A strained N-capping motif in α-helices of βαβ-units

A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions i - 2, i + 2 and i + 3, if N-cap is i). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure.

Current Approaches in Supersecondary Structures Investigation

Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research. The interest in the study of supersecondary structures in proteins is due to their autonomous stability outside the protein globule, which makes it possible to study folding processes, conformational changes in protein isoforms, and aberrant proteins with high productivity.

Left-handed βαβ-units: frequency of occurrence and arrangement in protein structure

Communicated by Ramaswamy H. Sarma.

Handedness of structural units depends on their mutual arrangement in protein structure

Communicated by Ramaswamy H. Sarma.