Characterization of non-planar peptide groups in protein crystal structures

Abstract

<span style="mso-bidi-language:HI">Peptide groups are generally assumed to be planar in protein structure, due to 'rigid' partial double bond character of peptide bonds, thus the value of peptide torsion angle ω should be restricted to 180<span style="mso-bidi-font-family:Arial;mso-bidi-language:HI">° <span style="mso-bidi-language:HI">for the <i>usual/rans </i>form of peptide unit. However, on analyzing the ultra-high resolution protein crystal database, we find that in some cases, ω deviates> 10<span style="mso-bidi-font-family:Arial; mso-bidi-language:HI">° <span style="mso-bidi-language:HI">from its usual value of 180<span style="mso-bidi-font-family:Arial;mso-bidi-language: HI">°, <span style="mso-bidi-language:HI">indicating significant non-planarity of peptide groups. Moreover, the non-planarity for most of the

<span style="mso-bidi-language:HI">amino acids is found to be 'biased' towards values of ω smaller than 180<span style="mso-bidi-font-family:Arial;mso-bidi-language: HI">°.

<span style="mso-bidi-language:HI">Similar trend for ω is confirmed by the neutron diffraction data for proteins. The neutron diffraction database also reveals that non-planar peptide groups are generally

<span style="mso-bidi-language:HI">correlated to 'pyramidal' structure of the peptide-nitrogen bonds. Consequently, the hydrogen atom of peptide group deviates from its planar position, as measured by the 'improper' torsion angle θ. Thus, we find that both the angles ω<span style="mso-bidi-font-family:Arial; mso-bidi-language:HI"> <span style="mso-bidi-language:HI">and θ point towards a significant amount of non-planarity of peptide groups, which cannot be ignored. The role of peptide non-planarity in protein function is, however, not yet clear.

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