title: Investigations of Ramachandran disallowed conformations in protein domain families.
abstract: 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 (≤1.2 Å). 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 1.2 Å 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.
authors.affiliation: Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: B
authors.initials: B
authors.lastname: Lakshmi
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
authors.forename: C
authors.initials: C
authors.lastname: Ramakrishnan
authors.affiliation: Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India.
authors.forename: G
authors.initials: G
authors.lastname: Archunan
authors.affiliation: National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore 560065, India.
authors.forename: R
authors.initials: R
authors.lastname: Sowdhamini
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: ns@mbu.iisc.ernet.in.
authors.forename: N
authors.initials: N
authors.lastname: Srinivasan
mesh_terms: D018360:Crystallography, X-Ray; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000145:classification; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry* / Q000145:classification
chemical_list: D010455:Peptides; D011506:Proteins
keywords: Disallowed conformations; Protein evolution; Protein structures; Ramachandran map; Steric clash