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Lu X, Huang J. Molecular mechanisms of Na +-driven bile acid transport in human NTCP. Biophys J 2024; 123:1195-1210. [PMID: 38544409 PMCID: PMC11140467 DOI: 10.1016/j.bpj.2024.03.033] [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: 01/01/2024] [Revised: 02/17/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Human Na+ taurocholate co-transporting protein (hNTCP) is a key bile salt transporter to maintain enterohepatic circulation and is responsible for the recognition of hepatitis B and D viruses. Despite landmark cryoelectron microscopy studies revealing open-pore and inward-facing states of hNTCP stabilized by antibodies, the transport mechanism remains largely unknown. To address this knowledge gap, we used molecular dynamics and enhanced sampling metadynamics simulations to elucidate the intrinsic mechanism of hNTCP-mediated taurocholate acid (TCA) transport driven by Na+ binding. We uncovered three TCA-binding modes, including one that closely matched the limited cryoelectron microscopy density observed in the open-pore hNTCP. We also captured several key hNTCP conformations in the substrate transport cycle, particularly including an outward-facing, substrate-bound state. Furthermore, we provided thermodynamic evidence supporting that changes in the Na+-binding state drive the TCA transport by exploiting the amphiphilic nature of the substrate and modulating the protein environment, thereby enabling the TCA molecule to flip through. Understanding these mechanistic details of Na+-driven bile acid transport may aid in the development of hNTCP-targeted therapies for liver diseases.
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Affiliation(s)
- Xiaoli Lu
- Westlake AI Therapeutics Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jing Huang
- Westlake AI Therapeutics Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
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2
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Hutchinson K, Schlessinger A. Comprehensive Characterization of LAT1 Cholesterol-Binding Sites. J Chem Theory Comput 2024; 20:3349-3358. [PMID: 38597304 DOI: 10.1021/acs.jctc.3c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The human L-type amino acid transporter 1 (LAT1; SLC7A5), is an amino acid exchanger protein, primarily found in the blood-brain barrier, placenta, and testis, where it plays a key role in amino acid homeostasis. Cholesterol is an essential lipid that has been highlighted to play a role in regulating the activity of membrane transporters, such as LAT1, yet little is known about the molecular mechanisms driving this phenomenon. Here we perform a comprehensive computational analysis to investigate cholesterol's role in LAT1 structure and function, focusing on four cholesterol-binding sites (CHOL1-4) identified in a recent LAT1-apo inward-open conformation cryo-EM structure. Through a series of independent molecular dynamics (MD) simulations, molecular docking, MM/GBSA free energy calculations, and other analysis tools, we explored the interactions between LAT1 and cholesterol. Our findings suggest that CHOL3 forms the most stable and favorable interactions with LAT1. Principal component analysis (PCA) and center of mass (COM) distance assessments show that CHOL3 binding stabilizes the inward-open state of LAT1 by preserving the spatial arrangement of the hash and bundle domains. Additionally, we propose an alternative cholesterol-binding site for originally assigned CHOL1. Overall, this study improves the understanding of cholesterol's modulatory effect on LAT1 and proposes candidate sites for the discovery of future allosteric ligands with rational design.
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Affiliation(s)
- Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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3
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Shao L, Yang M, Sun T, Xia H, Du D, Li X, Jie Z. Role of solute carrier transporters in regulating dendritic cell maturation and function. Eur J Immunol 2024; 54:e2350385. [PMID: 38073515 DOI: 10.1002/eji.202350385] [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: 07/02/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 02/27/2024]
Abstract
Dendritic cells (DCs) are specialized antigen-presenting cells that initiate and regulate innate and adaptive immune responses. Solute carrier (SLC) transporters mediate diverse physiological functions and maintain cellular metabolite homeostasis. Recent studies have highlighted the significance of SLCs in immune processes. Notably, upon activation, immune cells undergo rapid and robust metabolic reprogramming, largely dependent on SLCs to modulate diverse immunological responses. In this review, we explore the central roles of SLC proteins and their transported substrates in shaping DC functions. We provide a comprehensive overview of recent studies on amino acid transporters, metal ion transporters, and glucose transporters, emphasizing their essential contributions to DC homeostasis under varying pathological conditions. Finally, we propose potential strategies for targeting SLCs in DCs to bolster immunotherapy for a spectrum of human diseases.
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Affiliation(s)
- Lin Shao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Mengxin Yang
- School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Tao Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haotang Xia
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Dan Du
- Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xun Li
- Department of Laboratory Medicine, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zuliang Jie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
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Schlessinger A, Zatorski N, Hutchinson K, Colas C. Targeting SLC transporters: small molecules as modulators and therapeutic opportunities. Trends Biochem Sci 2023; 48:801-814. [PMID: 37355450 PMCID: PMC10525040 DOI: 10.1016/j.tibs.2023.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023]
Abstract
Solute carrier (SLCs) transporters mediate the transport of a broad range of solutes across biological membranes. Dysregulation of SLCs has been associated with various pathologies, including metabolic and neurological disorders, as well as cancer and rare diseases. SLCs are therefore emerging as key targets for therapeutic intervention with several recently approved drugs targeting these proteins. Unlocking this large and complex group of proteins is essential to identifying unknown SLC targets and developing next-generation SLC therapeutics. Recent progress in experimental and computational techniques has significantly advanced SLC research, including drug discovery. Here, we review emerging topics in therapeutic discovery of SLCs, focusing on state-of-the-art approaches in structural, chemical, and computational biology, and discuss current challenges in transporter drug discovery.
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Affiliation(s)
- Avner Schlessinger
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Nicole Zatorski
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claire Colas
- University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria.
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Dvorak V, Superti-Furga G. Structural and functional annotation of solute carrier transporters: implication for drug discovery. Expert Opin Drug Discov 2023; 18:1099-1115. [PMID: 37563933 DOI: 10.1080/17460441.2023.2244760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
INTRODUCTION Solute carriers (SLCs) represent the largest group of membrane transporters in the human genome. They play a central role in controlling the compartmentalization of metabolism and most of this superfamily is linked to human disease. Despite being in general considered druggable and attractive therapeutic targets, many SLCs remain poorly annotated, both functionally and structurally. AREAS COVERED The aim of this review is to provide an overview of functional and structural parameters of SLCs that play important roles in their druggability. To do this, the authors provide an overview of experimentally solved structures of human SLCs, with emphasis on structures solved in complex with chemical modulators. From the functional annotations, the authors focus on SLC localization and SLC substrate annotations. EXPERT OPINION Recent progress in the structural and functional annotations allows to refine the SLC druggability index. Particularly the increasing number of experimentally solved structures of SLCs provides insights into mode-of-action of a significant number of chemical modulators of SLCs.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - 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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Hou Y, Lu X, Xu Z, Qu J, Huang J. How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2. RSC Adv 2023; 13:4263-4274. [PMID: 36760301 PMCID: PMC9891203 DOI: 10.1039/d2ra07472a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase SHP2 is a key regulator modulating several signaling pathways. The oncogenic mutation E76K in SHP2 releases the enzyme from an autoinhibited, closed conformation into an active, open conformation. Here, we investigated the conformational dynamics of SHP2 and the effect of the E76K mutation on its conformational ensemble via extensive molecular dynamics (MD) and metadynamics (MetaD) simulations. Our simulations provide atomistic details on how the E76K mutated SHP2 prefers the open state and also reveal that the transition between the closed and the open states is highly collective. Several intermediate metastable states during the conformational transition between the closed and the open states were also investigated. Understanding how the single E76K mutation induces the conformational change in SHP2 could facilitate the further design of SHP2 inhibitors.
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Affiliation(s)
- Yingnan Hou
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Xiaoli Lu
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Ziyao Xu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jiarun Qu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jing Huang
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
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Smorodina E, Diankin I, Tao F, Qing R, Yang S, Zhang S. Structural informatic study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants. Sci Rep 2022; 12:20103. [PMID: 36418372 PMCID: PMC9684436 DOI: 10.1038/s41598-022-23764-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chemo-sensitivity. Here we report the study of 13 human solute carrier membrane transporters using the highly accurate AlphaFold2 predictions of 3D protein structures. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane alpha-helices. These hydrophobic amino acids L, I, V, F are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T) and tyrosine (Y), thus the QTY code. Therefore, these QTY variant transporters become water-soluble without requiring detergents. We present the superposed structures of these native solute carrier transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with RMSD ~ 1 Å-< 3 Å despite > 46% protein sequence substitutions in transmembrane alpha-helices. We also show the differences of surface hydrophobicity between the native solute carrier transporters and their QTY variants. Our study may further stimulate designs of water-soluble transmembrane proteins and other aggregated proteins for drug discovery and biotechnological applications.
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Affiliation(s)
- Eva Smorodina
- grid.55325.340000 0004 0389 8485Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Igor Diankin
- grid.78780.300000 0004 0613 1044Department of Computer Science, American University of Armenia, Yerevan, Armenia
| | - Fei Tao
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Rui Qing
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Steve Yang
- PT Metiska Farma, Daerah Khusus Ibukota, Jakarta, 12220 Indonesia
| | - Shuguang Zhang
- grid.116068.80000 0001 2341 2786Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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A structure and evolutionary-based classification of solute carriers. iScience 2022; 25:105096. [PMID: 36164651 PMCID: PMC9508557 DOI: 10.1016/j.isci.2022.105096] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 09/04/2022] [Indexed: 11/22/2022] Open
Abstract
Solute carriers are an operationally defined diverse family of membrane proteins involved in the transport of nutrients, metabolites, xenobiotics, and drugs. Here, we provide an integrative classification of solute carriers by combining evolutionary information with proteome-wide structure models recently made available through the AlphaFold resource. Analyses of orthologous relations among 455 protein-coding genes currently classified as human solute carriers, over the fully sequenced genomes of 2,100 species, suggest no more than approximately 180 independent evolutionary origins. Structural comparative analyses provided further insight revealing a total of 24 structurally distinct transmembrane folds, increasing by approximately 40% the number of previously described SLC structural folds. In addition, a structural comparative analysis identified a new human solute carrier member and revealed details of noncanonical ones. Our analyses uncover new ancestral relations between solute carrier genes, provide insights into the evolution of remote homologs and a platform to test hypotheses of functional deorphanization.
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Bernhofer M, Rost B. TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinformatics 2022; 23:326. [PMID: 35941534 PMCID: PMC9358067 DOI: 10.1186/s12859-022-04873-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4-5 times underrepresented compared to non-TMPs. Today's top methods such as AlphaFold2 accurately predict 3D structures for many TMPs, but annotating transmembrane regions remains a limiting step for proteome-wide predictions. RESULTS Here, we present TMbed, a novel method inputting embeddings from protein Language Models (pLMs, here ProtT5), to predict for each residue one of four classes: transmembrane helix (TMH), transmembrane strand (TMB), signal peptide, or other. TMbed completes predictions for entire proteomes within hours on a single consumer-grade desktop machine at performance levels similar or better than methods, which are using evolutionary information from multiple sequence alignments (MSAs) of protein families. On the per-protein level, TMbed correctly identified 94 ± 8% of the beta barrel TMPs (53 of 57) and 98 ± 1% of the alpha helical TMPs (557 of 571) in a non-redundant data set, at false positive rates well below 1% (erred on 30 of 5654 non-membrane proteins). On the per-segment level, TMbed correctly placed, on average, 9 of 10 transmembrane segments within five residues of the experimental observation. Our method can handle sequences of up to 4200 residues on standard graphics cards used in desktop PCs (e.g., NVIDIA GeForce RTX 3060). CONCLUSIONS Based on embeddings from pLMs and two novel filters (Gaussian and Viterbi), TMbed predicts alpha helical and beta barrel TMPs at least as accurately as any other method but at lower false positive rates. Given the few false positives and its outstanding speed, TMbed might be ideal to sieve through millions of 3D structures soon to be predicted, e.g., by AlphaFold2.
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Affiliation(s)
- Michael Bernhofer
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany. .,TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology ‑ i12, Technical University of Munich (TUM), Boltzmannstr. 3, 85748, Garching, Germany.,Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching, Germany.,TUM School of Life Sciences Weihenstephan (TUM-WZW), Alte Akademie 8, Freising, Germany
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