Table 1.
Values of the chloroquine cellular accumulation ratio in sensitive and resistant strains, in the presence and absence of FCCP, as estimated from figures 1A and 2A in Bray et al [29].
Table 2.
List of abbreviations used throughout the paper.
Table 3.
Values of the parameters used throughout the paper.
Figure 1.
Summary of the hypotheses analysed throughout the manuscript.
The columns refer to the mode of binding of the chloroquine to HM, the rows to mutated PfCRT, considering the possibility that the latter is a channel or an active carrier. Shaded cells correspond to combination of hypotheses inconsistent with the analysed data.
Figure 2.
Graphical representation of the results of the analytical model in comparison with the experimental data.
A) Computed values for the pH of the vacuole in the hypothesis that the concentration of the complex of HM with the indicated CQ species linearly increases with the concentration of the ligand (first four columns) or that the system is at saturation (last column). ALL refers to either CQ, CQ+, CQ++, CQTOT. Orange shaded area indicates the range of experimental values and their uncertainty measured by different authors in different experiments. As described in the text, the calculation only uses the CAR for sensitive strains (experiments A and B in Table 1) and therefore does not require any hypothesis on the nature of the mutated PfCRT. B) Computed values of the CAR compared with observed values obtained in experiment D (see Table 1). The different hypotheses are shown in the table at the bottom. The first row refers to the cells of the table in Figure 1. The second row reports the tested hypotheses on the mechanism of PfCRT (channel or carrier), on whether the binding of PfCRT with the indicated species is in the linear regime (linear) or at saturation (saturated) and on the protonation state of the transported molecule (CQ: neutral; CQ+: mono-protonated; CQ++: di-protonated). The third row refers to the tested hypotheses for the binding of the listed chloroquine species (CQ, CQ+, CQ++ or CQTOT; ALL refers to either CQ, CQ+, CQ++, CQTOT.) with HM in the hypotheses that the latter complex is at saturation or in the linear regime. Grey shaded cells indicate that the computed values are incompatible with the experimental ones. The orange shaded area indicates the range of experimental values and their experimental error. Dashed arrows indicate that the model provides an upper limit for the value. Question marks indicate that no conclusion can be derived using the indicated combination of hypotheses.
Figure 3.
Alignment between the PfCRT family and the DUF914 family.
Profile-profile alignment of PfCRT homologs (see Materials and Methods) and the Pfam family DUF914, a member of the DMY clan. Residues are colored according to their physico-chemical properties (green = hydrophobic, red = negatively charged, blue = positively charged, pink = polar, white = small, yellow = cysteine, gray = proline, orange = histidine). The image was generated using the MPI Bioinformatics Toolkit [52].
Figure 4.
The model of the transmembrane region of PfCRT.
Residues K76 (left side) and S163 (right side) are shown in red using a stick representation.
Figure 5.
Sequence alignment between the target PfCRT protein sequence and the sequence of the template (1PW4) as obtained by Phyre.