A closer look into the α-helix basin.

Abstract

α-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ). In this way, valuable information on the helical structure becomes directly available. Analysis of α-helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the α-helix backbone can be harmonically approximated on the (ρ, ϑ) space, which is not applicable to the (φ, ψ) space due to the diagonal distribution of the conformations. The observed trends of helical conformations obtained from the PDB are captured by four conceptual simulations that theoretically examine the effects of residue bulkiness, external electric field, and externally applied mechanical forces. Flory’s isolated pair hypothesis is shown to be partially correct for α-helical conformations.