Peptide Bond
Journal Title: Physical Science & Biophysics Journal - Year 2018, Vol 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.
Authors and Affiliations
Nandel FS*, Baskar M, Nandel V and Shafique M
Keywords
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