Investigations of Ramachandran disallowed conformations in protein domain families

• Published in: International journal of biological macromolecules Vol. 63; pp. 119 - 125
• Main Authors: Lakshmi, B., Ramakrishnan, C., Archunan, G., Sowdhamini, R., Srinivasan, N.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.2014
• Subjects: Crystallography, X-Ray; Disallowed conformations; Models, Molecular; Peptides - chemistry; Peptides - classification; Protein Conformation; Protein evolution; Protein Structure, Secondary; Protein Structure, Tertiary - genetics; Protein structures; Proteins - chemistry; Proteins - classification; Ramachandran map; Steric clash; Protein evolution; Ramachandran map; Steric clash; Protein structures; Disallowed conformations
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2013.10.032

In peptide and protein structures, occurrence of (ϕ,ψ) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (≤1.2Å). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2Å or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conserved in protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein.