The Ramachandran plots of glycine and pre-proline

BMC Struct Biol. 2005 Aug 16;5:14. doi: 10.1186/1472-6807-5-14.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Biophysical Phenomena
  • Biophysics
  • Carbon / chemistry
  • Computational Biology / methods*
  • Databases, Protein
  • Glycine / chemistry*
  • Hydrogen Bonding
  • Proline / chemistry*
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Software
  • Static Electricity
  • Stereoisomerism

Substances

  • Proteins
  • Carbon
  • Proline
  • Glycine