1
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Bai M, Shen Q, Wu Y, Ma Z, Wang Y, Chen M, Liu D, Zhou L. Evaluation of transport mechanisms of methotrexate in human choriocarcinoma cell lines by LC-MS/MS. J Pharm Biomed Anal 2024; 247:116268. [PMID: 38823222 DOI: 10.1016/j.jpba.2024.116268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024]
Abstract
Methotrexate (MTX) is commonly prescribed as the initial treatment for gestational trophoblastic neoplasia (GTN), but MTX monotherapy may not be effective for high-risk GTN and choriocarcinoma. The cellular uptake of MTX is essential for its pharmacological activity. Thus, our study aimed to investigate the cellular pharmacokinetics and transport mechanisms of MTX in choriocarcinoma cells. For the quantification of MTX concentrations in cellular matrix, a liquid chromatography-tandem mass spectrometry method was created and confirmed initially. MTX accumulation in BeWo, JEG-3, and JAR cells was minimal. Additionally, the mRNA levels of folate receptor α (FRα) and breast cancer resistance protein (BCRP) were relatively high in the three choriocarcinoma cell lines, whereas proton-coupled folate transporter (PCFT), reduced folate carrier (RFC), and organic anion transporter (OAT) 4 were low. Furthermore, the expression of other transporters was either very low or undetectable. Notably, the application of inhibitors and small interfering RNAs (siRNAs) targeting FRα, RFC, and PCFT led to a notable decrease in the accumulation of MTX in BeWo cells. Conversely, the co-administration of multidrug resistance protein 1 (MDR1) and BCRP inhibitors increased MTX accumulation. In addition, inhibitors of OATs and organic-anion transporting polypeptides (OATPs) reduced MTX accumulation, while peptide transporter inhibitors had no effect. Results from siRNA knockdown experiments and transporter overexpression cell models indicated that MTX was not a substrate of nucleoside transporters. In conclusion, the results indicate that FRα and multiple transporters such as PCFT, RFC, OAT4, and OATPs are likely involved in the uptake of MTX, whereas MDR1 and BCRP are implicated in the efflux of MTX from choriocarcinoma cells. These results have implications for predicting transporter-mediated drug interactions and offer potential directions for further research on enhancing MTX sensitivity.
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Affiliation(s)
- Mengru Bai
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou 310006, PR China
| | - Qian Shen
- Key Laboratory for Core Technology of Generic Drug Evaluation National Medical Product Administration, Zhejiang Institute for Food and Drug Control, Hangzhou 310052, PR China
| | - Yong Wu
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou 310006, PR China
| | - Zhiyuan Ma
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou 310006, PR China
| | - Yuqing Wang
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou 310006, PR China
| | - Mingyang Chen
- Laboratory of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Dan Liu
- Shanghai AB Sciex Analytical Instrument Trading Co., Ltd, Shanghai 200050, PR China
| | - Lin Zhou
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou 310006, PR China.
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2
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Gelová Z, Ingles-Prieto A, Bohstedt T, Frommelt F, Chi G, Chang YN, Garcia J, Wolf G, Azzollini L, Tremolada S, Scacioc A, Hansen JS, Serrano I, Droce A, Bernal JC, Burgess-Brown NA, Carpenter EP, Dürr KL, Kristensen P, Geertsma ER, Štefanić S, Scarabottolo L, Wiedmer T, Puetter V, Sauer DB, Superti-Furga G. Protein Binder Toolbox for Studies of Solute Carrier Transporters. J Mol Biol 2024; 436:168665. [PMID: 38878854 DOI: 10.1016/j.jmb.2024.168665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Transporters of the solute carrier superfamily (SLCs) are responsible for the transmembrane traffic of the majority of chemical substances in cells and tissues and are therefore of fundamental biological importance. As is often the case with membrane proteins that can be heavily glycosylated, a lack of reliable high-affinity binders hinders their functional analysis. Purifying and reconstituting transmembrane proteins in their lipidic environments remains challenging and standard approaches to generate binders for multi-transmembrane proteins, such as SLCs, channels or G protein-coupled receptors (GPCRs) are lacking. While generating protein binders to 27 SLCs, we produced full length protein or cell lines as input material for binder generation by selected binder generation platforms. As a result, we obtained 525 binders for 22 SLCs. We validated the binders with a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. Finally, we demonstrated the potential applications of the binders that passed our validation pipeline in structural, biochemical, and biological applications using the exemplary protein SLC12A6, an ion transporter relevant in human disease. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family. We hope that the process will serve as blueprint for the generation of binders against the entire superfamily of SLC transporters.
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Affiliation(s)
- Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Saša Štefanić
- Nanobody Service Facility, University of Zurich, AgroVet-Strickhof, Eschikon, Switzerland
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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3
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Hou X, Lu Z, Yu T, Zhang Y, Yao Q, Zhang C, Niu Y, Liang Q. Two maize homologs of mammalian proton-coupled folate transporter, ZmMFS_1-62 and ZmMFS_1-73, are essential to salt and drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108623. [PMID: 38626656 DOI: 10.1016/j.plaphy.2024.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Folates are essential to the maintenance of normal life activities in almost all organisms. Proton-coupled folate transporter (PCFT), belonging to the major facilitator superfamily, is one of the three major folate transporter types widely studied in mammals. However, information about plant PCFTs is limited. Here, a genome-wide identification of maize PCFTs was performed, and two PCFTs, ZmMFS_1-62 and ZmMFS_1-73, were functionally investigated. Both proteins contained the typical 12 transmembrane helixes with N- and C-termini located in the cytoplasm, and were localized in the plasma membrane. Molecular docking analysis indicated their binding activity with folates via hydrogen bonding. Interference with ZmMFS_1-62 and ZmMFS_1-73 in maize seedlings through virus-induced gene silencing disrupted folate homeostasis, mainly in the roots, and reduced tolerance to drought and salt stresses. Moreover, a molecular chaperone protein, ZmHSP20, was found to interact with ZmMFS_1-62 and ZmMFS_1-73, and interference with ZmHSP20 in maize seedlings also led to folate disruption and increased sensitivity to drought and salt stresses. Overall, this is the first report of functional identification of maize PCFTs, which play essential roles in salt and drought stress tolerance, thereby linking folate metabolism with abiotic stress responses in maize.
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Affiliation(s)
- Xiaowan Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China; Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Zhiwei Lu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Taifei Yu
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, the "Double-First Class" Application Characteristic Discipline of Hunan Province (Pharmaceutical Science), Changsha Medical University, Changsha 410219, China.
| | - Yuanyuan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Quansheng Yao
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China.
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, China.
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing 100081, China; National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572000, China.
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4
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Newstead S. Future opportunities in solute carrier structural biology. Nat Struct Mol Biol 2024; 31:587-590. [PMID: 38637662 DOI: 10.1038/s41594-024-01271-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024]
Abstract
Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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5
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Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
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Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
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6
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Kaku K, Ravindra MP, Tong N, Choudhary S, Li X, Yu J, Karim M, Brzezinski M, O’Connor C, Hou Z, Matherly LH, Gangjee A. Discovery of Tumor-Targeted 6-Methyl Substituted Pemetrexed and Related Antifolates with Selective Loss of RFC Transport. ACS Med Chem Lett 2023; 14:1682-1691. [PMID: 38116433 PMCID: PMC10726441 DOI: 10.1021/acsmedchemlett.3c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
Pemetrexed and related 5-substituted pyrrolo[2,3-d]pyrimidine antifolates are substrates for the ubiquitously expressed reduced folate carrier (RFC), and the proton-coupled folate transporter (PCFT) and folate receptors (FRs) which are more tumor-selective. A long-standing goal has been to discover tumor-targeted therapeutics that draw from one-carbon metabolic vulnerabilities of cancer cells and are selective for transport by FRs and PCFT over RFC. We discovered that a methyl group at the 6-position of the pyrrole ring in the bicyclic scaffold of 5-substituted 2-amino-4-oxo-pyrrolo[2,3-d]pyrimidine antifolates 1-4 (including pemetrexed) abolished transport by RFC with modest impacts on FRs or PCFT. From molecular modeling, loss of RFC transport involves steric repulsion in the scaffold binding site due to the 6-methyl moiety. 6-Methyl substitution preserved antiproliferative activities toward human tumor cells (KB, IGROV3) with selectivity over IOSE 7576 normal ovary cells and inhibition of de novo purine biosynthesis. Thus, adding a 6-methyl moiety to 5-substituted pyrrolo[2,3-d]pyrimidine antifolates affords tumor transport selectivity while preserving antitumor efficacy.
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Affiliation(s)
- Krishna Kaku
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Manasa P. Ravindra
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Nian Tong
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Shruti Choudhary
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Xinxin Li
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Jianming Yu
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Mohammad Karim
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Madelyn Brzezinski
- Department
of Oncology, Wayne State University School
of Medicine, Detroit, Michigan 48201, United States
| | - Carrie O’Connor
- Department
of Oncology, Wayne State University School
of Medicine, Detroit, Michigan 48201, United States
| | - Zhanjun Hou
- Molecular
Therapeutics Program, Barbara Ann Karmanos
Cancer Institute, 4100 John R, Detroit, Michigan 48201, United States
- Department
of Oncology, Wayne State University School
of Medicine, Detroit, Michigan 48201, United States
| | - Larry H. Matherly
- Molecular
Therapeutics Program, Barbara Ann Karmanos
Cancer Institute, 4100 John R, Detroit, Michigan 48201, United States
- Department
of Oncology, Wayne State University School
of Medicine, Detroit, Michigan 48201, United States
- Department
of Pharmacology, Wayne State University
School of Medicine, Detroit, Michigan 48201, United States
| | - Aleem Gangjee
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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7
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Parker JL, Kato T, Kuteyi G, Sitsel O, Newstead S. Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1. Nat Struct Mol Biol 2023; 30:1786-1793. [PMID: 37482561 PMCID: PMC10643130 DOI: 10.1038/s41594-023-01039-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023]
Abstract
In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Takafumi Kato
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Oleg Sitsel
- Department of Biochemistry, University of Oxford, Oxford, UK
- Max Planck Institute of Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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8
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Zeng YC, Sobti M, Quinn A, Smith NJ, Brown SHJ, Vandenberg JI, Ryan RM, O'Mara ML, Stewart AG. Structural basis of promiscuous substrate transport by Organic Cation Transporter 1. Nat Commun 2023; 14:6374. [PMID: 37821493 PMCID: PMC10567722 DOI: 10.1038/s41467-023-42086-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
Organic Cation Transporter 1 (OCT1) plays a crucial role in hepatic metabolism by mediating the uptake of a range of metabolites and drugs. Genetic variations can alter the efficacy and safety of compounds transported by OCT1, such as those used for cardiovascular, oncological, and psychological indications. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 remain poorly understood. Here, we present cryo-EM structures of full-length human OCT1 in the inward-open conformation, both ligand-free and drug-bound, indicating the basis for its broad substrate recognition. Comparison of our structures with those of outward-open OCTs provides molecular insight into the alternating access mechanism of OCTs. We observe that hydrophobic gates stabilize the inward-facing conformation, whereas charge neutralization in the binding pocket facilitates the release of cationic substrates. These findings provide a framework for understanding the structural basis of the promiscuity of drug binding and substrate translocation in OCT1.
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Affiliation(s)
- Yi C Zeng
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Meghna Sobti
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ada Quinn
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Nicola J Smith
- School of Biomedical Sciences, Faculty of Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Simon H J Brown
- School of Chemistry and Molecular Bioscience, Molecular Horizons, and Australian Research Council Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, NSW, Australia
| | - Jamie I Vandenberg
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Molecular Cardiology and Biophysics Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Renae M Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Megan L O'Mara
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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9
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Chen K, Liao J, Patel DJ, Xie W. Advances in structure-guided mechanisms impacting on the cGAS-STING innate immune pathway. Adv Immunol 2023; 159:1-32. [PMID: 37996205 DOI: 10.1016/bs.ai.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The metazoan cGAS-STING innate immunity pathway is triggered in response to cytoplasmic double-stranded DNA (dsDNA), thereby providing host defense against microbial pathogens. This pathway also impacts on autoimmune diseases, cellular senescence and anti-tumor immunity. The cGAS-STING pathway was also observed in the bacterial antiviral immune response, known as the cyclic oligonucleotide (CDN)-based anti-phage signaling system (CBASS). This review highlights a structure-based mechanistic perspective of recent advances in metazoan and bacterial cGAS-STING innate immune signaling by focusing on the cGAS sensor, cGAMP second messenger and STING adaptor components, thereby elucidating the specificity, activation, regulation and signal transduction features of the pathway.
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Affiliation(s)
- Kexin Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Jialing Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China; School of Biomedical Engineering, Hubei University of Medicine, Shiyan, Hubei, P.R. China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, United States.
| | - Wei Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China.
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10
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Kamegawa A, Suzuki S, Suzuki H, Nishikawa K, Numoto N, Fujiyoshi Y. Structural analysis of the water channel AQP2 by single-particle cryo-EM. J Struct Biol 2023; 215:107984. [PMID: 37315821 DOI: 10.1016/j.jsb.2023.107984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/19/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Water channels, which are small membrane proteins almost entirely buried in lipid membranes, are challenging research targets for single-particle cryo-electron microscopy (cryo-EM), a powerful technique routinely used to determine the structures of membrane proteins. Because the single-particle method enables structural analysis of a whole protein with flexible parts that interfere with crystallization, we have focused our efforts on analyzing water channel structures. Here, utilizing this system, we analyzed the structure of full-length aquaporin-2 (AQP2), a primary regulator of vasopressin-dependent reabsorption of water at the renal collecting ducts. The 2.9 Å resolution map revealed a cytoplasmic extension of the cryo-EM density that was presumed to be the highly flexible C-terminus at which the localization of AQP2 is regulated in the renal collecting duct cells. We also observed a continuous density along the common water pathway inside the channel pore and lipid-like molecules at the membrane interface. Observations of these constructions in the AQP2 structure analyzed without any fiducial markers (e.g., a rigidly bound antibody) indicate that single-particle cryo-EM will be useful for investigating water channels in native states as well as in complexes with chemical compounds.
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Affiliation(s)
- Akiko Kamegawa
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Shota Suzuki
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hiroshi Suzuki
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kouki Nishikawa
- Joint Research Course for Advanced Biomolecular Characterization, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Nobutaka Numoto
- Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8501, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
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11
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Katsube S, Willibal K, Vemulapally S, Hariharan P, Tikhonova E, Pardon E, Kaback HR, Steyaert J, Guan L. In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms. J Biol Chem 2023; 299:104967. [PMID: 37380079 PMCID: PMC10374971 DOI: 10.1016/j.jbc.2023.104967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well-studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under 4 ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable supercomplex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Katleen Willibal
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Sangama Vemulapally
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Els Pardon
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - H Ronald Kaback
- Department of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jan Steyaert
- VIB Center for Structural Biology Research, VIB, Brussel, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
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12
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Zhu A, Huang J, Kong F, Tan J, Lei J, Yuan Y, Yan C. Molecular basis for substrate recognition and transport of human GABA transporter GAT1. Nat Struct Mol Biol 2023:10.1038/s41594-023-00983-z. [PMID: 37400655 DOI: 10.1038/s41594-023-00983-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 03/31/2023] [Indexed: 07/05/2023]
Abstract
γ-Aminobutyric acid (GABA), an important inhibitory neurotransmitter in the central nervous system, is recycled through specific GABA transporters (GATs). GAT1, which is mainly expressed in the presynaptic terminals of axons, is a potential drug target of neurological disorders due to its essential role in GABA transport. Here we report four cryogenic electron microscopy structures of human GAT1, at resolutions of 2.2-3.2 Å. GAT1 in substrate-free form or in complex with the antiepileptic drug tiagabine exhibits an inward-open conformation. In the presence of GABA or nipecotic acid, inward-occluded structures are captured. The GABA-bound structure reveals an interaction network bridged by hydrogen bonds and ion coordination for GABA recognition. The substrate-free structure unwinds the last helical turn of transmembrane helix TM1a to release sodium ions and substrate. Complemented by structure-guided biochemical analyses, our studies reveal detailed mechanism of GABA recognition and transport, and elucidate mode of action of the inhibitors, nipecotic acid and tiagabine.
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Affiliation(s)
- Angqi Zhu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junhao Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fang Kong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaxin Tan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jianlin Lei
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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13
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Ray S, Gaudet R. Structures and coordination chemistry of transporters involved in manganese and iron homeostasis. Biochem Soc Trans 2023; 51:897-923. [PMID: 37283482 PMCID: PMC10330786 DOI: 10.1042/bst20210699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023]
Abstract
A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
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Affiliation(s)
- Shamayeeta Ray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
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14
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Jones SA, Gogoi P, Ruprecht JJ, King MS, Lee Y, Zögg T, Pardon E, Chand D, Steimle S, Copeman DM, Cotrim CA, Steyaert J, Crichton PG, Moiseenkova-Bell V, Kunji ER. Structural basis of purine nucleotide inhibition of human uncoupling protein 1. SCIENCE ADVANCES 2023; 9:eadh4251. [PMID: 37256948 PMCID: PMC10413660 DOI: 10.1126/sciadv.adh4251] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 06/02/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) gives brown adipose tissue of mammals its specialized ability to burn calories as heat for thermoregulation. When activated by fatty acids, UCP1 catalyzes the leak of protons across the mitochondrial inner membrane, short-circuiting the mitochondrion to generate heat, bypassing ATP synthesis. In contrast, purine nucleotides bind and inhibit UCP1, regulating proton leak by a molecular mechanism that is unclear. We present the cryo-electron microscopy structure of the GTP-inhibited state of UCP1, which is consistent with its nonconducting state. The purine nucleotide cross-links the transmembrane helices of UCP1 with an extensive interaction network. Our results provide a structural basis for understanding the specificity and pH dependency of the regulatory mechanism. UCP1 has retained all of the key functional and structural features required for a mitochondrial carrier-like transport mechanism. The analysis shows that inhibitor binding prevents the conformational changes that UCP1 uses to facilitate proton leak.
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Affiliation(s)
- Scott A. Jones
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Prerana Gogoi
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, 10-124 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5158, USA
| | - Jonathan J. Ruprecht
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Martin S. King
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Yang Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Thomas Zögg
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Deepak Chand
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Danielle M. Copeman
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Camila A. Cotrim
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul G. Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Vera Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, 10-124 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5158, USA
| | - Edmund R. S. Kunji
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Keith Peters Building, Cambridge CB2 0XY, UK
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15
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Bharadwaj R, Lusi CF, Mashayekh S, Nagar A, Subbarao M, Kane GI, Wodzanowski KA, Brown AR, Okuda K, Monahan A, Paik D, Nandy A, Anonick MV, Goldman WE, Kanneganti TD, Orzalli MH, Grimes CL, Atukorale PU, Silverman N. Methotrexate suppresses psoriatic skin inflammation by inhibiting muropeptide transporter SLC46A2 activity. Immunity 2023; 56:998-1012.e8. [PMID: 37116499 PMCID: PMC10195032 DOI: 10.1016/j.immuni.2023.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/04/2023] [Accepted: 04/03/2023] [Indexed: 04/30/2023]
Abstract
Cytosolic innate immune sensing is critical for protecting barrier tissues. NOD1 and NOD2 are cytosolic sensors of small peptidoglycan fragments (muropeptides) derived from the bacterial cell wall. These muropeptides enter cells, especially epithelial cells, through unclear mechanisms. We previously implicated SLC46 transporters in muropeptide transport in Drosophila immunity. Here, we focused on Slc46a2, which was highly expressed in mammalian epidermal keratinocytes, and showed that it was critical for the delivery of diaminopimelic acid (DAP)-muropeptides and activation of NOD1 in keratinocytes, whereas the related transporter Slc46a3 was critical for delivering the NOD2 ligand MDP to keratinocytes. In a mouse model, Slc46a2 and Nod1 deficiency strongly suppressed psoriatic inflammation, whereas methotrexate, a commonly used psoriasis therapeutic, inhibited Slc46a2-dependent transport of DAP-muropeptides. Collectively, these studies define SLC46A2 as a transporter of NOD1-activating muropeptides, with critical roles in the skin barrier, and identify this transporter as an important target for anti-inflammatory intervention.
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Affiliation(s)
- Ravi Bharadwaj
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Christina F Lusi
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | - Abhinit Nagar
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Malireddi Subbarao
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Griffin I Kane
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | | | - Ashley R Brown
- Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Kendi Okuda
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amanda Monahan
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Donggi Paik
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anubhab Nandy
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - William E Goldman
- Department of Microbiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | | | - Megan H Orzalli
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | | | - Prabhani U Atukorale
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Neal Silverman
- Program in Innate Immunity and Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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16
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Xie W, Patel DJ. Structure-based mechanisms of 2'3'-cGAMP intercellular transport in the cGAS-STING immune pathway. Trends Immunol 2023; 44:450-467. [PMID: 37147228 DOI: 10.1016/j.it.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023]
Abstract
Upon activation by double-stranded DNA (dsDNA), the cytosolic dsDNA sensor cyclic GMP-AMP synthase (cGAS) synthesizes the diffusible cyclic dinucleotide 2'3'-cGAMP (cyclic GMP-AMP), which subsequently binds to the adaptor STING, triggering a cascade of events leading to an inflammatory response. Recent studies have highlighted the role of 2'3'-cGAMP as an 'immunotransmitter' between cells, a process facilitated by gap junctions as well as by specialized membrane-spanning importer and exporter channels. This review highlights recent advances from a structural perspective of intercellular trafficking of 2'3'-cGAMP, with particular emphasis on the binding of importer SLC19A1 to 2'3'-cGAMP, as well as the significance of associated folate nutrients and antifolate therapeutics. This provides a path forward for structure-guided understanding of the transport cycle in immunology, as well as for candidate targeting approaches towards therapeutic intervention in inflammation.
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Affiliation(s)
- Wei Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 311027, China; Department of Infectious Diseases, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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17
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Patel DJ, Yu Y, Xie W. cGAMP-activated cGAS-STING signaling: its bacterial origins and evolutionary adaptation by metazoans. Nat Struct Mol Biol 2023; 30:245-260. [PMID: 36894694 DOI: 10.1038/s41594-023-00933-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023]
Abstract
The metazoan cGAMP-activated cGAS-STING innate immunity pathway is triggered in response to genomic instability and DNA damage, thereby providing host defense against microbial pathogens. This pathway also impacts on autophagy, cellular senescence and antitumor immunity, while its overactivation triggers autoimmune and inflammatory diseases. Metazoan cGAS generates cGAMP containing distinct combinations of 3'-5' and 2'-5' linkages, which target the adaptor protein STING and activate the innate immune response through a signaling cascade leading to upregulation of cytokine and interferon production. This Review highlights a structure-based mechanistic perspective of recent advances in cGAMP-activated cGAS-STING innate immune signaling by focusing on the cGAS sensor, cGAMP second messenger and STING adaptor components, thereby elucidating the specificity, activation, regulation and signal transduction features of the pathway. In addition, the Review addresses progress towards identification of inhibitors and activators targeting cGAS and STING, as well as strategies developed by pathogens to evade cGAS-STING immunity. Most importantly, it highlights cyclic nucleotide second messengers as ancient signaling molecules that elicit a potent innate immune response that originated in bacteria and evolved through evolutionary adaptation to metazoans.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| | - You Yu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Wei Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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18
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Dang Y, Zhou D, Du X, Zhao H, Lee CH, Yang J, Wang Y, Qin C, Guo Z, Zhang Z. Molecular mechanism of substrate recognition by folate transporter SLC19A1. Cell Discov 2022; 8:141. [PMID: 36575193 PMCID: PMC9794768 DOI: 10.1038/s41421-022-00508-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022] Open
Abstract
Folate (vitamin B9) is the coenzyme involved in one-carbon transfer biochemical reactions essential for cell survival and proliferation, with its inadequacy causing developmental defects or severe diseases. Notably, mammalian cells lack the ability to de novo synthesize folate but instead rely on its intake from extracellular sources via specific transporters or receptors, among which SLC19A1 is the ubiquitously expressed one in tissues. However, the mechanism of substrate recognition by SLC19A1 remains unclear. Here we report the cryo-EM structures of human SLC19A1 and its complex with 5-methyltetrahydrofolate at 3.5-3.6 Å resolution and elucidate the critical residues for substrate recognition. In particular, we reveal that two variant residues among SLC19 subfamily members designate the specificity for folate. Moreover, we identify intracellular thiamine pyrophosphate as the favorite coupled substrate for folate transport by SLC19A1. Together, this work establishes the molecular basis of substrate recognition by this central folate transporter.
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Affiliation(s)
- Yu Dang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Dong Zhou
- grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaojuan Du
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China ,grid.411472.50000 0004 1764 1621Present Address: Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Hongtu Zhao
- grid.240871.80000 0001 0224 711XDepartment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Chia-Hsueh Lee
- grid.240871.80000 0001 0224 711XDepartment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Jing Yang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
| | - Yijie Wang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
| | - Changdong Qin
- grid.11135.370000 0001 2256 9319Cryo-EM Platform, School of Life Sciences, Peking University, Beijing, China
| | - Zhenxi Guo
- grid.11135.370000 0001 2256 9319Cryo-EM Platform, School of Life Sciences, Peking University, Beijing, China
| | - Zhe Zhang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
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19
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Abstract
Structural insights into a long-studied folate-transport protein provide evidence that might lead to entirely new targeted anticancer treatments, or boost the success of immunotherapy approaches to tackling tumours.
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20
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Recognition of cyclic dinucleotides and folates by human SLC19A1. Nature 2022; 612:170-176. [PMID: 36265513 DOI: 10.1038/s41586-022-05452-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022]
Abstract
Cyclic dinucleotides (CDNs) are ubiquitous signalling molecules in all domains of life1,2. Mammalian cells produce one CDN, 2'3'-cGAMP, through cyclic GMP-AMP synthase after detecting cytosolic DNA signals3-7. 2'3'-cGAMP, as well as bacterial and synthetic CDN analogues, can act as second messengers to activate stimulator of interferon genes (STING) and elicit broad downstream responses8-21. Extracellular CDNs must traverse the cell membrane to activate STING, a process that is dependent on the solute carrier SLC19A122,23. Moreover, SLC19A1 represents the major transporter for folate nutrients and antifolate therapeutics24,25, thereby placing SLC19A1 as a key factor in multiple physiological and pathological processes. How SLC19A1 recognizes and transports CDNs, folate and antifolate is unclear. Here we report cryo-electron microscopy structures of human SLC19A1 (hSLC19A1) in a substrate-free state and in complexes with multiple CDNs from different sources, a predominant natural folate and a new-generation antifolate drug. The structural and mutagenesis results demonstrate that hSLC19A1 uses unique yet divergent mechanisms to recognize CDN- and folate-type substrates. Two CDN molecules bind within the hSLC19A1 cavity as a compact dual-molecule unit, whereas folate and antifolate bind as a monomer and occupy a distinct pocket of the cavity. Moreover, the structures enable accurate mapping and potential mechanistic interpretation of hSLC19A1 with loss-of-activity and disease-related mutations. Our research provides a framework for understanding the mechanism of SLC19-family transporters and is a foundation for the development of potential therapeutics.
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21
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Matherly LH, Schneider M, Gangjee A, Hou Z. Biology and therapeutic applications of the proton-coupled folate transporter. Expert Opin Drug Metab Toxicol 2022; 18:695-706. [PMID: 36239195 PMCID: PMC9637735 DOI: 10.1080/17425255.2022.2136071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 01/19/2023]
Abstract
INTRODUCTION The proton-coupled folate transporter (PCFT; SLC46A1) was discovered in 2006 as the principal mechanism by which folates are absorbed in the intestine and the causal basis for hereditary folate malabsorption (HFM). In 2011, it was found that PCFT is highly expressed in many tumors. This stimulated interest in using PCFT for cytotoxic drug targeting, taking advantage of the substantial levels of PCFT transport and acidic pH conditions commonly associated with tumors. AREAS COVERED We summarize the literature from 2006 to 2022 that explores the role of PCFT in the intestinal absorption of dietary folates and its role in HFM and as a transporter of folates and antifolates such as pemetrexed (Alimta) in relation to cancer. We provide the rationale for the discovery of a new generation of targeted pyrrolo[2,3-d]pyrimidine antifolates with selective PCFT transport and inhibitory activity toward de novo purine biosynthesis in solid tumors. We summarize the benefits of this approach to cancer therapy and exciting new developments in the structural biology of PCFT and its potential to foster refinement of active structures of PCFT-targeted anti-cancer drugs. EXPERT OPINION We summarize the promising future and potential challenges of implementing PCFT-targeted therapeutics for HFM and a variety of cancers.
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Affiliation(s)
- Larry H. Matherly
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Mathew Schneider
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Zhanjun Hou
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan 48201, United States
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
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22
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Wright NJ, Fedor JG, Zhang H, Jeong P, Suo Y, Yoo J, Hong J, Im W, Lee SY. Methotrexate recognition by the human reduced folate carrier SLC19A1. Nature 2022; 609:1056-1062. [PMID: 36071163 DOI: 10.1038/s41586-022-05168-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/01/2022] [Indexed: 02/01/2023]
Abstract
Folates are essential nutrients with important roles as cofactors in one-carbon transfer reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of amino acids during cell division1,2. Mammals lack de novo folate synthesis pathways and thus rely on folate uptake from the extracellular milieu3. The human reduced folate carrier (hRFC, also known as SLC19A1) is the major importer of folates into the cell1,3, as well as chemotherapeutic agents such as methotrexate4-6. As an anion exchanger, RFC couples the import of folates and antifolates to anion export across the cell membrane and it is a major determinant in methotrexate (antifolate) sensitivity, as genetic variants and its depletion result in drug resistance4-8. Despite its importance, the molecular basis of substrate specificity by hRFC remains unclear. Here we present cryo-electron microscopy structures of hRFC in the apo state and captured in complex with methotrexate. Combined with molecular dynamics simulations and functional experiments, our study uncovers key determinants of hRFC transport selectivity among folates and antifolate drugs while shedding light on important features of anion recognition by hRFC.
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Affiliation(s)
- Nicholas J Wright
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Justin G Fedor
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Han Zhang
- Departments of Biological Sciences, Chemistry and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | | | - Yang Suo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Jiho Yoo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.,College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
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23
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Structural basis for proton coupled cystine transport by cystinosin. Nat Commun 2022; 13:4845. [PMID: 35977944 PMCID: PMC9385667 DOI: 10.1038/s41467-022-32589-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Amino acid transporters play a key role controlling the flow of nutrients across the lysosomal membrane and regulating metabolism in the cell. Mutations in the gene encoding the transporter cystinosin result in cystinosis, an autosomal recessive metabolic disorder characterised by the accumulation of cystine crystals in the lysosome. Cystinosin is a member of the PQ-loop family of solute carrier (SLC) transporters and uses the proton gradient to drive cystine export into the cytoplasm. However, the molecular basis for cystinosin function remains elusive, hampering efforts to develop novel treatments for cystinosis and understand the mechanisms of ion driven transport in the PQ-loop family. To address these questions, we present the crystal structures of cystinosin from Arabidopsis thaliana in both apo and cystine bound states. Using a combination of in vitro and in vivo based assays, we establish a mechanism for cystine recognition and proton coupled transport. Mutational mapping and functional characterisation of human cystinosin further provide a framework for understanding the molecular impact of disease-causing mutations. Mutations in CTNS, the lysosomal cystine-proton symporter, cause cystinosis. Here authors report crystal structures of CTNS from Arabidopsis thaliana in complex with cystine, and establish the mode of ligand recognition and mechanism for proton-coupled cystine export from the lysosome.
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24
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Li T, Zhou B, Li Y, Huang S, Luo Z, Zhou Y, Lai Y, Gautam A, Bourgeau S, Wang S, Bao J, Tan J, Lavillette D, Li D. Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Int J Biol Macromol 2022; 209:1379-1388. [PMID: 35460753 PMCID: PMC9020654 DOI: 10.1016/j.ijbiomac.2022.04.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 engages with human cells through the binding of its Spike receptor-binding domain (S-RBD) to the receptor ACE2. Molecular blocking of this engagement represents a proven strategy to treat COVID-19. Here, we report a single-chain antibody (nanobody, DL4) isolated from immunized alpaca with picomolar affinity to RBD. DL4 neutralizes SARS-CoV-2 pseudoviruses with an IC50 of 0.101 μg mL-1 (6.2 nM). A crystal structure of the DL4-RBD complex at 1.75-Å resolution unveils the interaction detail and reveals a direct competition mechanism for DL4's ACE2-blocking and hence neutralizing activity. The structural information allows us to rationally design a mutant with higher potency. Our work adds diversity of neutralizing nanobodies against SARS-CoV-2 and should encourage protein engineering to improve antibody affinities in general.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Bingjie Zhou
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Yaning Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Suqiong Huang
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,College of Pharmacy, Chongqing Medical University, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yuanze Zhou
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China,University of CAS, Beijing 101408, China
| | - Anupriya Gautam
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China
| | - Salome Bourgeau
- University of CAS, Beijing 101408, China,CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China,Institut National de la Santé et de la Recherche Médicale, École des Hautes Etudes en Santé Publique, Institut de Recherche en Santé, Environnement et Travail, Université de Rennes, F-35000 Rennes, France
| | - Shurui Wang
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China
| | - Jingquan Tan
- Nanjing Crycision Biotech Co., Ltd., Nanjing, China
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, 320 Yueyang Road, Shanghai 200031, China; Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai 200030, China.
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25
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Zhang M, Liu G, Zhang Y, Chen T, Feng S, Cai R, Lu C. The Second Class of Tetrahydrofolate (THF-II) Riboswitches Recognizes the Tetrahydrofolic Acid Ligand via Local Conformation Changes. Int J Mol Sci 2022; 23:ijms23115903. [PMID: 35682583 PMCID: PMC9180208 DOI: 10.3390/ijms23115903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
Riboswitches are regulatory noncoding RNAs found in bacteria, fungi and plants, that modulate gene expressions through structural changes in response to ligand binding. Understanding how ligands interact with riboswitches in solution can shed light on the molecular mechanisms of this ancient regulators. Previous studies showed that riboswitches undergo global conformation changes in response to ligand binding to relay information. Here, we report conformation switching models of the recently discovered tetrahydrofolic acid-responsive second class of tetrahydrofolate (THF-II) riboswitches in response to ligand binding. Using a combination of selective 2′-hydroxyl acylation, analyzed by primer extension (SHAPE) assay, 3D modeling and small-angle X-ray scattering (SAXS), we found that the ligand specifically recognizes and reshapes the THF-II riboswitch loop regions, but does not affect the stability of the P3 helix. Our results show that the THF-II riboswitch undergoes only local conformation changes in response to ligand binding, rearranging the Loop1-P3-Loop2 region and rotating Loop1 from a ~120° angle to a ~75° angle. This distinct conformation changes suggest a unique regulatory mechanism of the THF-II riboswitch, previously unseen in other riboswitches. Our findings may contribute to the fields of RNA sensors and drug design.
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Affiliation(s)
- Minmin Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China;
| | - Yunlong Zhang
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Ting Chen
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Shanshan Feng
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
| | - Rujie Cai
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
| | - Changrui Lu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China; (M.Z.); (Y.Z.); (T.C.); (S.F.)
- Correspondence: (R.C.); (C.L.); Tel.: +86-21-6779-2740 (C.L.)
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26
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Giacomini KM, Yee SW, Koleske ML, Zou L, Matsson P, Chen EC, Kroetz DL, Miller MA, Gozalpour E, Chu X. New and Emerging Research on Solute Carrier and ATP Binding Cassette Transporters in Drug Discovery and Development: Outlook from the International Transporter Consortium. Clin Pharmacol Ther 2022; 112:540-561. [PMID: 35488474 PMCID: PMC9398938 DOI: 10.1002/cpt.2627] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Enabled by a plethora of new technologies, research in membrane transporters has exploded in the past decade. The goal of this state‐of‐the‐art article is to describe recent advances in research on membrane transporters that are particularly relevant to drug discovery and development. This review covers advances in basic, translational, and clinical research that has led to an increased understanding of membrane transporters at all levels. At the basic level, we describe the available crystal structures of membrane transporters in both the solute carrier (SLC) and ATP binding cassette superfamilies, which has been enabled by the development of cryogenic electron microscopy methods. Next, we describe new research on lysosomal and mitochondrial transporters as well as recently deorphaned transporters in the SLC superfamily. The translational section includes a summary of proteomic research, which has led to a quantitative understanding of transporter levels in various cell types and tissues and new methods to modulate transporter function, such as allosteric modulators and targeted protein degraders of transporters. The section ends with a review of the effect of the gut microbiome on modulation of transporter function followed by a presentation of 3D cell cultures, which may enable in vivo predictions of transporter function. In the clinical section, we describe new genomic and pharmacogenomic research, highlighting important polymorphisms in transporters that are clinically relevant to many drugs. Finally, we describe new clinical tools, which are becoming increasingly available to enable precision medicine, with the application of tissue‐derived small extracellular vesicles and real‐world biomarkers.
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Affiliation(s)
- Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Sook W Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Megan L Koleske
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Ling Zou
- Pharmacokinetics and Drug Metabolism, Amgen Inc., South San Francisco, California, USA
| | - Pär Matsson
- Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eugene C Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elnaz Gozalpour
- Drug Safety and Metabolism, IMED Biotech Unit, Safety and ADME Translational Sciences Department, AstraZeneca R&D, Cambridge, UK
| | - Xiaoyan Chu
- Department of ADME and Discovery Toxicology, Merck & Co. Inc, Kenilworth, New Jersey, USA
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27
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Konuksever D, Yücel SP. Evaluation of correlation between vitamin D with vitamin B12 and folate in children. Nutrition 2022; 99-100:111683. [DOI: 10.1016/j.nut.2022.111683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/23/2022] [Accepted: 04/02/2022] [Indexed: 02/07/2023]
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28
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Newstead S. Structural basis for recognition and transport of folic acid in mammalian cells. Curr Opin Struct Biol 2022; 74:102353. [PMID: 35303537 PMCID: PMC7612623 DOI: 10.1016/j.sbi.2022.102353] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 12/19/2022]
Abstract
Structural studies on mammalian vitamin transport lag behind other metabolites. Folates, also known as B9 vitamins, are essential cofactors in one-carbon transfer reactions in biology. Three different systems control folate uptake in the human body; folate receptors function to capture and internalise extracellular folates via endocytosis, whereas two major facilitator superfamily transporters, the reduced folate carrier (RFC; SLC19A1) and proton-coupled folate transporter (PCFT; SLC46A1) control the transport of folates across cellular membranes. Targeting specific folate transporters is being pursued as a route to developing new antifolates with improved pharmacology. Recent structures of the proton-coupled folate transporter, PCFT, revealed key insights into antifolate recognition and the mechanism of proton-coupled transport. Combined with previously determined structures of folate receptors and new predictions for the structure of the RFC, we are now able to develop a structure-based understanding of folate and antifolate recognition to accelerate efforts in antifolate drug development.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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29
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Kühlbrandt W. Forty years in cryoEM of membrane proteins. Microscopy (Oxf) 2022; 71:i30-i50. [PMID: 35275191 PMCID: PMC8855526 DOI: 10.1093/jmicro/dfab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
In a surprisingly short time, electron cryo-microscopy (cryoEM) has developed from a niche technique in structural biology to a mainstream method practiced in a rapidly growing number of laboratories around the world. From its beginnings about 40 years ago, cryoEM has had a major impact on the study of membrane proteins, in particular the energy-converting systems from bacterial, mitochondrial and chloroplast membranes. Early work on two-dimensional crystals attained resolutions ∼3.5 Å, but at present, single-particle cryoEM delivers much more detailed structures without crystals. Electron cryo-tomography of membranes and membrane-associated proteins adds valuable context, usually at lower resolution. The review ends with a brief outlook on future prospects.
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Affiliation(s)
- Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue Str. 3, Frankfurt am Main 60438, Germany
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30
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Hou Z, Gangjee A, Matherly LH. The evolving biology of the proton‐coupled folate transporter: New insights into regulation, structure, and mechanism. FASEB J 2022; 36:e22164. [PMID: 35061292 PMCID: PMC8978580 DOI: 10.1096/fj.202101704r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/15/2021] [Accepted: 01/03/2022] [Indexed: 01/19/2023]
Abstract
The human proton‐coupled folate transporter (PCFT; SLC46A1) or hPCFT was identified in 2006 as the principal folate transporter involved in the intestinal absorption of dietary folates. A rare autosomal recessive hereditary folate malabsorption syndrome is attributable to human SLC46A1 variants. The recognition that hPCFT was highly expressed in many tumors stimulated substantial interest in its potential for cytotoxic drug targeting, taking advantage of its high‐level transport activity under acidic pH conditions that characterize many tumors and its modest expression in most normal tissues. To better understand the basis for variations in hPCFT levels between tissues including human tumors, studies have examined the transcriptional regulation of hPCFT including the roles of CpG hypermethylation and critical transcription factors and cis elements. Additional focus involved identifying key structural and functional determinants of hPCFT transport that, combined with homology models based on structural homologies to the bacterial transporters GlpT and LacY, have enabled new structural and mechanistic insights. Recently, cryo‐electron microscopy structures of chicken PCFT in a substrate‐free state and in complex with the antifolate pemetrexed were reported, providing further structural insights into determinants of (anti)folate recognition and the mechanism of pH‐regulated (anti)folate transport by PCFT. Like many major facilitator proteins, hPCFT exists as a homo‐oligomer, and evidence suggests that homo‐oligomerization of hPCFT monomeric proteins may be important for its intracellular trafficking and/or transport function. Better understanding of the structure, function and regulation of hPCFT should facilitate the rational development of new therapeutic strategies for conditions associated with folate deficiency, as well as cancer.
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Affiliation(s)
- Zhanjun Hou
- Molecular Therapeutics Program Barbara Ann Karmanos Cancer Institute Detroit Michigan USA
- Department of Oncology Wayne State University School of Medicine Detroit Michigan USA
| | - Aleem Gangjee
- Division of Medicinal Chemistry Graduate School of Pharmaceutical Sciences Duquesne University Pittsburgh Pennsylvania USA
| | - Larry H. Matherly
- Molecular Therapeutics Program Barbara Ann Karmanos Cancer Institute Detroit Michigan USA
- Department of Oncology Wayne State University School of Medicine Detroit Michigan USA
- Department of Pharmacology Wayne State University School of Medicine Detroit Michigan USA
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31
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Do HQ, Jansen M. Cell-Free Expression of Proton-Coupled Folate Transporter in the Presence of Nanodiscs. Methods Mol Biol 2022; 2507:425-444. [PMID: 35773596 DOI: 10.1007/978-1-0716-2368-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proton coupled folate transporter (PCFT) is an integral membrane protein with 12 transmembrane segments localized to the plasma membrane. PCFT is the main route by which folate, vitamin B9, from dietary sources enters mammalian cells in the small intestine. Loss-of-function mutations in this membrane transport protein cause hereditary folate malabsorption, and upregulation of PCFT has been reported in cancer cells. Currently, a complete translocation mechanism of folate via PCFT is still missing. To reveal this mechanism via studies of structural architecture and structure-function relationships, soluble and stable PCFT in a phospholipid bilayer environment is needed. We therefore develop an approach to screen lipid environments in which PCFT is most soluble. Traditional in vitro expression and reconstitution into lipid bilayers of integral membrane proteins requires separate steps, which are costly and time-consuming. In this chapter, we describe a protocol for in vitro translation of PCFT into preformed lipid nanodiscs using a cell-free expression system, which helps to accelerate and reduce the cost of the sample preparation.
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Affiliation(s)
- Hoa Quynh Do
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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32
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Folate Transport and One-Carbon Metabolism in Targeted Therapies of Epithelial Ovarian Cancer. Cancers (Basel) 2021; 14:cancers14010191. [PMID: 35008360 PMCID: PMC8750473 DOI: 10.3390/cancers14010191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 12/20/2022] Open
Abstract
New therapies are urgently needed for epithelial ovarian cancer (EOC), the most lethal gynecologic malignancy. To identify new approaches for targeting EOC, metabolic vulnerabilities must be discovered and strategies for the selective delivery of therapeutic agents must be established. Folate receptor (FR) α and the proton-coupled folate transporter (PCFT) are expressed in the majority of EOCs. FRβ is expressed on tumor-associated macrophages, a major infiltrating immune population in EOC. One-carbon (C1) metabolism is partitioned between the cytosol and mitochondria and is important for the synthesis of nucleotides, amino acids, glutathione, and other critical metabolites. Novel inhibitors are being developed with the potential for therapeutic targeting of tumors via FRs and the PCFT, as well as for inhibiting C1 metabolism. In this review, we summarize these exciting new developments in targeted therapies for both tumors and the tumor microenvironment in EOC.
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33
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Do HQ, Bassil CM, Andersen EI, Jansen M. Impact of nanodisc lipid composition on cell-free expression of proton-coupled folate transporter. PLoS One 2021; 16:e0253184. [PMID: 34793461 PMCID: PMC8601550 DOI: 10.1371/journal.pone.0253184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/31/2021] [Indexed: 01/19/2023] Open
Abstract
The Proton-Coupled Folate Transporter (PCFT) is a transmembrane transport protein that controls the absorption of dietary folates in the small intestine. PCFT also mediates uptake of chemotherapeutically used antifolates into tumor cells. PCFT has been identified within lipid rafts observed in phospholipid bilayers of plasma membranes, a micro environment that is altered in tumor cells. The present study aimed at investigating the impact of different lipids within Lipid-protein nanodiscs (LPNs), discoidal lipid structures stabilized by membrane scaffold proteins, to yield soluble PCFT expression in an E. coli lysate-based cell-free transcription/translation system. In the absence of detergents or lipids, we observed PCFT quantitatively as precipitate in this system. We then explored the ability of LPNs to support solubilized PCFT expression when present during in-vitro translation. LPNs consisted of either dimyristoyl phosphatidylcholine (DMPC), palmitoyl-oleoyl phosphatidylcholine (POPC), or dimyristoyl phosphatidylglycerol (DMPG). While POPC did not lead to soluble PCFT expression, both DMPG and DMPC supported PCFT translation directly into LPNs, the latter in a concentration dependent manner. The results obtained through this study provide insights into the lipid preferences of PCFT. Membrane-embedded or solubilized PCFT will enable further studies with diverse biophysical approaches to enhance the understanding of the structure and molecular mechanism of folate transport through PCFT.
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Affiliation(s)
- Hoa Quynh Do
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Carla M. Bassil
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
- The Clark Scholar Program, Texas Tech University, Lubbock, TX, United States of America
| | - Elizabeth I. Andersen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
| | - Michaela Jansen
- Department of Cell Physiology and Molecular Biophysics and Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, United States of America
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34
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Birch J, Quigley A. The high-throughput production of membrane proteins. Emerg Top Life Sci 2021; 5:655-663. [PMID: 34623416 PMCID: PMC8726054 DOI: 10.1042/etls20210196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/11/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
Membrane proteins, found at the junctions between the outside world and the inner workings of the cell, play important roles in human disease and are used as biosensors. More than half of all therapeutics directly affect membrane protein function while nanopores enable DNA sequencing. The structural and functional characterisation of membrane proteins is therefore crucial. However, low levels of naturally abundant protein and the hydrophobic nature of membrane proteins makes production difficult. To maximise success, high-throughput strategies were developed that rely upon simple screens to identify successful constructs and rapidly exclude those unlikely to work. Parameters that affect production such as expression host, membrane protein origin, expression vector, fusion-tags, encapsulation reagent and solvent composition are screened in parallel. In this way, constructs with divergent requirements can be produced for a variety of structural applications. As structural techniques advance, sample requirements will change. Single-particle cryo-electron microscopy requires less protein than crystallography and as cryo-electron tomography and time-resolved serial crystallography are developed new sample production requirements will evolve. Here we discuss different methods used for the high-throughput production of membrane proteins for structural biology.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, U.K
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, U.K
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Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. SCIENCE ADVANCES 2021; 7:eabh3355. [PMID: 34433568 PMCID: PMC8386928 DOI: 10.1126/sciadv.abh3355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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