Minimum distance measurements and mapping of significant LiP-MS peptides to structures of other putative MIPS2673-interacting proteins. Related to Fig. 5.
Distance measurement analyses were performed for other putative MIPS2673-interacting proteins identified with thermal stability proteomics and LiP-MS (experiment one) where a protein structure was available and significant LiP-MS peptides were identified. Only peptides detected in both LiP-MS experiments were considered for analysis. Significant LiP peptides were defined as any peptide that passed the relative abundance (absolute fold-change >1.5), statistical significance (q<0.01) and proteolytic peptide pattern (i.e. increased fully tryptic or decreased half tryptic) filters at any concentration in both LiP-MS experiments. For the metalloproteins PfA-M17, PfAPP and PfADA (PDB: 7RIE, 5JR6 and 6II7, respectively) the active site metal ions were used as a reference point for minimum distance measurements. For PfMIF (PDB: 4P7S), the bound ligand 20K, and TRXR1 (PDB: 2ZZC), the bound ligands FAD and NADP, were used for minimum distance measurements. For RAB39A, which is not a metalloprotein and where no ligand-bound structure is available, the GTP binding site residues (blue) were used (AlphaFold: AF-Q14964-F1). Significant LiP-MS peptides are in pink, metal ions are in light blue and ligands are in dark blue or orange (NADP only). Peptide mapping for multimeric proteins was performed for one chain only (chain A for PfA-M17, PfAPP and TRXR1 and chain B for PfMIF). The putative PfApiAP2 transcription factor, PF3D7_1239200, was excluded as no protein structure is available and the AlphaFold predicted structure is of very low quality (pLDDT score 36.67). No peptides met the significance criteria for PfA-M18 and the conserved parasite proteins, PF3D7_1026000 and PF3D7_0604300. * p < 0.05, Mann-Whitney test. For RAB39A and TRXR1, where only one significant LiP-MS peptide was identified per protein, statistical significance was not determined