Quantitative use of chemical shifts for the modeling of protein complexes

Despite recent advances in the modeling of protein-protein complexes by docking, additional information is often required to identify the best solutions. For this purpose, NMR data deliver valuable restraints that can be used in the sampling and/or the scoring stage, like in the data-driven docking approach HADDOCK that can make use of NMR chemical shift perturbation (CSP) data to define the binding site on each protein and drive the docking. We show here that a quantitative use of chemical shifts (CS) in the scoring stage can help to resolve ambiguities. A quantitative CS-RMSD score based on (1)H(alpha), (13)C(alpha), and (15)N chemical shifts ranks the best solutions always at the top, as demonstrated on a small benchmark of four complexes. It is implemented in a new docking protocol, CS-HADDOCK, which combines CSP data as ambiguous interaction restraints in the sampling stage with the CS-RMSD score in the final scoring stage. This combination of qualitative and quantitative use of chemical shifts increases the reliability of data-driven docking for the structure determination of complexes from limited NMR data.