Structural Basis of Sirtuin 6 Activation by Synthetic Small Molecules

Sirtuins are protein deacylases regulating metabolism and stress responses, and are implicated in aging‐related diseases. Small molecule activators for the human sirtuins Sirt1‐7 are sought as chemical tools and potential therapeutics, such as for cancer. Activators are available for Sirt1 and exploit its unique N‐terminus, whereas drug‐like activators for Sirt2–7 are lacking. We synthesized and screened pyrrolo[1,2‐a]quinoxaline derivatives, yielding the first synthetic Sirt6 activators. Biochemical assays show direct, substrate‐independent compound binding to the Sirt6 catalytic core and potent activation of Sirt6‐dependent deacetylation of peptide substrates and complete nucleosomes. Crystal structures of Sirt6/activator complexes reveal that the compounds bind to a Sirt6‐specific acyl channel pocket and identify key interactions. Our results establish potent Sirt6 activation with small molecules and provide a structural basis for further development of Sirt6 activators as tools and therapeutics.     

Pac13 is a Small,Monomeric Dehydratase that Mediates the Formation of the 3′‐Deoxy Nucleoside of Pacidamycins

The uridyl peptide antibiotics (UPAs), of which pacidamycin is a member, have a clinically unexploited mode of action and an unusual assembly. Perhaps the most striking feature of these molecules is the biosynthetically unique 3′‐deoxyuridine that they share. This moiety is generated by an unusual, small and monomeric dehydratase, Pac13, which catalyses the dehydration of uridine‐5′‐aldehyde. Here we report the structural characterisation of Pac13 with a series of ligands, and gain insight into the enzyme's mechanism demonstrating that H42 is critical to the enzyme's activity and that the reaction is likely to proceed via an E1cB mechanism. The resemblance of the 3′‐deoxy pacidamycin moiety with the synthetic anti‐retrovirals, presents a potential opportunity for the utilisation of Pac13 in the biocatalytic generation of antiviral compounds.     

High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints

There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid‐state NMR restraints with physics‐based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi‐quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid‐state NMR data for the model protein GB1 labeled with Cu²⁺‐EDTA at six different sites. We are able to determine the structure to 0.9 Å accuracy within a single day of computation on a GPU cluster. We further show that in some cases, the data from only a single paramagnetic tag are sufficient for accurate folding.