title: Investigating diproline segments in proteins: occurrences, conformation and classification.
abstract: The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60 °± 30° for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (( L) Pro-( L) Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II) -P(II) and P(II) -α are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the Xaa-Pro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies.
authors: Department of Physics, Indian Institute of Science, Bangalore, India. indranil.saha@elettra.trieste.it
authors: Indranil
authors: I
authors: Saha
authors: Narayanaswamy
authors: N
authors: Shamala
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs / Q000502:physiology; D004151:Dipeptides / Q000737:chemistry* / Q000145:classification*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary / Q000502:physiology; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D013237:Stereoisomerism
chemical_list: D004151:Dipeptides; D011506:Proteins; D011392:Proline