The refinement of the parameters of β-turns using neutron diffraction data

Abstract

Beta-bends are a difficult to interpret type of polypeptide chain backbone structure of globular proteins. Beta-bends are usually classified according to the dihedral angles φ and ψ of amino acid residues i + 1 and i + 2. Ramachandran map analysis of amino acid residues i + 1 and i + 2 indicates the resulting conformational stresses in bending. The mechanism of stabilization of their energetically disadvantageous conformations is still unclear. This kind of conformation stresses can only be compensated by additional interactions, such as additional hydrogen bonds, whose geometry and energy compensates for the beta-bending stress. Neutronography is the only available direct method for determining the position of hydrogen atoms in the structures of chemical compounds, including proteins. In this work, beta-bends from 176 protein structures from PDB established by neutronography are studied. In these structures, 3733 beta-bends were found using the i → i + 3 hydrogen bonding criterion. Using clustering by the magnitude of conformational angles, eight types of bends were newly identified. The magnitudes of conformational angles for each type of bend were determined. The hypothesis of additional hydrogen bonding to stabilize the bend was not confirmed, suggesting that the bending stress is compensated by other factors.