Mining and Structural Characterization of S···X Chalcogen Bonds in Protein Database

GRAPHICAL ABSTRACT

Abstract

Existence of specific secondary bonding interactions around a divalent sulfur atom, i.e., S···X (X˭O, N, and S) interactions (or chalcogen bonds), has recently become evident in proteins by virtue of statistical studies using protein structure databases. In this work, to reinvestigate structural properties of the S···X chalcogen bonds in proteins, statistical analysis of S···X contacts found in TOP500 database was carried out. Four types of chalcogen bonds, i.e., S‒S···O˭C, C‒S···O˭C, C‒S···N, and S‒S···S‒S interactions, were characterized. The directionalities strongly suggested the importance of π_O→σ*_S, π_N→σ*_S, or n_S→σ*_S orbital interaction for the stability. Contribution from the dispersion force would also play roles in the chalcogen bonds because the distances between the interacting atoms were close to or slightly larger than the sum of the van der Waals radii. These observations were essentially the same as previous studies using a different set of protein structures. Thus, existence and structural features of S···X chalcogen bonds in proteins were unambiguously reconfirmed.

Keywords:

• Secondary bonding interaction
• orbital interaction
• statistical analysis
• directionality