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.


CONCLUSIONS
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.
Ho
Bosco K
BK
Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, San Francisco, CA 94107, USA. bosco@maxwell.ucsf.edu
Brasseur
Robert
R
D020816:Amino Acid Motifs; D055592:Biophysical Phenomena; D001703:Biophysics; D002244:Carbon / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005998:Glycine / Q000737:chemistry*; D006860:Hydrogen Bonding; D011392:Proline / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013237:Stereoisomerism
D011506:Proteins; D002244:Carbon; D011392:Proline; D005998:Glycine