Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies

Abstract

The distinguishing property of Sm/LSm protein assemblies is their high stability. In order to better understand the nature of Sm/LSm protein oligomers in this study we have analyzed the contribution of non-canonical interactions to the stability of assemblies. The predominant types of non-canonical interactions at Sm/LSm protein interfaces are CH⋅⋅⋅O, and CH⋅⋅⋅N interactions represented at interfaces. Our results show low percentages of XH-π and non-canonical interactions involving sulfur atoms, while the backbone groups were less frequently involved. The data show a high percentage of non-canonical interactions in interfaces formed by charged residues with Lys and Arg, these being the major charged donors. The main chain non-canonical interactions might be slightly more linear than the side chain interactions, and they have somewhat shorter median distances. Comparing the stabilizing amino acid residues with amino acids which build non-canonical interactions at interfaces shows that certain amino acids like Phe, Pro, His and Tyr are involved with a high percentage. The high conservation score of amino acids that are involved in non-canonical interactions in protein interfaces is an additional strong argument for their importance in the stabilization of Sm/LSm protein assemblies.

Keywords: Computational chemistry; Interfaces; Noncovalent interactions; Proteins; Stabilization centers.