1
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. Structure 2024; 32:1528-1543.e3. [PMID: 39025067 PMCID: PMC11380583 DOI: 10.1016/j.str.2024.06.015] [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: 01/24/2024] [Revised: 05/30/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters, the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Samuel P Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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2
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George A, Zuckerman DM. From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis. J Phys Chem B 2024; 128:1830-1842. [PMID: 38373358 DOI: 10.1021/acs.jpcb.3c07025] [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: 02/21/2024]
Abstract
Electrophysiology studies of secondary active transporters have revealed quantitative mechanistic insights over many decades of research. However, the emergence of new experimental and analytical approaches calls for investigation of the capabilities and limitations of the newer methods. We examine the ability of solid-supported membrane electrophysiology (SSME) to characterize discrete-state kinetic models with >10 rate constants. We use a Bayesian framework applied to synthetic data for three tasks: to quantify and check (i) the precision of parameter estimates under different assumptions, (ii) the ability of computation to guide the selection of experimental conditions, and (iii) the ability of our approach to distinguish among mechanisms based on SSME data. When the general mechanism, i.e., event order, is known in advance, we show that a subset of kinetic parameters can be "practically identified" within ∼1 order of magnitude, based on SSME current traces that visually appear to exhibit simple exponential behavior. This remains true even when accounting for systematic measurement bias and realistic uncertainties in experimental inputs (concentrations) are incorporated into the analysis. When experimental conditions are optimized or different experiments are combined, the number of practically identifiable parameters can be increased substantially. Some parameters remain intrinsically difficult to estimate through SSME data alone, suggesting that additional experiments are required to fully characterize parameters. We also demonstrate the ability to perform model selection and determine the order of events when that is not known in advance, comparing Bayesian and maximum-likelihood approaches. Finally, our studies elucidate good practices for the increasingly popular but subtly challenging Bayesian calculations for structural and systems biology.
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Affiliation(s)
- August George
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon 97239, United States
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3
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577062. [PMID: 38352416 PMCID: PMC10862720 DOI: 10.1101/2024.01.24.577062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A. Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Samuel P. Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael A. Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Novartis Biomedical Research, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Lead contact
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4
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Hiraizumi M, Akashi T, Murasaki K, Kishida H, Kumanomidou T, Torimoto N, Nureki O, Miyaguchi I. Transport and inhibition mechanism of the human SGLT2-MAP17 glucose transporter. Nat Struct Mol Biol 2024; 31:159-169. [PMID: 38057552 PMCID: PMC10803289 DOI: 10.1038/s41594-023-01134-0] [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: 01/10/2023] [Accepted: 09/22/2023] [Indexed: 12/08/2023]
Abstract
Sodium-glucose cotransporter 2 (SGLT2) is imporant in glucose reabsorption. SGLT2 inhibitors suppress renal glucose reabsorption, therefore reducing blood glucose levels in patients with type 2 diabetes. We and others have developed several SGLT2 inhibitors starting from phlorizin, a natural product. Using cryo-electron microscopy, we present the structures of human (h)SGLT2-MAP17 complexed with five natural or synthetic inhibitors. The four synthetic inhibitors (including canagliflozin) bind the transporter in the outward conformations, while phlorizin binds it in the inward conformation. The phlorizin-hSGLT2 interaction exhibits biphasic kinetics, suggesting that phlorizin alternately binds to the extracellular and intracellular sides. The Na+-bound outward-facing and unbound inward-open structures of hSGLT2-MAP17 suggest that the MAP17-associated bundle domain functions as a scaffold, with the hash domain rotating around the Na+-binding site. Thus, Na+ binding stabilizes the outward-facing conformation, and its release promotes state transition to inward-open conformation, exhibiting a role of Na+ in symport mechanism. These results provide structural evidence for the Na+-coupled alternating-access mechanism proposed for the transporter family.
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Affiliation(s)
- Masahiro Hiraizumi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Tomoya Akashi
- DMPK Research Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Kouta Murasaki
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Hiroyuki Kishida
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Taichi Kumanomidou
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Nao Torimoto
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ikuko Miyaguchi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
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5
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Azizogli AR, Vitti MR, Mishra R, Osorno L, Heffernan C, Kumar VA. Comparison of SGLT1, SGLT2, and Dual Inhibitor biological activity in treating Type 2 Diabetes Mellitus. ADVANCED THERAPEUTICS 2023; 6:2300143. [PMID: 38223846 PMCID: PMC10783160 DOI: 10.1002/adtp.202300143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 01/16/2024]
Abstract
Diabetes Mellitus Type 2 (T2D) is an emerging health burden in the USand worldwide, impacting approximately 15% of Americans. Current front-line therapeutics for T2D patients include sulfonylureas that act to reduce A1C and/or fasting blood glucose levels, or Metformin that antagonizes the action of glucagon to reduce hepatic glucose production. Next generation glucomodulatory therapeutics target members of the high-affinity glucose transporter Sodium-Glucose-Linked-Transporter (SGLT) family. SGLT1 is primarily expressed in intestinal epithelium, whose inhibition reduces dietary glucose uptake, whilst SGLT2 is highly expressed in kidney - regulating glucose reabsorption. A number of SGLT2 inhibitors are FDA approved whilst SGLT1 and dual SGLT1 & 2 inhibitor are currently in clinical trials. Here, we discuss and compare SGLT2, SGLT1, and dual inhibitors' biochemical mechanism and physiological effects.
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Affiliation(s)
- Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Michael R Vitti
- University of Virginia School of Medicine, Charlottesville, VA, 22903
| | - Richa Mishra
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Laura Osorno
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Vivek A Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103
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6
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Khan F, Elgeti M, Grandfield S, Paz A, Naughton FB, Marcoline FV, Althoff T, Ermolova N, Wright EM, Hubbell WL, Grabe M, Abramson J. Membrane potential accelerates sugar uptake by stabilizing the outward facing conformation of the Na/glucose symporter vSGLT. Nat Commun 2023; 14:7511. [PMID: 37980423 PMCID: PMC10657379 DOI: 10.1038/s41467-023-43119-z] [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: 09/08/2022] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Sodium-dependent glucose transporters (SGLTs) couple a downhill Na+ ion gradient to actively transport sugars. Here, we investigate the impact of the membrane potential on vSGLT structure and function using sugar uptake assays, double electron-electron resonance (DEER), electrostatic calculations, and kinetic modeling. Negative membrane potentials, as present in all cell types, shift the conformational equilibrium of vSGLT towards an outward-facing conformation, leading to increased sugar transport rates. Electrostatic calculations identify gating charge residues responsible for this conformational shift that when mutated reduce galactose transport and eliminate the response of vSGLT to potential. Based on these findings, we propose a comprehensive framework for sugar transport via vSGLT, where the cellular membrane potential facilitates resetting of the transporter after cargo release. This framework holds significance not only for SGLTs but also for other transporters and channels.
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Affiliation(s)
- Farha Khan
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Matthias Elgeti
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
| | - Samuel Grandfield
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, 11794, USA
| | - Aviv Paz
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Fiona B Naughton
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Frank V Marcoline
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Thorsten Althoff
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Natalia Ermolova
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Ernest M Wright
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Wayne L Hubbell
- Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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7
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Cui W, Niu Y, Sun Z, Liu R, Chen L. Structures of human SGLT in the occluded state reveal conformational changes during sugar transport. Nat Commun 2023; 14:2920. [PMID: 37217492 DOI: 10.1038/s41467-023-38720-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open conformations are emerging from structural studies, the trajectory of how SGLTs transit from the outward-facing to the inward-facing conformation remains unknown. Here, we present the cryo-EM structures of human SGLT1 and SGLT2 in the substrate-bound state. Both structures show an occluded conformation, with not only the extracellular gate but also the intracellular gate tightly sealed. The sugar substrate are caged inside a cavity surrounded by TM1, TM2, TM3, TM6, TM7, and TM10. Further structural analysis reveals the conformational changes associated with the binding and release of substrates. These structures fill a gap in our understanding of the structural mechanisms of SGLT transporters.
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Affiliation(s)
- Wenhao Cui
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Yange Niu
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Zejian Sun
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Rui Liu
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China
| | - Lei Chen
- State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, 100871, Beijing, China.
- National Biomedical Imaging Center, Peking University, 100871, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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8
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Transcriptome Analysis Reveals the Effect of Low NaCl Concentration on Osmotic Stress and Type III Secretion System in Vibrio parahaemolyticus. Int J Mol Sci 2023; 24:ijms24032621. [PMID: 36768942 PMCID: PMC9916905 DOI: 10.3390/ijms24032621] [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: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Vibrio parahaemolyticus is a moderately halophilic foodborne pathogen that is mainly distributed in marine and freshwater environments. The transition of V. parahaemolyticus between aquatic ecosystems and hosts is essential for infection. Both freshwater and host environments have low salinity. In this study, we sought to further investigate the effects of low salinity (0.5% NaCl) on the fitness and virulence of V. parahaemolyticus. We found that V. parahaemolyticus could survive in Luria-Bertani (LB) and M9 mediums with different NaCl concentrations, except for the M9 medium containing 9% NaCl. Our results further showed that V. parahaemolyticus cultured in M9 medium with 0.5% NaCl had a higher cell density than that cultured at other NaCl concentrations when it entered the stationary phase. Therefore, we compared the transcriptomes of V. parahaemolyticus wild type (WT) cultured in an M9 medium with 0.5% and 3% NaCl at the stationary phase using RNA-seq. A total of 658 genes were significantly differentially expressed in the M9 medium with 0.5% NaCl, including regulators, osmotic adaptive responses (compatible solute synthesis systems, transporters, and outer membrane proteins), and virulence factors (T3SS1 and T6SS1). Furthermore, a low salinity concentration in the M9 medium induced the expression of T3SS1 to mediate the cytotoxicity of V. parahaemolyticus to HeLa cells. Similarly, low salinity could also induce the secretion of the T3SS2 translocon protein VPA1361. These factors may result in the high pathogenicity of V. parahaemolyticus in low-salinity environments. Taken together, these results suggest that low salinity (0.5% NaCl) could affect gene expression to mediate fitness and virulence, which may contribute to the transition of V. parahaemolyticus between aquatic ecosystems and the host.
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9
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Ding L, Chen X, Zhang W, Dai X, Guo H, Pan X, Xu Y, Feng J, Yuan M, Gao X, Wang J, Xu X, Li S, Wu H, Cao J, He Q, Yang B. Canagliflozin primes antitumor immunity by triggering PD-L1 degradation in endocytic recycling. J Clin Invest 2023; 133:e154754. [PMID: 36594471 PMCID: PMC9797339 DOI: 10.1172/jci154754] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2022] [Indexed: 01/04/2023] Open
Abstract
Understanding the regulatory mechanisms of PD-L1 expression in tumors provides key clues for improving immune checkpoint blockade efficacy or developing novel oncoimmunotherapy. Here, we showed that the FDA-approved sodium-glucose cotransporter-2 (SGLT2) inhibitor canagliflozin dramatically suppressed PD-L1 expression and enhanced T cell-mediated cytotoxicity. Mechanistic study revealed that SGLT2 colocalized with PD-L1 at the plasma membrane and recycling endosomes and thereby prevented PD-L1 from proteasome-mediated degradation. Canagliflozin disturbed the physical interaction between SGLT2 and PD-L1 and subsequently allowed the recognition of PD-L1 by Cullin3SPOP E3 ligase, which triggered the ubiquitination and proteasome-mediated degradation of PD-L1. In mouse models and humanized immune-transformation models, either canagliflozin treatment or SGLT2 silencing significantly reduced PD-L1 expression and limited tumor progression - to a level equal to the PD-1 mAb - which was correlated with an increase in the activity of antitumor cytotoxic T cells. Notably, prolonged progression-free survival and overall survival curves were observed in the group of PD-1 mAb-treated patients with non-small cell lung cancer with high expression of SGLT2. Therefore, our study identifies a regulator of cell surface PD-L1, provides a ready-to-use small-molecule drug for PD-L1 degradation, and highlights a potential therapeutic target to overcome immune evasion by tumor cells.
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Affiliation(s)
- Ling Ding
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Xi Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Wenxin Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Xiaoyang Dai
- Center of Drug Safety Evaluation and Research, Zhejiang University, Hangzhou, China
| | - Hongjie Guo
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Xiaohui Pan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Yanjun Xu
- Department of Medical Thoracic Oncology and
| | - Jianguo Feng
- Institute of Basic Medicine and Cancer, The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Chinese Academy of Sciences, Hangzhou, China
| | - Meng Yuan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Xiaomeng Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Jian Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Xiaqing Xu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Sicheng Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Honghai Wu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
- The Innovation Institute for Artificial Intelligence in Medicine and
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, and
- The Innovation Institute for Artificial Intelligence in Medicine and
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10
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Sanguinetti M, Silva Santos LH, Dourron J, Alamón C, Idiarte J, Amillis S, Pantano S, Ramón A. Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter. Int J Mol Sci 2022; 23:16039. [PMID: 36555682 PMCID: PMC9783183 DOI: 10.3390/ijms232416039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and acetamide in the Aspergillus nidulans urea transporter, UreA. To deepen the structural characterization of UreA, we employed the artificial intelligence (AI) based AlphaFold2 (AF2) program. In this analysis, the resulting AF2 models lacked inward- and outward-facing cavities, suggesting a structural intermediate state of UreA. Moreover, the orientation of the W82, W84, N279, and T282 side chains showed a large variability, which in the case of W82 and W84, may operate as a gating mechanism in the ligand pathway. To test this hypothesis non-conservative and conservative substitutions of these amino acids were introduced, and binding and transport assessed for urea and its toxic analogue 2-thiourea, as well as binding of the structural analogue acetamide. As a result, residues W82, W84, N279, and T282 were implicated in substrate identification, selection, and translocation. Using molecular docking with Autodock Vina with flexible side chains, we corroborated the AF2 theoretical intermediate model, showing a remarkable correlation between docking scores and experimental affinities determined in wild-type and UreA mutants. The combination of AI-based modeling with classical docking, validated by comprehensive mutational analysis at the binding region, would suggest an unforeseen option to determine structural level details on a challenging family of proteins.
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Affiliation(s)
- Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | | | - Juliette Dourron
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Catalina Alamón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
- Neurodegeneration Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Juan Idiarte
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
- Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
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11
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Niu Y, Cui W, Liu R, Wang S, Ke H, Lei X, Chen L. Structural mechanism of SGLT1 inhibitors. Nat Commun 2022; 13:6440. [PMID: 36307403 PMCID: PMC9616851 DOI: 10.1038/s41467-022-33421-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/16/2022] [Indexed: 12/25/2022] Open
Abstract
Sodium glucose co-transporters (SGLT) harness the electrochemical gradient of sodium to drive the uphill transport of glucose across the plasma membrane. Human SGLT1 (hSGLT1) plays a key role in sugar uptake from food and its inhibitors show promise in the treatment of several diseases. However, the inhibition mechanism for hSGLT1 remains elusive. Here, we present the cryo-EM structure of the hSGLT1-MAP17 hetero-dimeric complex in the presence of the high-affinity inhibitor LX2761. LX2761 locks the transporter in an outward-open conformation by wedging inside the substrate-binding site and the extracellular vestibule of hSGLT1. LX2761 blocks the putative water permeation pathway of hSGLT1. The structure also uncovers the conformational changes of hSGLT1 during transitions from outward-open to inward-open states.
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Affiliation(s)
- Yange Niu
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China
| | - Wenhao Cui
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China ,grid.27255.370000 0004 1761 1174Taishan College, Shandong University, Qingdao, China
| | - Rui Liu
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China
| | - Sanshan Wang
- grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China ,grid.454727.7Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing, China
| | - Han Ke
- grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China ,grid.454727.7Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing, China
| | - Xiaoguang Lei
- grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China ,grid.454727.7Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing, China
| | - Lei Chen
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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12
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del Alamo D, DeSousa L, Nair RM, Rahman S, Meiler J, Mchaourab HS. Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter. Proc Natl Acad Sci U S A 2022; 119:e2206129119. [PMID: 35969794 PMCID: PMC9407458 DOI: 10.1073/pnas.2206129119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
The Amino Acid-Polyamine-Organocation (APC) transporter GadC contributes to the survival of pathogenic bacteria under extreme acid stress by exchanging extracellular glutamate for intracellular γ-aminobutyric acid (GABA). Its structure, determined in an inward-facing conformation at alkaline pH, consists of the canonical LeuT-fold with a conserved five-helix inverted repeat, thereby resembling functionally divergent transporters such as the serotonin transporter SERT and the glucose-sodium symporter SGLT1. However, despite this structural similarity, it is unclear if the conformational dynamics of antiporters such as GadC follow the blueprint of these or other LeuT-fold transporters. Here, we used double electron-electron resonance (DEER) spectroscopy to monitor the conformational dynamics of GadC in lipid bilayers in response to acidification and substrate binding. To guide experimental design and facilitate the interpretation of the DEER data, we generated an ensemble of structural models in multiple conformations using a recently introduced modification of AlphaFold2 . Our experimental results reveal acid-induced conformational changes that dislodge the Cterminus from the permeation pathway coupled with rearrangement of helices that enables isomerization between inward- and outward-facing states. The substrate glutamate, but not GABA, modulates the dynamics of an extracellular thin gate without shifting the equilibrium between inward- and outward-facing conformations. In addition to introducing an integrated methodology for probing transporter conformational dynamics, the congruence of the DEER data with patterns of structural rearrangements deduced from ensembles of AlphaFold2 models illuminates the conformational cycle of GadC underpinning transport and exposes yet another example of the divergence between the dynamics of different families in the LeuT-fold.
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Affiliation(s)
- Diego del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212
| | - Lillian DeSousa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Rahul M. Nair
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Suhaila Rahman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany 04109
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
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13
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Sala D, Del Alamo D, Mchaourab HS, Meiler J. Modeling of protein conformational changes with Rosetta guided by limited experimental data. Structure 2022; 30:1157-1168.e3. [PMID: 35597243 PMCID: PMC9357069 DOI: 10.1016/j.str.2022.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/25/2022] [Indexed: 11/24/2022]
Abstract
Conformational changes are an essential component of functional cycles of many proteins, but their characterization often requires an integrative structural biology approach. Here, we introduce and benchmark ConfChangeMover (CCM), a new method built into the widely used macromolecular modeling suite Rosetta that is tailored to model conformational changes in proteins using sparse experimental data. CCM can rotate and translate secondary structural elements and modify their backbone dihedral angles in regions of interest. We benchmarked CCM on soluble and membrane proteins with simulated Cα-Cα distance restraints and sparse experimental double electron-electron resonance (DEER) restraints, respectively. In both benchmarks, CCM outperformed state-of-the-art Rosetta methods, showing that it can model a diverse array of conformational changes. In addition, the Rosetta framework allows a wide variety of experimental data to be integrated with CCM, thus extending its capability beyond DEER restraints. This method will contribute to the biophysical characterization of protein dynamics.
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Affiliation(s)
- Davide Sala
- Institute for Drug Discovery, Leipzig University, Leipzig, Saxony 04103, Germany
| | - Diego Del Alamo
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University, Leipzig, Saxony 04103, Germany; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.
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14
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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15
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Hustedt EJ, Stein RA, Mchaourab HS. Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations. J Gen Physiol 2021; 153:212643. [PMID: 34529007 PMCID: PMC8449309 DOI: 10.1085/jgp.201711954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
The potential of spin labeling to reveal the dynamic dimension of macromolecules has been recognized since the dawn of the methodology in the 1960s. However, it was the development of pulsed electron paramagnetic resonance spectroscopy to detect dipolar coupling between spin labels and the availability of turnkey instrumentation in the 21st century that realized the full promise of spin labeling. Double electron-electron resonance (DEER) spectroscopy has seen widespread applications to channels, transporters, and receptors. In these studies, distance distributions between pairs of spin labels obtained under different biochemical conditions report the conformational states of macromolecules, illuminating the key movements underlying biological function. These experimental studies have spurred the development of methods for the rigorous analysis of DEER spectroscopic data along with methods for integrating these distributions into structural models. In this tutorial, we describe a model-based approach to obtaining a minimum set of components of the distance distribution that correspond to functionally relevant protein conformations with a set of fractional amplitudes that define the equilibrium between these conformations. Importantly, we review and elaborate on the error analysis reflecting the uncertainty in the various parameters, a critical step in rigorous structural interpretation of the spectroscopic data.
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Affiliation(s)
- Eric J Hustedt
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Richard A Stein
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Hassane S Mchaourab
- Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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16
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Function Trumps Form in Two Sugar Symporters, LacY and vSGLT. Int J Mol Sci 2021; 22:ijms22073572. [PMID: 33808202 PMCID: PMC8037263 DOI: 10.3390/ijms22073572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 11/21/2022] Open
Abstract
Active transport of sugars into bacteria occurs through symporters driven by ion gradients. LacY is the most well-studied proton sugar symporter, whereas vSGLT is the most characterized sodium sugar symporter. These are members of the major facilitator (MFS) and the amino acid-Polyamine organocation (APS) transporter superfamilies. While there is no structural homology between these transporters, they operate by a similar mechanism. They are nano-machines driven by their respective ion electrochemical potential gradients across the membrane. LacY has 12 transmembrane helices (TMs) organized in two 6-TM bundles, each containing two 3-helix TM repeats. vSGLT has a core structure of 10 TM helices organized in two inverted repeats (TM 1–5 and TM 6–10). In each case, a single sugar is bound in a central cavity and sugar selectivity is determined by hydrogen- and hydrophobic- bonding with side chains in the binding site. In vSGLT, the sodium-binding site is formed through coordination with carbonyl- and hydroxyl-oxygens from neighboring side chains, whereas in LacY the proton (H3O+) site is thought to be a single glutamate residue (Glu325). The remaining challenge for both transporters is to determine how ion electrochemical potential gradients drive uphill sugar transport.
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17
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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18
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Prokaryotic Solute/Sodium Symporters: Versatile Functions and Mechanisms of a Transporter Family. Int J Mol Sci 2021; 22:ijms22041880. [PMID: 33668649 PMCID: PMC7918813 DOI: 10.3390/ijms22041880] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
The solute/sodium symporter family (SSS family; TC 2.A.21; SLC5) consists of integral membrane proteins that use an existing sodium gradient to drive the uphill transport of various solutes, such as sugars, amino acids, vitamins, or ions across the membrane. This large family has representatives in all three kingdoms of life. The human sodium/iodide symporter (NIS) and the sodium/glucose transporter (SGLT1) are involved in diseases such as iodide transport defect or glucose-galactose malabsorption. Moreover, the bacterial sodium/proline symporter PutP and the sodium/sialic acid symporter SiaT play important roles in bacteria–host interactions. This review focuses on the physiological significance and structural and functional features of prokaryotic members of the SSS family. Special emphasis will be given to the roles and properties of proteins containing an SSS family domain fused to domains typically found in bacterial sensor kinases.
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19
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Conserved binding site in the N-lobe of prokaryotic MATE transporters suggests a role for Na + in ion-coupled drug efflux. J Biol Chem 2021; 296:100262. [PMID: 33837745 PMCID: PMC7949106 DOI: 10.1016/j.jbc.2021.100262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
In both prokaryotes and eukaryotes, multidrug and toxic-compound extrusion (MATE) transporters catalyze the efflux of a broad range of cytotoxic compounds, including human-made antibiotics and anticancer drugs. MATEs are secondary-active antiporters, i.e., their drug-efflux activity is coupled to, and powered by, the uptake of ions down a preexisting transmembrane electrochemical gradient. Key aspects of this mechanism, however, remain to be delineated, such as its ion specificity and stoichiometry. We previously revealed the existence of a Na+-binding site in a MATE transporter from Pyroccocus furiosus (PfMATE) and hypothesized that this site might be broadly conserved among prokaryotic MATEs. Here, we evaluate this hypothesis by analyzing VcmN and ClbM, which along with PfMATE are the only three prokaryotic MATEs whose molecular structures have been determined at atomic resolution, i.e. better than 3 Å. Reinterpretation of existing crystallographic data and molecular dynamics simulations indeed reveal an occupied Na+-binding site in the N-terminal lobe of both structures, analogous to that identified in PfMATE. We likewise find this site to be strongly selective against K+, suggesting it is mechanistically significant. Consistent with these computational results, DEER spectroscopy measurements for multiple doubly-spin-labeled VcmN constructs demonstrate Na+-dependent changes in protein conformation. The existence of this binding site in three MATE orthologs implicates Na+ in the ion-coupled drug-efflux mechanisms of this class of transporters. These results also imply that observations of H+-dependent activity likely stem either from a site elsewhere in the structure, or from H+ displacing Na+ under certain laboratory conditions, as has been noted for other Na+-driven transport systems.
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20
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Wright EM, Loo DDF. Active Glucose Transport 2020 and Beyond. FUNCTION (OXFORD, ENGLAND) 2020; 2:zqaa047. [PMID: 33511351 PMCID: PMC7812037 DOI: 10.1093/function/zqaa047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/06/2023]
Affiliation(s)
| | - Donald D F Loo
- Physiology Department, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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21
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Bisignano P, Lee MA, George A, Zuckerman DM, Grabe M, Rosenberg JM. A kinetic mechanism for enhanced selectivity of membrane transport. PLoS Comput Biol 2020; 16:e1007789. [PMID: 32614861 PMCID: PMC7331977 DOI: 10.1371/journal.pcbi.1007789] [Citation(s) in RCA: 15] [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: 07/30/2019] [Accepted: 03/13/2020] [Indexed: 01/06/2023] Open
Abstract
Membrane transport is generally thought to occur via an alternating access mechanism in which the transporter adopts at least two states, accessible from two different sides of the membrane to exchange substrates from the extracellular environment and the cytoplasm or from the cytoplasm and the intracellular matrix of the organelles (only in eukaryotes). In recent years, a number of high resolution structures have supported this general framework for a wide class of transport molecules, although additional states along the transport pathway are emerging as critically important. Given that substrate binding is often weak in order to enhance overall transport rates, there exists the distinct possibility that transporters may transport the incorrect substrate. This is certainly the case for many pharmaceutical compounds that are absorbed in the gut or cross the blood brain barrier through endogenous transporters. Docking studies on the bacterial sugar transporter vSGLT reveal that many highly toxic compounds are compatible with binding to the orthosteric site, further motivating the selective pressure for additional modes of selectivity. Motivated by recent work in which we observed failed substrate delivery in a molecular dynamics simulation where the energized ion still goes down its concentration gradient, we hypothesize that some transporters evolved to harness this 'slip' mechanism to increase substrate selectivity and reduce the uptake of toxic molecules. Here, we test this idea by constructing and exploring a kinetic transport model that includes a slip pathway. While slip reduces the overall productive flux, when coupled with a second toxic molecule that is more prone to slippage, the overall substrate selectivity dramatically increases, suppressing the accumulation of the incorrect compound. We show that the mathematical framework for increased substrate selectivity in our model is analogous to the classic proofreading mechanism originally proposed for tRNA synthase; however, because the transport cycle is reversible we identified conditions in which the selectivity is essentially infinite and incorrect substrates are exported from the cell in a 'detoxification' mode. The cellular consequences of proofreading and membrane slippage are discussed as well as the impact on future drug development.
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Affiliation(s)
- Paola Bisignano
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael A. Lee
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - August George
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Michael Grabe
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John M. Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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22
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Transporters of glucose and other carbohydrates in bacteria. Pflugers Arch 2020; 472:1129-1153. [PMID: 32372286 DOI: 10.1007/s00424-020-02379-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
Glucose arguably is the most important energy carrier, carbon source for metabolites and building block for biopolymers in all kingdoms of life. The proper function of animal organs and tissues depends on the continuous supply of glucose from the bloodstream. Most animals can resorb only a small number of monosaccharides, mostly glucose, galactose and fructose, while all other sugars oligosaccharides and dietary fibers are degraded and metabolized by the microbiota of the lower intestine. Bacteria, in contrast, are omnivorous. They can import and metabolize structurally different sugars and, as a consortium of different species, utilize almost any sugar, sugar derivative and oligosaccharide occurring in nature. Bacteria have membrane transport systems for the uptake of sugars against steep concentration gradients energized by ATP, the proton motive force and the high energy glycolytic intermediate phosphoenolpyruvate (PEP). Different uptake mechanisms and the broad range of overlapping substrate specificities allow bacteria to quickly adapt to and colonize changing environments. Here, we review the structures and mechanisms of bacterial representatives of (i) ATP-dependent cassette (ABC) transporters, (ii) major facilitator (MFS) superfamily proton symporters, (iii) sodium solute symporters (SSS) and (iv) enzyme II integral membrane subunits of the bacterial PEP-dependent phosphotransferase system (PTS). We give a short overview on the distribution of transporter genes and their phylogenetic relationship in different bacterial species. Some sugar transporters are hijacked for import of bacteriophage DNA and antibacterial toxins (bacteriocins) and they facilitate the penetration of polar antibiotics. Finally, we describe how the expression and activity of certain sugar transporters are controlled in response to the availability of sugars and how the presence and uptake of sugars may affect pathogenicity and host-microbiota interactions.
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23
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Gupta K, Toombes GE, Swartz KJ. Exploring structural dynamics of a membrane protein by combining bioorthogonal chemistry and cysteine mutagenesis. eLife 2019; 8:50776. [PMID: 31714877 PMCID: PMC6850778 DOI: 10.7554/elife.50776] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
The functional mechanisms of membrane proteins are extensively investigated with cysteine mutagenesis. To complement cysteine-based approaches, we engineered a membrane protein with thiol-independent crosslinkable groups using azidohomoalanine (AHA), a non-canonical methionine analogue containing an azide group that can selectively react with cycloalkynes through a strain-promoted azide-alkyne cycloaddition (SPAAC) reaction. We demonstrate that AHA can be readily incorporated into the Shaker Kv channel in place of methionine residues and modified with azide-reactive alkyne probes in Xenopus oocytes. Using voltage-clamp fluorometry, we show that AHA incorporation permits site-specific fluorescent labeling to track voltage-dependent conformational changes similar to cysteine-based methods. By combining AHA incorporation and cysteine mutagenesis in an orthogonal manner, we were able to site-specifically label the Shaker Kv channel with two different fluorophores simultaneously. Our results identify a facile and straightforward approach for chemical modification of membrane proteins with bioorthogonal chemistry to explore their structure-function relationships in live cells. Living cells can sense cues from their environment via molecules located at the interface between the inside and the outside of the cell. These molecules are mostly proteins and are made up of building blocks known as amino acids. To understand how these proteins work, fluorescent probes can be attached to amino acids within them – which can then tell when different parts of proteins move in response to a signal. Scientists often target fluorescent probes at the amino acid cysteine, because it has a chemically reactive side group and is rare enough so that unique positions can be labeled in the protein of interest. However, being able to target other amino acids would allow scientists to ask, and potentially solve, more precise questions about these proteins. Methionine is another amino acid that has a low abundance in most proteins. Previous research has shown that the cell’s normal protein-building machinery can incorporate synthetic versions of methionine into proteins. This suggested that the introduction of chemically reactive alternatives to methionine could offer a way to label membrane proteins with fluorescent probes and free up the cysteines to be targeted with other approaches. Gupta et al. set out to develop a straightforward method to achieve this and started with a well-studied membrane protein, called Shaker, and cells from female African clawed frogs, which are widely used to study membrane proteins. Gupta et al. found that the cells could readily take up a chemically reactive methionine alternative called azidohomoalanine (AHA) from their surrounding solution and incorporate it within the Shaker protein. The AHA took the place of the methionines that are normally found in Shaker, and just like in cysteine-based methods, fluorescent probes could be easily attached to the AHAs in this membrane protein. Shaker is a protein that allows potassium ions to flow across the cell membrane by changing shape in response to the membrane voltage. The fluorescence from those probes also changed with the membrane voltage in a way that was comparable to cysteine-mediated approaches. This indicated that the AHA modification could also be used to track structural changes in the Shaker protein. Finally, Gupta et al. showed that AHA- and cysteine-mediated labeling approaches could be combined to attach two different fluorescent probes onto the Shaker protein. This method will expand the toolbox for researchers studying the relationship between the structure and function of membrane proteins in live cells. In future, it could be applied more widely once the properties of the fluorescent probes for AHA-mediated labeling can be optimized.
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Affiliation(s)
- Kanchan Gupta
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Gilman Es Toombes
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, United States
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24
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LeVine MV, Terry DS, Khelashvili G, Siegel ZS, Quick M, Javitch JA, Blanchard SC, Weinstein H. The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor. Proc Natl Acad Sci U S A 2019; 116:15947-15956. [PMID: 31324743 PMCID: PMC6689989 DOI: 10.1073/pnas.1903020116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. Results from many structural, functional, and computational studies on LeuT, a bacterial NSS homolog, have provided critical insight into the mechanism of sodium-coupled transport, but the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of molecular dynamics simulations, single-molecule fluorescence resonance energy transfer (smFRET) imaging, and measurements of Na+ binding and substrate transport that reveals an allosteric substrate specificity mechanism. In this mechanism, residues F259 and I359 in the substrate binding pocket couple the binding of substrate to Na+ release from the Na2 site by allosterically modulating the stability of a partially open, inward-facing state. We propose a model for transport selectivity in which residues F259 and I359 act as a volumetric sensor that inhibits the transport of bulky amino acids.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Zarek S Siegel
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Matthias Quick
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
- Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
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25
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Golan Y, Alhadeff R, Warshel A, Assaraf YG. ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion. PLoS Comput Biol 2019; 15:e1006882. [PMID: 30893306 PMCID: PMC6443192 DOI: 10.1371/journal.pcbi.1006882] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 04/01/2019] [Accepted: 02/18/2019] [Indexed: 01/29/2023] Open
Abstract
Zinc is a vital trace element crucial for the proper function of some 3,000 cellular proteins. Specifically, zinc is essential for key physiological processes including nucleic acid metabolism, regulation of gene expression, signal transduction, cell division, immune- and nervous system functions, wound healing, and apoptosis. Consequently, impairment of zinc homeostasis disrupts key cellular functions resulting in various human pathologies. Mammalian zinc transport proceeds via two transporter families ZnT and ZIP. However, the detailed mechanism of action of ZnT2, which is responsible for vesicular zinc accumulation and zinc secretion into breast milk during lactation, is currently unknown. Moreover, although the putative coupling of zinc transport to the proton gradient in acidic vesicles has been suggested, it has not been conclusively established. Herein we modeled the mechanism of action of ZnT2 and demonstrated both computationally and experimentally, using functional zinc transport assays, that ZnT2 is indeed a proton-coupled zinc antiporter. Bafilomycin A1, a specific inhibitor of vacuolar-type proton ATPase (V-ATPase) which alkalizes acidic vesicles, abolished ZnT2-dependent zinc transport into intracellular vesicles. Moreover, using LysoTracker Red and Lyso-pHluorin, we further showed that upon transient ZnT2 overexpression in intracellular vesicles and addition of exogenous zinc, the vesicular pH underwent alkalization, presumably due to a proton-zinc antiport; this phenomenon was reversed in the presence of TPEN, a specific zinc chelator. Finally, based on computational energy calculations, we propose that ZnT2 functions as an antiporter with a stoichiometry of 2H+/Zn2+ ion. Hence, ZnT2 is a proton motive force-driven, electroneutral vesicular zinc exchanger, concentrating zinc in acidic vesicles on the expense of proton extrusion to the cytoplasm. Herein we explored the mechanism of action of the human ZnT2 zinc transporter. ZnT2 is essential for zinc accumulation in breast milk and is therefore of paramount medical significance. Expanding on our previous study, we herein present energy calculations suggesting that ZnT2 functions as a proton/zinc antiporter. Our calculations consist of electrostatic and pKa calculations as well as zinc binding free-energy curves. Upon integration of our calculation results, we conclude that ZnT2 functions as an antiporter with a 2H+/Zn2+ stoichiometry, construct a Monte Carlo model to test this mode of ZnT2 transport activity, and validate our computational results experimentally using live human breast epithelial cells. These functional experiments reveal that ZnT2 cannot function in the absence of protons suggesting that it operates as a substrate-induced alternating-access transporter, displaying an apparent 2H+/Zn2+ stoichiometry.
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Affiliation(s)
- Yarden Golan
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Raphael Alhadeff
- Department of Chemistry, University of Southern California, Los Angeles, California
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California
| | - Yehuda G. Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- * E-mail:
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26
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Leone V, Waclawska I, Kossmann K, Koshy C, Sharma M, Prisner TF, Ziegler C, Endeward B, Forrest LR. Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP. J Gen Physiol 2019; 151:381-394. [PMID: 30728216 PMCID: PMC6400524 DOI: 10.1085/jgp.201812111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 11/26/2018] [Accepted: 01/11/2019] [Indexed: 11/20/2022] Open
Abstract
Mechanistic understanding of dynamic membrane proteins such as transporters, receptors, and channels requires accurate depictions of conformational ensembles, and the manner in which they interchange as a function of environmental factors including substrates, lipids, and inhibitors. Spectroscopic techniques such as electron spin resonance (ESR) pulsed electron-electron double resonance (PELDOR), also known as double electron-electron resonance (DEER), provide a complement to atomistic structures obtained from x-ray crystallography or cryo-EM, since spectroscopic data reflect an ensemble and can be measured in more native solvents, unperturbed by a crystal lattice. However, attempts to interpret DEER data are frequently stymied by discrepancies with the structural data, which may arise due to differences in conditions, the dynamics of the protein, or the flexibility of the attached paramagnetic spin labels. Recently, molecular simulation techniques such as EBMetaD have been developed that create a conformational ensemble matching an experimental distance distribution while applying the minimal possible bias. Moreover, it has been proposed that the work required during an EBMetaD simulation to match an experimentally determined distribution could be used as a metric with which to assign conformational states to a given measurement. Here, we demonstrate the application of this concept for a sodium-coupled transport protein, BetP. Because the probe, protein, and lipid bilayer are all represented in atomic detail, the different contributions to the work, such as the extent of protein backbone movements, can be separated. This work therefore illustrates how ranking simulations based on EBMetaD can help to bridge the gap between structural and biophysical data and thereby enhance our understanding of membrane protein conformational mechanisms.
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Affiliation(s)
- Vanessa Leone
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | | | - Katharina Kossmann
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Caroline Koshy
- Max Planck Institute for Biophysics, Frankfurt am Main, Germany
| | - Monika Sharma
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Regensburg, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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27
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Inhibitor binding mode and allosteric regulation of Na +-glucose symporters. Nat Commun 2018; 9:5245. [PMID: 30532032 PMCID: PMC6286348 DOI: 10.1038/s41467-018-07700-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
Sodium-dependent glucose transporters (SGLTs) exploit sodium gradients to transport sugars across the plasma membrane. Due to their role in renal sugar reabsorption, SGLTs are targets for the treatment of type 2 diabetes. Current therapeutics are phlorizin derivatives that contain a sugar moiety bound to an aromatic aglycon tail. Here, we develop structural models of human SGLT1/2 in complex with inhibitors by combining computational and functional studies. Inhibitors bind with the sugar moiety in the sugar pocket and the aglycon tail in the extracellular vestibule. The binding poses corroborate mutagenesis studies and suggest a partial closure of the outer gate upon binding. The models also reveal a putative Na+ binding site in hSGLT1 whose disruption reduces the transport stoichiometry to the value observed in hSGLT2 and increases inhibition by aglycon tails. Our work demonstrates that subtype selectivity arises from Na+-regulated outer gate closure and a variable region in extracellular loop EL5. Sodium-dependent glucose transporters (SGLTs) transport sugars across the plasma membrane and play important roles in renal sugar reabsorption. Here authors develop structural models of human SGLT1/2 (hSGLT1/2) in complex with inhibitors which helps to understand inhibitor subtype selectivity.
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28
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Hellwig N, Peetz O, Ahdash Z, Tascón I, Booth PJ, Mikusevic V, Diskowski M, Politis A, Hellmich Y, Hänelt I, Reading E, Morgner N. Native mass spectrometry goes more native: investigation of membrane protein complexes directly from SMALPs. Chem Commun (Camb) 2018; 54:13702-13705. [PMID: 30452022 PMCID: PMC6289172 DOI: 10.1039/c8cc06284f] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/06/2018] [Indexed: 01/07/2023]
Abstract
Other than more widely used methods, the use of styrene maleic acid allows the direct extraction of membrane proteins from the lipid bilayer into SMALPs keeping it in its native lipid surrounding. Here we present the combined use of SMALPs and LILBID-MS, allowing determination of oligomeric states of membrane proteins of different functionality directly from the native nanodiscs.
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Affiliation(s)
- Nils Hellwig
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
| | - Zainab Ahdash
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Igor Tascón
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Paula J. Booth
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Vedrana Mikusevic
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Marina Diskowski
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Argyris Politis
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Yvonne Hellmich
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Inga Hänelt
- Institute of Biochemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 9
, 60438 Frankfurt
, Germany
| | - Eamonn Reading
- Department of Chemistry
, King's College London
,
7 Trinity Street
, SE1 1DB
, London
, UK
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry
, Goethe University Frankfurt
,
Max-von-Laue-Straße 7
, 60438 Frankfurt
, Germany
.
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29
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Kumar S, Rubino FA, Mendoza AG, Ruiz N. The bacterial lipid II flippase MurJ functions by an alternating-access mechanism. J Biol Chem 2018; 294:981-990. [PMID: 30482840 DOI: 10.1074/jbc.ra118.006099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/14/2018] [Indexed: 11/06/2022] Open
Abstract
The peptidoglycan (PG) cell wall is an essential extracytoplasmic glycopeptide polymer that safeguards bacteria against osmotic lysis and determines cellular morphology. Bacteria use multiprotein machineries for the synthesis of the PG cell wall during cell division and elongation that can be targeted by antibiotics such as the β-lactams. Lipid II, the lipid-linked precursor for PG biogenesis, is synthesized in the inner leaflet of the cytoplasmic membrane and then translocated across the bilayer, where it is ultimately polymerized into PG. In Escherichia coli, MurJ, a member of the MOP exporter superfamily, has been recently shown to have lipid II flippase activity that depends on membrane potential. Because of its essentiality, MurJ could potentially be targeted by much needed novel antibiotics. Recent structural information suggests that a central cavity in MurJ alternates between inward- and outward-open conformations to flip lipid II, but how these conformational changes occur are unknown. Here, we utilized structure-guided cysteine cross-linking and proteolysis-coupled gel analysis to probe the conformational changes of MurJ in E. coli cells. We found that paired cysteine substitutions in transmembrane domains 2 and 8 and periplasmic loops of MurJ could be cross-linked with homobifunctional cysteine cross-linkers, indicating that MurJ can adopt both inward- and outward-facing conformations in vivo Furthermore, we show that dissipating the membrane potential with an ionophore decreases the prevalence of the inward-facing, but not the outward-facing state. Our study provides in vivo evidence that MurJ uses an alternating-access mechanism during the lipid II transport cycle.
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Affiliation(s)
- Sujeet Kumar
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Frederick A Rubino
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Alicia G Mendoza
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
| | - Natividad Ruiz
- From the Department of Microbiology, The Ohio State University, Columbus, Ohio 43210 and
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