title: Conformational studies on beta-bend containing a cis peptide unit.
abstract: Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds--either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C gamma-endo and C gamma-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
authors: H A
authors: HA
authors: Nagarajaram
authors: P K
authors: PK
authors: Paul
authors: K
authors: K
authors: Ramanarayanan
authors: K V
authors: KV
authors: Soman
authors: C
authors: C
authors: Ramakrishnan
mesh_terms: D000409:Alanine / Q000737:chemistry; D000595:Amino Acid Sequence; D005998:Glycine / Q000737:chemistry; D007536:Isomerism; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011392:Proline / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D009842:Oligopeptides; D011392:Proline; D000409:Alanine; D005998:Glycine