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.
Highlights
Many proteins carry out their functional role acting as part of protein assemblies, i.e. a combination of different proteins or of multiple copies of the same monomeric unit
The difficult step in the coevolution analysis of hetero-oligomers is the proper pairing of orthologs of interacting proteins and the corresponding removal of paralogs
Once this has been achieved, the creation of a joint multiple sequence alignment (MSA) in which each line contains a pair of interacting proteins allows the straightforward use of predicted inter-protein contacts as restraints to drive the modelling of the quaternary structure [6,26,40]
Summary
Many proteins carry out their functional role acting as part of protein assemblies, i.e. a combination of different proteins (hetero-complexes) or of multiple copies of the same monomeric unit (homo-complexes). DARR experiments yield a list of ambiguous contacts in which the quaternary contacts must be separated from intra-monomeric contacts to determine the 3D structure of the complex. In heterocomplexes this problem can be alleviated by using different schemes for enrichment in stable NMR-active isotopes (13C, 15N) in the various subunits of the complex [23]; for instance, one subunit can be uniformly enriched while all other subunits are not.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Computational and Structural Biotechnology Journal
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
