Supramolecular protein assemblies are an emerging area within the chemical sciences, which combine the topological structures of the field of supramolecular chemistry and the state-of-the-art chemical biology approaches to unravel the formation and function of protein assemblies. Recent chemical and biological studies on natural multimeric protein structures, including fibers, rings, tubes, catenanes, knots, and cages, have shown that the quaternary structures of proteins are a prerequisite for their highly specific biological functions. In this review, we illustrate that a striking structural diversity of protein assemblies is present in nature. Furthermore, we describe structure-function relationship studies for selected classes of protein architectures, and we highlight the techniques that enable the characterisation of supramolecular protein structures.

A large number of structurally diverse epigenetic reader proteins specifically recognize methylated lysine residues on histone proteins. Here we describe comparative thermodynamic, structural and computational studies on recognition of the positively charged natural trimethyllysine and its neutral analogues by reader proteins. This work provides experimental and theoretical evidence that reader proteins predominantly recognize trimethyllysine via a combination of favourable cation–π interactions and the release of the high-energy water molecules that occupy the aromatic cage of reader proteins on the association with the trimethyllysine side chain. These results have implications in rational drug design by specifically targeting the aromatic cage of readers of trimethyllysine.

Histone lysine methylation is regulated by N-methyltransferases, demethylases, and N-methyl lysine binding proteins. Thermodynamic, catalytic and computational studies were carried out to investigate the interaction of three epigenetic protein classes with synthetic histone substrates containing l- and d-lysine residues. The results reveal that out of the three classes, N-methyl lysine binding proteins are superior in accepting lysines with the d-configuration.

Histone N-lysine methylation is a widespread posttranslational modification that is specifically recognised by a diverse class of N-methyllysine binding reader proteins. Combined thermodynamic data, molecular dynamics simulations, and quantum chemical studies reveal that reader proteins efficiently bind trimethylornithine and trimethylhomolysine, the simplest N-trimethyllysine analogues that differ in the length of the side chain.

Thermodynamic analyses of associations between reader domain proteins and histone H3K4me3 peptides demonstrated that the shortest recognised histone substrate contains just the first four amino acids in histone 3. Deletion or addition at the N terminus resulted in a substantial decrease of binding affinity for most readers, thus verifying the importance of the H3A1 binding pocket.