The Ramachandran Plots Of Glycine And Pre-Proline

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 psi angle is typically clustered at psi = 180 degrees
and psi = 0 degrees. We show that these clusters correspond to conformations
where either the N(i+1) or O atom is sandwiched between the two Halpha atoms of
glycine. We show that the shape of the 5 distinct regions of density (the alpha,
alphaL, betaS, betaP and betaPR regions) can be reproduced with electrostatic
dipole-dipole interactions. In pre-proline, we analyse the origin of the zeta
region of the Ramachandran plot, a region unique to pre-proline. We show that it
is stabilized by a CO(i-1)...CdeltaHdelta(i+1) weak hydrogen bond. This is
analogous to the CO(i-1)...NH(i+1) hydrogen bond that stabilizes the gamma 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.