Nearest neighbour interactions between amino acid residues in short peptides and coil libraries

Abstract

Intrinsically disordered proteins (IDP) or proteins with intrinsically disordered regions (IDR) perform a plethora of functions mostly in a cellular environment. As unfolded proteins, IDPs can adopt molten globule or coil ensembles of conformations. Regarding the latter, the question arises as to whether they are describable as a self-avoiding random coil. Locally, this requires that amino acid residues sample the entire sterically allowed region of the Ramachandran plot with very similar probabilities and independent of the conformational dynamics of their neighbours. However, various lines of experimental and bioinformatic evidence suggest a more restricted, side chain and nearest neighbor dependent conformational space for individual residues. Over the last 25 years, short peptides and coil libraries were employed to determine conformational propensities of amino acid residues in unfolded states. The question arises as to whether conformational ensembles obtained from these two sources are comparable. In this paper, a variety of metrics were used to compare Ramachandran plots of a limited number of GXYG peptides (X,Y: guest residues) with XY dimers in the coil library of Ting et al. (Ting D., Wang G., Shapovalov M., Mitra R., Jordan M. I., Dunbrack R. L., Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical dirichlet process model, PLoS Comput. Biol., 2010, 6(4), e1000763-1–21, 10.1371/journal.pcbi.1000763). The results reveal major differences between corresponding plots, which might in part be due to the fact that solely the influence of one of the two neighbours of a given residue is probed by the above coil library while averages were taken over the respective opposite neighbours. The presented results suggest that coil libraries alone might not be a sufficient tool for determining the characteristics of statistical coils of IDPS and IDRs alike.