The Ramachandran plots of glycine and pre-proline

Ho, Bosco K.; Brasseur, Robert
January 2005
BMC Structural Biology;2005, Vol. 5, p14
Academic Journal
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 Ni+1 or O atom is sandwiched between the two Hα atoms of glycine. We show that the shape of the 5 distinct regions of density (the α, αL, βS, βP and βPR regions) can be reproduced with electrostatic dipole-dipole interactions. In preproline, we analyse the origin of the ζ region of the Ramachandran plot, a region unique to preproline. We show that it is stabilized by a COi-l…CδHi+lδ weak hydrogen bond. This is analogous to the COi-l…NHi+l 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.


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