ABSTRACT
Using a data set of 454 crystal structures of peptides and 80 crystal structures of non-homologous proteins solved at ultra high resolution of 1.2 A or better we have analyzed the occurrence of disallowed Ramachandran (phi, psi) angles. Out of 1492 and 13508 non-glycyl residues in peptides and proteins respectively 12 and 76 residues in the two datasets adopt clearly disallowed combinations of Ramachandran angles. These examples include a number of conformational points which are far away from any of the allowed regions in the Ramachandran map. According to the Ramachandran map a given (phi, psi) combination is considered disallowed when two non-bonded atoms in a system of two-linked peptide units with ideal geometry are prohibitively proximal in space. However, analysis of the disallowed conformations in peptide and protein structures reveals that none of the observations of disallowed conformations in the crystal structures correspond to a short contact between non-bonded atoms. A further analysis of deviations of bond lengths and angles, from the ideal peptide geometry, at the residue positions of disallowed conformations in the crystal structures suggest that individual bond lengths and angles are all within acceptable limits. Thus, it appears that the rare tolerance of disallowed conformations is possible by gentle and acceptable deviations in a number of bond lengths and angles, from ideal geometry, over a series of bonds resulting in a net gross effect of acceptable non-bonded inter-atomic distances.
Subject(s)
Bacterial Proteins/chemistry , Peptides/chemistry , Amino Acid Sequence , Computational Biology , Genome , Molecular Sequence Data , Mycobacterium/chemistry , Protein ConformationABSTRACT
Medicinal plants play a key role in human health care. Pterocarpus marsupium is one of the plants used in treatment of diabetes mellitus and the present study was aimed to assess hepatoprotective effect of the plant against CCl(4) induced hepatotoxicity. Wistar albino rats were divided into four groups. Group I was normal control group; Group II, the hepatotoxic group was given CCl(4) (2ml/kg body weight intraperitoneally); Groups III received CC1(4) + Plant extract (100 mg/kg b.w orally); Group IV received only the plant extract. Liver markers were assayed in serum and liver tissue. Levels of marker enzymes such as alanine transminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), and lactate dehydrogenase (LDH) and bilirubin were increased significantly in Group II. These enzymes were significantly decreased in Group III treated with plant extracts. The present investigation suggest that the plant had a good protective effect on CCl(4) induced hepatic injury.
