AMP activated protein kinase is a protein complex that plays an important role in energy metabolism in nearly all eukaryotes. AMPK is a heterotrimeric protein consisting of three different subunits, catalytic alpha (α1, α2), regulatory beta (β1, β2) and regulatory gamma (γ1, γ2, γ3). Following activation by phosphorylation AMPK can be further regulated by the AMP:ATP ratio and localisation/regulation by glycogen. Once activated AMPK increases ATP producing pathways while at the same time inhibiting ATP consuming pathways. For its roles in metabolism AMPK is considered a good target for treating metabolic disorders such as type-2 diabetes.

The β subunit contains a carbohydrate binding module (CBM) that binds to glycogen. Our lab has found that the isolated β2-CBM always binds to oligosaccharides more tightly than the β1-CBM. The greatest difference in affinity was found for oligosaccharides with a single α1,6 branch. β1- and β2-CBM show better than 80% sequence identity with all residues in contact with carbohydrate strictly conserved. The difference in affinity may in part be due to an extra threonine residue located in a loop in β2-CBM, however, the structural reasons for the difference are not resolved. An additional difference in the two CBMs is that β2-CBM shows microsecond motions which are absent in β1-CBM.

The aim of this project is to i) determine if the CBM within full length AMPK shows the same oligosaccharide binding results as the isolated CBMs, and observe activity differences with branched oligosaccharides ii) resolve the structural reasons for the carbohydrate affinity differences between the β1- and β2-CBMs iii) find and develop novel non-carbohydrate ligands that show isoform specificity. The methods that will be used include protein mutagenesis combined with NMR experiments to assess structural changes , dynamic changes and screening experiments.