Fig. 3
Development of KArGO, a hetero-bifunctional reagent for arginine-lysine cross-linking. a Structure of KArGO and an initially synthesised hetero-bifunctional cross-linker possessing ArGO and NHS functional groups. b Major cross-linked peptide structure identified from protein cross-linking with KArGO. The reaction of OPA with lysine residues forms a single phthalimidine product. c Comparison of the numbers of identified peptide pairs cross-linked by ArGO (blue dots) or by KArGO (purple squares) on model proteins. The four conditions of the ArGO experiment: 0.5 or 1.0 mM of either ArGO1 or ArGO2. The four conditions of the KArGO experiment: 0.1 or 0.2 mM of KArGO cross-link followed by trypsin or trypsin/Asp-N digestion. The derived mean and standard deviation (s.d.) values are shown in the figure. The number of ArGO- or KArGO-linked peptide pairs obtained from each of the four conditions can be found in the source data file. d The data in c are merged and reorganized by cross-linked R–R or K–R pairs. All cross-linked sites of ArGO2 and KArGO are provided in the source data file. e Histogram depicting the distribution of Cα–Cα distances of KArGO-linked residues, validated by comparison to the crystal structures of the model proteins. The structural compatibility rate, the proportion of cross-linked K–R pairs within the maximum distance restraint imposed by KArGO (32.2 Å), is 85.5%. See source data file for the calculated distance of each K–R pair
