Tripeptide analysis of protein structures

BACKGROUND: An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (≤ 2.0°A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures. RESULTS: Tripeptides have been classified into three categories: rigid, non-rigid and intermediate, based on the relative structural rigidity between C(α )and C(β )atoms in a tripeptide. We found that 18% of the tripeptides in the dataset can be classified as rigid, 4% as non-rigid and 78% as intermediate. Many rigid tripeptides are made of hydrophobic residues, however, there are tripeptides with polar side chains forming rigid structures. The bulk of the tripeptides fall in the intermediate class while very small numbers actually fall in the non-rigid class. Structurally all rigid tripeptides essentially form two structural classes while the intermediate and non-rigid tripeptides fall into one structural class. This notion of rigidity and non-rigidity is designed to capture side chain interactions but not secondary structures. CONCLUSIONS: Rigid tripeptides have no correlation with the secondary structures in proteins and hence this work is complementary to such studies. Tripeptide data may be used to predict plausible structures for oligopeptides and for denovo protein design

Quark Propagator and Chiral Symmetry with String Tension

General properties of the light and heavy quark propagators have been investigated in the context of string tension interaction. Confinement, chiral symmetry breaking, spectral properties of the propagator are analytically studied and numerically validated. We show that the propagator is analytic in the infrared region even for massless quarks with a non zero radius of convergence. Emergence of more than one mass scale is exemplified. Massless limit of the quark propagator does exhibit critical behaviour.Comment: 15 pages, 6 eps figures, LaTe