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Title: Characterization of non-planar peptide groups in protein crystal structures
Authors: Dasgupta, Anjan Kumar
Majumdar, Rabi
Bhattacharyya, Dhananjay
Keywords: X-ray diffraction;Database analysis;Neutron diffraction;Non-planar peptide;Peptide bond;Protein crystal structure
Issue Date: Oct-2004
Publisher: NISCAIR-CSIR, India
IPC Code: C 07 K
Abstract: 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° for the usual/rans form of peptide unit. However, on analyzing the ultra-high resolution protein crystal database, we find that in some cases, ω deviates> 10° from its usual value of 180°, indicating significant non-planarity of peptide groups. Moreover, the non-planarity for most of the amino acids is found to be 'biased' towards values of ω smaller than 180°. 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 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 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.
Page(s): 233-240
ISSN: 0975-0959 (Online); 0301-1208 (Print)
Appears in Collections:IJBB Vol.41(5) [October 2004]

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