Chalcogen bonds in protein architecture

Abstract

Nonbonded interactions between a divalent sulfur atom and polar functional groups, i.e., S···X (X=O, N, and S) interactions, have recently been demonstrated to stabilize protein structures to some extent and play putative roles in their function and evolution, thanks to the interplay of statistical analysis of protein structure databases and theoretical calculation using simple molecular cluster models. The directional features observed between the interacting S and X atoms suggest that they can also be called S···X chalcogen bonds in analogy to halogen bonds. While the existence of chalcogen bonds in proteins may be accepted today by the protein scientist community, there are still several issues that should be addressed clearly before going forward to applications of the interactions to protein engineering and the ligand design. Herein, the current status of the research on the S···X chalcogen bonds in proteins is reviewed from several points of view, including the historical aspects and the analytical methods for mining chalcogen bonds in protein structures. Statistical, directional, and energetic features of four typical S···X chalcogen bonds in proteins are presented. Possibility of analogous Se···X chalcogen bonds in selenoproteins is also pointed out. Implications of S···X chalcogen bonds in the structural control and in the function and evolution of some particular proteins are subsequently summarized from the recent literature. Finally, it is proposed that the concept of S···X chalcogen bonds will be a useful tool for fully understanding not only protein structures but also the biological aspects. Thus, the chalcogen bonds, though their interaction energy is smaller than that of classical hydrogen bonds, can be an element of weak noncovalent interactions that control chemical and biological properties of protein architecture.