Affinage · Plasmodium

FKBP35

PF3D7_1247400 · peptidyl-prolyl cis-trans isomerase FKBP35

Annotated
2026-09-08
25 papers in source corpus 18 papers cited in narrative 20 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

FKBP35 (PF3D7_1247400) is an essential Plasmodium chaperone-immunophilin that couples peptidyl-prolyl cis-trans isomerase activity to protein-folding and regulatory functions required for parasite viability (PMID:15850699, PMID:15664653, PMID:37934560). Recombinant P. falciparum FKBP35 possesses both PPIase and chaperone (protein-folding) activities that are inhibited by ascomycin and rapamycin but not by cyclosporin A, placing it firmly in the FKBP family (PMID:15850699, PMID:15664653). The protein is bipartite: an FK506-binding domain (FKBD) that carries the catalytic PPIase machinery and binds FK506, rapamycin, and small-molecule inhibitors with high affinity (PMID:17289400, PMID:18465874, PMID:26057671), and a tetratricopeptide-repeat (TPR) domain that mediates dimerization and directly engages the Hsp90 C-terminal MEEVD pentapeptide through carboxylate-clamp residues (PMID:19691130). FKBP35 also inhibits parasite calcineurin phosphatase activity basally, an effect that is FK506-independent but enhanced by FK506 and that requires the FKBD, with the TPR domain augmenting calcineurin binding (PMID:15850699, PMID:15664653, PMID:17289400, PMID:31120120). Genetic depletion of FKBP35 is lethal and produces a delayed-death-like phenotype of defective ribosome homeostasis and stalled protein synthesis, defining its cellular role in translational/proteostatic homeostasis (PMID:37934560). Crystallographic and NMR analyses of the FKBD identify Cys106 as a non-canonical residue adjacent to the drug-binding pocket that enables selective covalent inhibitor targeting, supporting FKBP35 as an antimalarial target (PMID:18465874, PMID:26057671, PMID:33209191), although cellular thermal shift data indicate that FK506's antiproliferative activity operates largely through targets beyond FKBP35 itself (PMID:37934560).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2005 High

    Establishing that the P. falciparum gene product is a bona fide FKBP-family enzyme was the necessary first step, distinguishing it functionally from cyclophilins and defining its drug sensitivity profile.

    Evidence Recombinant protein PPIase and chaperone assays with FK506-class and cyclosporin drug inhibition, replicated in two concurrent papers

    PMID:15664653 PMID:15850699

    Open questions at the time
    • In vitro substrate specificity in the parasite not defined
    • Physiological folding clients unidentified
  2. 2005 High

    Showing FKBP35 inhibits calcineurin phosphatase without requiring FK506 raised the question of whether the immunophilin regulates a parasite phosphatase pathway directly.

    Evidence In vitro phosphatase assay with purified plasmodial calcineurin and recombinant FKBP35

    PMID:15664653 PMID:15850699

    Open questions at the time
    • Whether the FKBP35-calcineurin interaction occurs in vivo not shown
    • Localization data indicate no co-localization with calcineurin
  3. 2005 Medium

    Localization and Hsp90-association findings began to place FKBP35 in a chaperone network and cast doubt on a direct calcineurin regulatory role in the cell.

    Evidence Immunofluorescence across intra-erythrocytic stages; TPR-domain association assay; geldanamycin/ascomycin synergy growth assay

    PMID:15850699

    Open questions at the time
    • Nucleocytoplasmic shuttling trigger unknown
    • FKBP35 does not co-localize with calcineurin, leaving the phosphatase inhibition context unresolved
  4. 2005 Medium

    Testing FK520 analogues that dissociate PPIase from chaperone inhibition asked which enzymatic activity underlies the antimalarial effect.

    Evidence In vitro PPIase and chaperone assays with multiple structurally distinct compounds plus growth inhibition

    PMID:15776382

    Open questions at the time
    • Single lab
    • Direct in-parasite target engagement not established at this stage
  5. 2008 High

    Structural determination of the FKBD in complex with FK506 revealed parasite-specific pocket residues (Cys106, Ser109) that diverge from human FKBP12, opening a route to selective inhibitor design.

    Evidence X-ray crystallography at 2.35 A plus NMR of ligand-induced conformational changes; solution NMR structure of the isolated FKBD

    PMID:17876830 PMID:18465874

    Open questions at the time
    • Full-length domain architecture not crystallized
    • Functional consequence of divergent residues not tested here
  6. 2009 High

    Structural and biochemical dissection of the TPR domain established the molecular basis for direct Hsp90 recruitment via carboxylate-clamp binding to the MEEVD motif.

    Evidence TPR-domain crystal structure with SPR, NMR binding, and clamp-residue mutagenesis abolishing Hsp90 binding

    PMID:19691130

    Open questions at the time
    • Functional consequence of Hsp90 binding for chaperone clients not defined
    • Stoichiometry of the FKBP35-Hsp90 assembly unresolved
  7. 2013 High

    Substrate-bound and inhibitor-bound FKBD structures in Plasmodium orthologs pinned down catalytic contact residues and demonstrated that PPIase-targeting chemotypes arrest parasite growth stage-specifically.

    Evidence X-ray structures of PvFKBP35 with tetrapeptide substrate and of Pf/Pv FKBD with D44 and adamantyl inhibitors; PPIase assays, mutagenesis (Y100), and stage-specific growth inhibition

    PMID:23435727 PMID:23974147 PMID:24900611

    Open questions at the time
    • P. vivax catalytic residues inferred to apply to PfFKBP35 by homology, not directly tested in Pf
    • Endogenous substrate identity unknown
  8. 2015 Medium

    Identification of histones as FKBP35 interactors introduced a candidate nuclear/gene-regulatory function consistent with its stage-specific nuclear shuttling.

    Evidence Co-immunoprecipitation and yeast two-hybrid screening in P. falciparum

    PMID:26156578

    Open questions at the time
    • No functional readout linking FKBP35 to gene expression
    • Specific histone(s) and modification context not defined
  9. 2015 High

    Rapamycin-bound FKBD structures confirmed a shared binding site with FK506 and positioned Cys106 within reach of bound ligand, reinforcing the covalent-targeting hypothesis.

    Evidence Two crystal structures (oxidized and reduced) of PfFKBD-rapamycin complex

    PMID:26057671

    Open questions at the time
    • Reactivity of Cys106 not directly demonstrated in this study
    • Selectivity over human FKBPs not quantified here
  10. 2017 Medium

    Comparing FK506 and rapamycin action and re-examining calcineurin inhibition argued against calcineurin as the antimalarial mechanism and refocused attention on FKBP35 itself as the target.

    Evidence P. falciparum stage-specificity and drug-interaction assays plus calcineurin phosphatase assays under varied conditions

    PMID:28274284

    Open questions at the time
    • Single lab
    • Did not genetically prove FKBP35 dependence
  11. 2018 High

    Domain-deletion and mutagenesis analysis in P. knowlesi partitioned FKBP35 functions: FKBD carries catalysis and calcineurin inhibition, while the TPRD drives dimerization and enhances calcineurin binding.

    Evidence Recombinant domain expression, PPIase assays, mutagenesis of catalytic residues, oligomerization analysis, and calcineurin inhibition assays in P. knowlesi

    PMID:31120120

    Open questions at the time
    • P. knowlesi assignments not directly reproduced in PfFKBP35
    • In-cell relevance of dimerization not tested
  12. 2020 High

    Targeted covalent inhibitors demonstrated that Cys106 can be selectively modified and that FKBP35 is engaged in living blood-stage parasites, validating the covalent chemistry predicted by the structures.

    Evidence Covalent inhibitor synthesis, mass spectrometry of C106 modification, cellular target engagement, and blood-stage growth inhibition

    PMID:33209191

    Open questions at the time
    • On-target contribution to killing not fully separated from off-target effects
    • Downstream consequences of FKBD inhibition not mapped
  13. 2023 High

    Conditional genetic depletion resolved the essentiality question and revealed the cellular process FKBP35 supports, while CETSA reframed FK506's mechanism as largely FKBP35-independent.

    Evidence Conditional knockdown with delayed-death phenotyping, ribosome/translation assays, and cellular thermal shift assay in P. falciparum

    PMID:37934560

    Open questions at the time
    • Molecular link between FKBP35 and ribosome homeostasis unresolved
    • Identity of FK506 targets beyond FKBP35 not determined
  14. 2026 Medium

    Quantitative binding analysis in P. knowlesi confirmed TPRD-exclusive MEEVD engagement and showed Hsp90 binding does not alter PPIase activity, clarifying functional independence of the two domains.

    Evidence SPR MEEVD binding (KD ~55 uM), PPIase assays, CD, and domain/CBM-deletion variants in P. knowlesi

    PMID:42376286

    Open questions at the time
    • Data paper without extensive functional follow-up
    • Function of the calmodulin-binding motif not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • The endogenous PPIase/chaperone substrates of FKBP35 and the molecular basis for its requirement in ribosome homeostasis and protein synthesis remain undefined.
  • No physiological folding client identified
  • Mechanistic link between FKBP35 loss and stalled translation not established
  • Functional significance of histone interaction and nuclear shuttling unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification
Partners
CALCINEURIN (PROTEIN PHOSPHATASE 2B)HSP90 (C-TERMINAL MEEVD PENTAPEPTIDE)PARASITE HISTONES
Complex memberships
FKBP35 homodimer (TPR domain-mediated)FKBP35-Hsp90 (via TPR domain-MEEVD interaction)

Evidence

Reading pass · 20 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 Recombinant FKBP35 from P. falciparum exhibits PPIase activity and protein-folding (chaperone) activity in vitro; both activities are inhibited by ascomycin and rapamycin but not by cyclosporin A, confirming membership in the FKBP family. Recombinant protein expression in bacteria; in vitro PPIase activity assay; in vitro chaperone/protein-folding assay; drug inhibition studies Molecular and biochemical parasitology High 15664653 15850699
2005 FKBP35 inhibits purified P. falciparum calcineurin (protein phosphatase 2B) phosphatase activity in the absence of FK506, demonstrating a drug-independent calcineurin-inhibitory activity. In vitro phosphatase activity assay using purified plasmodial calcineurin and recombinant FKBP35 Molecular and biochemical parasitology High 15664653 15850699
2005 FKBP35 undergoes stage-specific nucleocytoplasmic shuttling in P. falciparum but does not co-localize with calcineurin inside the parasite cell. Subcellular localization by immunofluorescence/co-localization microscopy across intra-erythrocytic stages Molecular and biochemical parasitology Medium 15850699
2005 FKBP35 associates with P. falciparum Hsp90 via its TPR domain; geldanamycin (Hsp90 inhibitor) and ascomycin synergistically inhibit P. falciparum growth. Co-association/interaction assay (reported as association); drug synergy growth assay in culture Molecular and biochemical parasitology Medium 15850699
2005 FK520 and non-immunosuppressive FK520 analogues inhibit both the PPIase and chaperone activities of recombinant PfFKBP35 in vitro and inhibit parasite growth; compounds that do not inhibit PPIase activity still inhibit chaperone activity, suggesting the antimalarial effect may be mediated via chaperone inhibition rather than PPIase inhibition. In vitro PPIase activity assay; in vitro chaperone activity assay; P. falciparum culture growth inhibition assay The Journal of infectious diseases Medium 15776382
2006 Full-length PfFKBP35 inhibits calcineurin phosphatase activity basally; the presence of FK506 greatly enhances this calcineurin-inhibitory activity. The FKBD binds FK506 with high affinity as shown by NMR. In vitro phosphatase activity assay; NMR ligand-binding studies Protein expression and purification Medium 17289400
2008 Crystal structure of the FK506-binding domain of PfFKBP35 in complex with FK506 at 2.35 Å resolution reveals structural differences in the β5–β6 segment and identifies Cys-106 and Ser-109 (substituting His-87 and Ile-90 in human FKBP12) near the FK506 binding site; NMR shows conformational changes in aromatic residues shaping the binding pocket upon ligand binding. X-ray crystallography at 2.35 Å; NMR spectroscopy Biochemistry High 18465874
2008 Solution NMR structure of the FK506-binding domain of PfFKBP35 was determined, providing structural characterization of the isolated FKBD in solution. NMR spectroscopy (solution structure determination) Proteins Medium 17876830
2009 Crystal structure of the TPR domain of PfFKBP35 was determined; it interacts directly with the Hsp90 C-terminal pentapeptide MEEVD. Surface plasmon resonance and NMR binding studies confirmed this interaction. Mutagenesis of positively charged clamp residues critical for carboxylate-clamping of Hsp90 abolished Hsp90 binding, identifying specific residues essential for the interaction. X-ray crystallography; surface plasmon resonance; NMR binding studies; site-directed mutagenesis Protein science : a publication of the Protein Society High 19691130
2010 The FK506-binding domain of P. vivax FKBP35 (PvFKBP35) was structurally determined by NMR (apo form) and X-ray crystallography (FK506 complex); it exhibits a canonical FKBD fold and shares kinetic PPIase profiles similar to those of PfFKBP35, with differences in ligand-binding mode relative to human FKBP12. NMR spectroscopy (apo structure); X-ray crystallography (FK506 complex); PPIase kinetic assays Protein science : a publication of the Protein Society High 20572013
2013 Crystal structures of the FK506-binding domains of PfFKBP35 and PvFKBP35 in complex with the novel small-molecule inhibitor D44 were determined; D44 modulates the PPIase activity of FKBP35 and inhibits P. falciparum growth in a stage-specific manner. X-ray crystallography; in vitro PPIase activity assay; P. falciparum growth inhibition assay (stage-specific) Scientific reports High 23974147
2013 Crystal structure of PvFKBP35 FKBD in complex with tetrapeptide substrate sALPFp at 1.65 Å reveals substrate binds in cis conformation; NMR chemical shift perturbations identify D55, H67, V73, and I74 as contact residues; mutagenesis identifies Y100 as a key catalytic residue for PPIase activity. X-ray crystallography at 1.4 Å (apo) and 1.65 Å (substrate complex); NMR chemical shift perturbation; site-directed mutagenesis with PPIase activity assay Eukaryotic cell High 23435727
2013 Adamantyl derivatives (SRA/4a and analogues) inhibit PfFKBP35 FKBD PPIase activity at submicromolar concentrations and inhibit P. falciparum 3D7 growth in a stage-specific manner, with activity concentrated at the trophozoite stage; crystal structure of PvFKBD35 in complex with SRA provides structural basis for selective inhibition. In vitro PPIase inhibition assay; P. falciparum culture growth inhibition; X-ray crystallography of PvFKBD35-SRA complex ACS medicinal chemistry letters High 24900611
2015 PfFKBP35 interacts with parasite histones in P. falciparum, as identified by co-immunoprecipitation and yeast two-hybrid screening, suggesting a possible role in modulating gene expression. Co-immunoprecipitation; yeast two-hybrid screening Parasitology Medium 26156578
2015 Two crystal structures of rapamycin in complex with the FK506-binding domain of PfFKBP35 (oxidized and reduced forms) reveal the same binding-site residues as FK506, with Cys106 4–5 Å from the bound rapamycin, and structural differences from human FKBP12 in the β4–β6 segment. X-ray crystallography (two structures of PfFKBD–rapamycin complex) Acta crystallographica. Section D, Biological crystallography High 26057671
2017 FK506 and rapamycin act indistinguishably on P. falciparum in culture (same stage-specificity, killing kinetics, and drug interactions), and PfFKBP35's calcineurin-inhibitory activity is independent of FK506 under a range of conditions, making it unlikely that calcineurin inhibition is the mechanism of FK506 antimalarial action; the findings support FKBP35 itself as the relevant antimalarial target. P. falciparum culture growth/stage-specificity assays; drug interaction experiments; in vitro calcineurin phosphatase assay under varied conditions Parasitology Medium 28274284
2018 In P. knowlesi, FKBP35 PPIase activity is confined to the FKBD; the TPRD is essential for dimerization; Asp55, Arg60, Trp77 and Phe117 in the FKBD are important for catalysis (significant PPIase activity reduction upon mutation); inhibition of calcineurin requires the FKBD, while the TPRD enhances calcineurin binding efficiency. Recombinant domain expression; in vitro PPIase activity assay; site-directed mutagenesis; oligomerization analysis; calcineurin phosphatase inhibition assay Protein engineering, design & selection : PEDS High 31120120
2020 Targeted covalent inhibitors of PfFKBP35 selectively and covalently modify C106 (adjacent to the rapamycin binding pocket), directly bind FKBP35 in a cellular setting, and exhibit antiplasmodium activity in blood-stage cultured parasites. Covalent inhibitor synthesis; mass spectrometry-based covalent modification confirmation; cell-based target engagement assay; P. falciparum blood-stage growth inhibition assay ACS medicinal chemistry letters High 33209191
2023 Genetic depletion of PfFKBP35 is lethal to P. falciparum and produces a delayed death-like phenotype characterized by defective ribosome homeostasis and stalled protein synthesis, establishing FKBP35 as essential for parasite viability. Furthermore, cellular thermal shift assays suggest FK506 exerts its antiproliferative activity in a PfFKBP35-independent manner, identifying putative FK506 targets beyond PfFKBP35. Conditional knockdown/depletion (genetic validation); cellular thermal shift assay (CETSA); ribosome/translation assays eLife High 37934560
2026 In P. knowlesi, FL-FKBP35 binds the Hsp90 C-terminal MEEVD pentapeptide via its TPRD (KD ~55 µM by SPR); the FKBD alone shows no detectable MEEVD binding; MEEVD binding does not significantly affect PPIase activity. A calmodulin-binding motif deletion variant (del-CBM) retains PPIase activity comparable to full-length. Surface plasmon resonance; in vitro PPIase activity assay; circular dichroism; recombinant domain expression Data in brief Medium 42376286

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 The FK506-binding protein of the malaria parasite, Plasmodium falciparum, is a FK506-sensitive chaperone with FK506-independent calcineurin-inhibitory activity. Molecular and biochemical parasitology 56 15850699
2005 A Plasmodium falciparum FK506-binding protein (FKBP) with peptidyl-prolyl cis-trans isomerase and chaperone activities. Molecular and biochemical parasitology 51 15664653
2005 Antimalarial effects of macrolactones related to FK520 (ascomycin) are independent of the immunosuppressive properties of the compounds. The Journal of infectious diseases 31 15776382
2008 Crystal structure of the FK506 binding domain of Plasmodium falciparum FKBP35 in complex with FK506. Biochemistry 27 18465874
2013 Small molecule Plasmodium FKBP35 inhibitor as a potential antimalaria agent. Scientific reports 26 23974147
2010 NMR and crystallographic structures of the FK506 binding domain of human malarial parasite Plasmodium vivax FKBP35. Protein science : a publication of the Protein Society 24 20572013
2009 Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide. Protein science : a publication of the Protein Society 23 19691130
2014 Co-chaperones of Hsp90 in Plasmodium falciparum and their concerted roles in cellular regulation. Parasitology 17 24560171
2013 Structural insights into substrate binding by PvFKBP35, a peptidylprolyl cis-trans isomerase from the human malarial parasite Plasmodium vivax. Eukaryotic cell 17 23435727
2008 Solution structure of FK506 binding domain (FKBD) of Plasmodium falciparum FK506 binding protein 35 (PfFKBP35). Proteins 16 17876830
2006 Expression, purification, and molecular characterization of Plasmodium falciparum FK506-binding protein 35 (PfFKBP35). Protein expression and purification 16 17289400
2013 Adamantyl derivative as a potent inhibitor of Plasmodium FK506 binding protein 35. ACS medicinal chemistry letters 15 24900611
2020 Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35. ACS medicinal chemistry letters 12 33209191
2015 Two crystal structures of the FK506-binding domain of Plasmodium falciparum FKBP35 in complex with rapamycin at high resolution. Acta crystallographica. Section D, Biological crystallography 11 26057671
2017 The antimalarial action of FK506 and rapamycin: evidence for a direct effect on FK506-binding protein PfFKBP35. Parasitology 10 28274284
2015 Immunophilin-protein interactions in Plasmodium falciparum. Parasitology 10 26156578
2009 NMR assignments of the FK506-binding domain of FK506-binding protein 35 from Plasmodium vivax. Biomolecular NMR assignments 10 19774494
2023 Genetic validation of PfFKBP35 as an antimalarial drug target. eLife 9 37934560
2015 Computational insights into the suicide inhibition of Plasmodium falciparum Fk506-binding protein 35. Bioorganic & medicinal chemistry letters 6 26091727
2022 Structural insights into Plasmodium PPIases. Frontiers in cellular and infection microbiology 4 36118020
2018 Expression and characterization of functional domains of FK506-binding protein 35 from Plasmodium knowlesi. Protein engineering, design & selection : PEDS 4 31120120
2015 Molecular docking study of macrocycles as Fk506-binding protein inhibitors. Journal of molecular graphics & modelling 4 25978804
2020 Understanding the potency of malarial ligand (D44) in plasmodium FKBP35 and modelled halogen atom (Br, Cl, F) functional groups. Journal of molecular graphics & modelling 3 32035313
2007 1H, 13C, and 15N resonance assignments of FK506-binding domain of Plasmodium falciparum FKBP35. Biomolecular NMR assignments 1 19636818
2026 Data sets on the interaction of FKBP35 from Plasmodium knowlesi and Hsp90 C-terminal pentapeptide. Data in brief 0 42376286