A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts

Abstract

Protein assemblies are involved in many important biological processes. Solid-state NMR (SSNMR) spectroscopy is a technique suitable for the structural characterization of samples with high molecular weight and thus can be applied to such assemblies. A significant bottleneck in terms of both effort and time required is the manual identification of unambiguous intermolecular contacts. This is particularly challenging for homo-oligomeric complexes, where simple uniform labeling may not be effective. We tackled this challenge by exploiting coevolution analysis to extract information on homo-oligomeric interfaces from NMR-derived ambiguous contacts. After removing the evolutionary couplings (ECs) that are already satisfied by the 3D structure of the monomer, the predicted ECs are matched with the automatically generated list of experimental contacts. This approach provides a selection of potential interface residues that is used directly in monomer–monomer docking calculations. We validated the protocol on tetrameric L-asparaginase II and dimeric Sod1.

Keywords

• Homo-oligomers
• Coevolution
• NMR
• Evolutionary constraints
• Protein-protein interactions
• Solid-state NMR