The Ramachandran plots of glycine and pre-proline

Abstract

Background: The Ramachandran plot is a fundamental tool in the analysis of protein structures. Of the 4 basic types of Ramachandran plots, the interactions that determine the generic and proline Ramachandran plots are well understood. The interactions of the glycine and pre-proline Ramachandran plots are not. Results: In glycine, the ψ angle is typically clustered at ψ = 180° and ψ = 0°. We show that these clusters correspond to conformations where either the N i+1 or O atom is sandwiched between the two H α atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, α L, β S, β P and β PR regions) can be reproduced with electrostatic dipole-dipole interactions. In pre-proline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to pre-proline. We show that it is stabilized by a CO i-1···C δ H δ i+1 weak hydrogen bond. This is analogous to the CO i-1···NH i+1 hydrogen bond that stabilizes the γ region in the generic Ramachandran plot. Conclusion: We have identified the specific interactions that affect the backbone of glycine and pre-proline. Knowledge of these interactions will improve current force-fields, and help understand structural motifs containing these residues.