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  • Zheng, Y. & Cantley, L. C. Toward a better understanding of folate metabolism in health and disease. J. Exp. Med. 216, 253–266 (2019).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Clare, C. E., Brassington, A. H., Kwong, W. Y. & Sinclair, K. D. One-carbon metabolism: linking nutritional biochemistry to epigenetic programming of long-term development. Annu. Rev. Anim. Biosci. 7, 263–287 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hou, Z. & Matherly, L. H. Biology of the major facilitative folate transporters SLC19A1 and SLC46A1. Curr. Top. Membr. 73, 175–204 (2014).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Matherly, L. H., Hou, Z. & Deng, Y. Human reduced folate carrier: translation of basic biology to cancer etiology and therapy. Cancer Metastasis Rev. 26, 111–128 (2007).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • O’Connor, C. et al. Folate transporter dynamics and therapy with classic and tumor-targeted antifolates. Sci. Rep. 11, 6389 (2021).

    PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kanarek, N. et al. Histidine catabolism is a major determinant of methotrexate sensitivity. Nature 559, 632–636 (2018).

    ADS 
    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Kobayashi, H., Takemura, Y. & Ohnuma, T. Variable expression of RFC1 in human leukemia cell lines resistant to antifolates. Cancer Lett. 124, 135–142 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Girardi, E. et al. A widespread role for SLC transmembrane transporters in resistance to cytotoxic drugs. Nat. Chem. Biol. 16, 469–478 (2020).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R. et al. Rescue of embryonic lethality in reduced folate carrier-deficient mice by maternal folic acid supplementation reveals early neonatal failure of hematopoietic organs. J. Biol. Chem. 276, 10224–10228 (2001).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Svaton, M. et al. A homozygous deletion in the SLC19A1 gene as a cause of folate-dependent recurrent megaloblastic anemia. Blood 135, 2427–2431 (2020).

    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Yang, R. et al. Sequence alterations in the reduced folate carrier are observed in osteosarcoma tumor samples. Clin. Cancer Res. 9, 837–844 (2003).

    CAS 
    PubMed 

    Google Scholar 

  • Matherly, L. H. & Hou, Z. Structure and function of the reduced folate carrier a paradigm of a major facilitator superfamily mammalian nutrient transporter. Vitam. Horm. 79, 145–184 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Yee, S. W. et al. SLC19A1 pharmacogenomics summary. Pharmacogenet. Genomics 20, 708–715 (2010).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Guo, W. et al. Mechanisms of methotrexate resistance in osteosarcoma. Clin. Cancer Res. 5, 621–627 (1999).

    CAS 
    PubMed 

    Google Scholar 

  • Luteijn, R. D. et al. SLC19A1 transports immunoreactive cyclic dinucleotides. Nature 573, 434–438 (2019).

    ADS 
    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Ritchie, C., Cordova, A. F., Hess, G. T., Bassik, M. C. & Li, L. SLC19A1 is an importer of the immunotransmitter cGAMP. Mol. Cell 75, 372–381.e5 (2019).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Alam, C., Hoque, M. T., Finnell, R. H., Goldman, I. D. & Bendayan, R. Regulation of reduced folate carrier (RFC) by vitamin D receptor at the blood-brain barrier. Mol. Pharm. 14, 3848–3858 (2017).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Hou, Z., Ye, J., Haska, C. L. & Matherly, L. H. Transmembrane domains 4, 5, 7, 8, and 10 of the human reduced folate carrier are important structural or functional components of the transmembrane channel for folate substrates. J. Biol. Chem. 281, 33588–33596 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Ganapathy, V., Smith, S. B. & Prasad, P. D. SLC19: the folate/thiamine transporter family. Pflugers Arch. 447, 641–646 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Henderson, G. B. & Zevely, E. M. Anion exchange mechanism for transport of methotrexate in L1210 cells. Biochem. Biophys. Res. Commun. 99, 163–169 (1981).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R., Gao, F. & Goldman, I. D. Reduced folate carrier transports thiamine monophosphate: an alternative route for thiamine delivery into mammalian cells. Am. J. Physiol. Cell Physiol. 282, C1512–C1517 (2002).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Goldman, I. D. The characteristics of the membrane transport of amethopterin and the naturally occurring folates. Ann. NY Acad. Sci. 186, 400–422 (1971).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R., Gao, F., Hanscom, M. & Goldman, I. D. A prominent low-pH methotrexate transport activity in human solid tumors: contribution to the preservation of methotrexate pharmacologic activity in HeLa cells lacking the reduced folate carrier. Clin. Cancer Res. 10, 718–727 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Desmoulin, S. K., Hou, Z., Gangjee, A. & Matherly, L. H. The human proton-coupled folate transporter: biology and therapeutic applications to cancer. Cancer Biol. Ther. 13, 1355–1373 (2012).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Parker, J. L. et al. Structural basis of antifolate recognition and transport by PCFT. Nature 595, 130–134 (2021).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Jansen, G. et al. Sulfasalazine is a potent inhibitor of the reduced folate carrier: implications for combination therapies with methotrexate in rheumatoid arthritis. Arthritis Rheum. 50, 2130–2139 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Straub, M. S., Alvadia, C., Sawicka, M. & Dutzler, R. Cryo-EM structures of the caspase-activated protein XKR9 involved in apoptotic lipid scrambling. Elife 10, e69800 (2021).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Chun, E. et al. Fusion partner toolchest for the stabilization and crystallization of G protein-coupled receptors. Structure 20, 967–976 (2012).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Gao, X. et al. Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 463, 828–832 (2010).

    ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Henderson, G. B. & Zevely, E. M. Affinity labeling of the 5-methyltetrahydrofolate/methotrexate transport protein of L1210 cells by treatment with an N-hydroxysuccinimide ester of [3H]methotrexate. J. Biol. Chem. 259, 4558–4562 (1984).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hou, Z., Stapels, S. E., Haska, C. L. & Matherly, L. H. Localization of a substrate binding domain of the human reduced folate carrier to transmembrane domain 11 by radioaffinity labeling and cysteine-substituted accessibility methods. J. Biol. Chem. 280, 36206–36213 (2005).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Deng, Y. et al. Role of lysine 411 in substrate carboxyl group binding to the human reduced folate carrier, as determined by site-directed mutagenesis and affinity inhibition. Mol. Pharmacol. 73, 1274–1281 (2008).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Liu, X. Y. & Matherly, L. H. Functional interactions between arginine-133 and aspartate-88 in the human reduced folate carrier: evidence for a charge-pair association. Biochem. J. 358, 511–516 (2001).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Brigle, K. E., Spinella, M. J., Sierra, E. E. & Goldman, I. D. Characterization of a mutation in the reduced folate carrier in a transport defective L1210 murine leukemia cell line. J. Biol. Chem. 270, 22974–22979 (1995).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R., Sharina, I. G. & Goldman, I. D. Pattern of mutations that results in loss of reduced folate carrier function under antifolate selective pressure augmented by chemical mutagenesis. Mol. Pharmacol. 56, 68–76 (1999).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Rothem, L. et al. Resistance to multiple novel antifolates is mediated via defective drug transport resulting from clustered mutations in the reduced folate carrier gene in human leukaemia cell lines. Biochem. J. 367, 741–750 (2002).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Tse, A., Brigle, K., Taylor, S. M. & Moran, R. G. Mutations in the reduced folate carrier gene which confer dominant resistance to 5,10-dideazatetrahydrofolate. J. Biol. Chem. 273, 25953–25960 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Gifford, A. J. et al. Role of the E45K-reduced folate carrier gene mutation in methotrexate resistance in human leukemia cells. Leukemia 16, 2379–2387 (2002).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R., Assaraf, Y. G. & Goldman, I. D. A mutated murine reduced folate carrier (RFC1) with increased affinity for folic acid, decreased affinity for methotrexate, and an obligatory anion requirement for transport function. J. Biol. Chem. 273, 19065–19071 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Jansen, G. et al. A structurally altered human reduced folate carrier with increased folic acid transport mediates a novel mechanism of antifolate resistance. J. Biol. Chem. 273, 30189–30198 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Drori, S., Jansen, G., Mauritz, R., Peters, G. J. & Assaraf, Y. G. Clustering of mutations in the first transmembrane domain of the human reduced folate carrier in GW1843U89-resistant leukemia cells with impaired antifolate transport and augmented folate uptake. J. Biol. Chem. 275, 30855–30863 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zhao, R., Assaraf, Y. G. & Goldman, I. D. A reduced folate carrier mutation produces substrate-dependent alterations in carrier mobility in murine leukemia cells and methotrexate resistance with conservation of growth in 5-formyltetrahydrofolate. J. Biol. Chem. 273, 7873–7879 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Rosowsky, A., Wright, J. E., Vaidya, C. M. & Forsch, R. A. The effect of side-chain, para-aminobenzoyl region, and B-ring modifications on dihydrofolate reductase binding, influx via the reduced folate carrier, and cytotoxicity of the potent nonpolyglutamatable antifolate Nα-(4-amino-4-deoxypteroyl)-Nδ-hemiphthaloyl-L-ornithine. Pharmacol. Ther. 85, 191–205 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Rhee, M. S., Galivan, J., Wright, J. E. & Rosowsky, A. Biochemical studies on PT523, a potent nonpolyglutamatable antifolate, in cultured cells. Mol. Pharmacol. 45, 783–791 (1994).

    CAS 
    PubMed 

    Google Scholar 

  • Furst, D. E. The rational use of methotrexate in rheumatoid arthritis and other rheumatic diseases. Br. J. Rheumatol. 36, 1196–1204 (1997).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Schroder, O. & Stein, J. Low dose methotrexate in inflammatory bowel disease: current status and future directions. Am. J. Gastroenterol. 98, 530–537 (2003).

    Article 
    PubMed 

    Google Scholar 

  • Hou, Z. et al. Dual targeting of epithelial ovarian cancer via folate receptor alpha and the proton-coupled folate transporter with 6-substituted pyrrolo[2,3-d]pyrimidine antifolates. Mol. Cancer Ther. 16, 819–830 (2017).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Aluri, S. et al. Substitutions that lock and unlock the proton-coupled folate transporter (PCFT-SLC46A1) in an inward-open conformation. J. Biol. Chem. 294, 7245–7258 (2019).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Desmoulin, S. K. et al. Targeting the proton-coupled folate transporter for selective delivery of 6-substituted pyrrolo[2,3-d]pyrimidine antifolate inhibitors of de novo purine biosynthesis in the chemotherapy of solid tumors. Mol. Pharmacol. 78, 577–587 (2010).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Drew, D., North, R. A., Nagarathinam, K. & Tanabe, M. Structures and general transport mechanisms by the major facilitator superfamily (MFS). Chem. Rev. 121, 5289–5335 (2021).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Jurrus, E. et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 27, 112–128 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 44, W344–W350 (2016).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Harris, M., Firsov, D., Vuagniaux, G., Stutts, M. J. & Rossier, B. C. A novel neutrophil elastase inhibitor prevents elastase activation and surface cleavage of the epithelial sodium channel expressed in Xenopus laevis oocytes. J. Biol. Chem. 282, 58–64 (2007).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Di Francesco, V., Di Francesco, M., Decuzzi, P., Palomba, R. & Ferreira, M. Synthesis of two methotrexate prodrugs for optimizing drug loading into liposomes. Pharmaceutics 13, 332 (2021).

    PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Goehring, A. et al. Screening and large-scale expression of membrane proteins in mammalian cells for structural studies. Nat. Protoc. 9, 2574–2585 (2014).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Shinkarev, V. P., Crofts, A. R. & Wraight, C. A. Spectral analysis of the bc1 complex components in situ: beyond the traditional difference approach. Biochim. Biophys. Acta 1757, 67–77 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Asarnow, D., Palovcak, E., Cheng, Y. UCSF pyem v0.5. Zenodo https://doi.org/10.5281/zenodo.3576630 (2019).

  • Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).

    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    CAS 
    Article 

    Google Scholar 

  • Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lee, J. et al. CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM simulations using the CHARMM36 Additive Force Field. Biophys. J. 110, 641a–641a (2016).

    ADS 
    Article 

    Google Scholar 

  • Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20, 1160–1166 (2019).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Gabler, F. et al. Protein sequence analysis using the MPI Bioinformatics Toolkit. Curr. Protoc. Bioinformatics 72, e108 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Jo, S., Kim, T. & Im, W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS ONE 2, e880 (2007).

    ADS 
    PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Tian, C. et al. ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. J. Chem. Theory Comput. 16, 528–552 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • He, X., Man, V. H., Yang, W., Lee, T. S. & Wang, J. A fast and high-quality charge model for the next generation general AMBER force field. J. Chem. Phys. 153, 114502 (2020).

    ADS 
    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Case, D. A. et al. AMBER 2021 (Univ. California, 2021).

  • Gotz, A. W. et al. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. J. Chem. Theory Comput. 8, 1542–1555 (2012).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Salomon-Ferrer, R., Gotz, A. W., Poole, D., Le Grand, S. & Walker, R. C. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J. Chem. Theory Comput. 9, 3878–3888 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lee, J. et al. CHARMM-GUI supports the Amber force fields. J. Chem. Phys. 153, 035103 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Hopkins, C. W., Le Grand, S., Walker, R. C. & Roitberg, A. E. Long-time-step molecular dynamics through hydrogen mass repartitioning. J. Chem. Theory Comput. 11, 1864–1874 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Gao, Y. et al. CHARMM-GUI supports hydrogen mass repartitioning and different protonation states of phosphates in lipopolysaccharides. J. Chem. Inf. Model. 61, 831–839 (2021).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar 

  • Darden, T., York, D. & Pedersen, L. Particle mesh Ewald – an N.Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).

    ADS 
    CAS 
    Article 

    Google Scholar 

  • Roe, D. R. & Cheatham, T. E. 3rd PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084–3095 (2013).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Kaufman, Y., Ifergan, I., Rothem, L., Jansen, G. & Assaraf, Y. G. Coexistence of multiple mechanisms of PT523 resistance in human leukemia cells harboring 3 reduced folate carrier alleles: transcriptional silencing, inactivating mutations, and allele loss. Blood 107, 3288–3294 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Kaufman, Y. et al. Reduced folate carrier mutations are not the mechanism underlying methotrexate resistance in childhood acute lymphoblastic leukemia. Cancer 100, 773–782 (2004).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Roy, K., Tolner, B., Chiao, J. H. & Sirotnak, F. M. A single amino acid difference within the folate transporter encoded by the murine RFC-1 gene selectively alters its interaction with folate analogues. Implications for intrinsic antifolate resistance and directional orientation of the transporter within the plasma membrane of tumor cells. J. Biol. Chem. 273, 2526–2531 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 



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