Peptide Bond Planarity

Authors:

Nandel FS*, Baskar M, Nandel V and Shafique M

DOI: 10.23880/psbj-16000107

Volume 2, Issue 1

Abstract

Peptide bond is treated planar with ω=180° or ω=0° representing trans and cis peptide bond respectively. Deviations in
ω from 180°and 0° are referred as distortions of individual peptide units from planarity. Different interpretations have
appeared to explain the deviations/non-planarity in terms of: i) pyramidalization of carbonyl carbon and amide nitrogen
atoms, ii) ψ dihedral angle, iii) handedness of protein main chain, iv) tightening default restrictions on the peptide
planarity angle ω. Recently, Mathews has argued that the quality of a refined model of a protein needs to be assessed not
just from its R-factors but together with the “Fo – Fc” electron density difference maps. Thus, then non-planarity of
peptide bond continued to be a debatable issue.
Analysis of high resolution pdb structures for the bond angels around carbonyl carbon’s and amide nitrogen’s is found to
be 360°.This rules out the change in hybridization and hence pyramidalization of these atoms as claimed earlier.
Likewise, there is no change in the hybridization of Cα and there is only readjustment of bond angels. Thus, the peptide
bond is planar.
Both expansion and contraction of the angle N-Cα-C was observed up to 10° & 5° respectively. The position of Cα’s with
respect to the C-N bond is governed by the angle’s N-Cα-C and this will be clearly reflected in the electron density
difference map. Minimum deviations both in ω and in the angle N-Cα-C (Δτ) are found in helical and compact structures.

Keywords:

Peptide Bond; High Resolution Structures; Pyramidalization

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