Fig. 4: Molecular effects of CBQ treatment revealed by thermal PISA, integrated cell montages and quantitative proteomics.

a, Graph of percentages of EF-bound states in CBQ-treated and DMSO control parasites, across four time points and four technical replicates. Percentages are based on total identified ribosomes after particle curation (n = 230,471). b, Volcano plot of differential abundance of soluble proteins in parasites treated with CBQ, relative to the DMSO vehicle control. Each protein is represented as a function of the log₂ fold change (x axis) and −log₁₀ P value (y axis) based on moderated t-test analysis carried out for each gradient independently. Hit selection cutoffs of P < 0.01 and a log₂ fold change of >0.2 are represented by dashed lines. Drug-stabilized proteins, red; destabilized proteins, blue; proteins exhibiting no significant (NS) abundance change, gray. c, Relative soluble protein abundance of eEF2 and eEF1α identified in a. Protein abundance under CBQ treatment is plotted relative to the DMSO vehicle in each respective thermal gradient (n = 4 biological replicates). Significance changes (moderated t-test) are represented by asterisks (**P < 0.01 and ***P < 0.001). eEF2, P = 0.00037; eEF1α, P = 0.000064. Error bars represent the s.d. d, Integrated cell montage of a CBQ-treated parasite frozen, milled and imaged at 18 h after treatment. Segmented features are color-coded as indicated by corresponding colored labels. Mapped back ribosomes are colored as follows: orange, monomers; pale yellow, dimers and polysomes; red, membrane-bound ribosomes. e, Volcano plot of differentially expressed proteins in CBQ-treated parasites comparing 36 h to 18 h after treatment (52 versus 38 hpi). The mean average of each protein from three replicates (n = 3) is shown. The y axes show the log₁₀ P value and x axes show the log₂ fold change using a nested study design. Blue and red circles indicate proteins with significant change. Gray circles indicate proteins with no significant (P > 0.05) change in expression. Hit selection cutoffs of P < 0.05 and log₂ fold change > 0.1 are represented by dashed lines. f, REVIGO-generated GO enrichment analysis of enriched proteins in CBQ-treated parasites at 36 h compared to 18 h. Bars are colored by REVIGO-designated cluster. A one-way ANOVA and pairwise comparison were used to compare each condition. The y axes represent the log₁₀ number of annotated GO terms in P. falciparum. Each bar represents a subcluster.