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BMC Struct Biol. 2005 Aug 16;5:14.

The Ramachandran plots of glycine and pre-proline.

Author information

1
Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, San Francisco, CA 94107, USA. bosco@maxwell.ucsf.edu

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 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.

PMID:
16105172
PMCID:
PMC1201153
DOI:
10.1186/1472-6807-5-14
[Indexed for MEDLINE]
Free PMC Article

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