Analyses of experiment based ramachandran plots of tri-, tetra- and pentapeptides reveal residue dependent interactions between neighbors

Abstract

Flory's canonical random coil model is based on the assumption that conformational fluctuations of amino acid residues in unfolded poly(oligo)peptides and proteins are uncorrelated (isolated pair hypothesis, IPH). It implies that conformational energies, entropies, and solvation free energies are all additive. Nearly 25 years ago, analyses of coil libraries casted some doubt on this notion in that they revealed that aromatic residues could change the 3J(HNHCα) coupling of their neighbors. Since then multiple lines of bioinformatical, computational and lately also experimental evidence indicate that the conformational propensities of amino acids in unfolded peptides and proteins depend on their nearest neighbors and possibly even on the nature of the second neighbor.