Strong and weak hydrogen bonds in sm/lsm oligomeric assemblies: a comparison of intra- and interchain interaction

Abstract

The Sm and Sm-like (LSm) proteins are a widespread protein family with members in all kingdoms of life. Sm proteins form complexes engaging in various RNA-processing events. Sm proteins do form and act as oligomeric assemblies whose characteristic is their exceptional stability. This study compares strong and weak hydrogen bonds in the interior of monomers and at interfaces of Sm/LSm proteins in order to better understand the stability of oligomers. According to our results, the stability of oligomeric assemblies is achieved by CH center dot center dot center dot O, NH center dot center dot center dot O and CH center dot center dot center dot N interactions including, NH center dot center dot center dot N, OH center dot center dot center dot O, XH center dot center dot center dot pi interactions present in small percentages. Intrachain hydrogen bonds behave in respect to geometry, distances and angles, like interchain hydrogen bonds. It is also shown that amino acids Arg and Lys participate significantly as donors or acceptors in some of the strong or weak interactions at interfaces to a higher extent than in the monomers. There is a trend for most polar amino acids to cross into more solvent exposed position in interfaces, which is not the case for nonpolar or charged amino acids. There is no exclusive preference for particular secondary structure both for intrachains and for interfaces.