularly folded and disordered proteins – termed as Dual Personality Fragments (DPF). DPF have sequence and structural features that identifies them as distinct structural state. The study is inspired by the work of Zhang. Y, Godzik. A et al published a decade ago in Cell press Structure. Strikingly, that is the only existing literature on DPF so far. We identify DPF from a redundant set of PDB_r_2015 based on pairwise alignments using PALI database. Noteworthy is that the number of such fragments have increased with each new PDB release. We analyse DPF based on its amino acid composition, solvent accessibility and local structural information. We employ structural alphabets – known as protein blocks (PB) – to approximate the local structure of these fragments. The amino acid composition of DPF is similar to that found in 2007 and therefore provides the basis of distinction for DPF from ordered and disordered fragments. For instance, a composition of high L, G, P and D in missing region can be isolated from disorder to DPF. The structural composition based on secondary structure assignments and PB reveals that helical local structures are more abundant in DPF thus supporting the fact that they are not involved in amyloid formations. Functional analysis of DPF shows that ~ 68% of DPF lie in the sites of post translational modifications like phosphorylations and N-glycosylations. This is an indicative of the importance of DPF in regulatory proteins since the PTM modifies their local structure. Our study focuses on the characterisation of such modifying fragments, like DPF. It would be helpful in understanding the structural spectra of Disorder to Order.