Structure and features of amino acid sequences of Π-modules in OB-folds

Abstract

Stereochemical analysis has been performed for П-modules from the large set of non-homologous protein structures containing the OB-fold. That module consists of two β-strands connected by a loop and placed in different sheets in such a way which looks as Greek letter П. Total 70 non-homologous proteins at resolution not less than 2.5Å have been selected for the analysis from 265 suitable structures belonging to sixteen OB-fold super families. We have disclosed two types of П-modules: the fist with the connecting loop containing α-helix, and second one without helix. Entrance of protein chain into second β-sheet is carried out by the same arch with conformation βββαLβp. In most cases, 85 % of total, α-positions are occupied by glycine residue, while at entrance in the loop such residues are absent. Occupancy frequency of П-modules has been obtained in dependence on the loop length. Spatial pathway of structures of all modules are superimposed very well. Structural alignment of amino acid for П-module sequences allows us to determine the key positions of the hydrophobic, hydrophilic, and glycine residues.