Characterization of non-planar peptide groups in protein crystal structures.
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 omega should be restricted to 180 degrees for the usual trans form of peptide unit. However, on analyzing the ultra-high resolution protein crystal database, we find that in some cases, omega deviates >10 degrees from its usual value of 180 degrees, 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 omega smaller than 180 degrees. Similar trend for to 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 theta. Thus, we find that both the angles omega and theta point towards a significant amount of non-planarity of peptide groups, which cannot be ignored. The role of peptide nonplanarity in protein function is, however, not yet clear.
Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019.
Anjan Kumar
AK
Dasgupta
Rabi
R
Majumdar
Dhananjay
D
Bhattacharyya
D000818:Animals; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D015233:Models, Statistical; D008968:Molecular Conformation; D009502:Neutrons; D009584:Nitrogen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
D008024:Ligands; D010455:Peptides; D011506:Proteins; D009584:Nitrogen