1
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Jiang Y, Miyagi A, Wang X, Qiu B, Boudker O, Scheuring S. HS-AFM single-molecule structural biology uncovers basis of transporter wanderlust kinetics. Nat Struct Mol Biol 2024:10.1038/s41594-024-01260-3. [PMID: 38632360 DOI: 10.1038/s41594-024-01260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
The Pyrococcus horikoshii amino acid transporter GltPh revealed, like other channels and transporters, activity mode switching, previously termed wanderlust kinetics. Unfortunately, to date, the basis of these activity fluctuations is not understood, probably due to a lack of experimental tools that directly access the structural features of transporters related to their instantaneous activity. Here, we take advantage of high-speed atomic force microscopy, unique in providing simultaneous structural and temporal resolution, to uncover the basis of kinetic mode switching in proteins. We developed membrane extension membrane protein reconstitution that allows the analysis of isolated molecules. Together with localization atomic force microscopy, principal component analysis and hidden Markov modeling, we could associate structural states to a functional timeline, allowing six structures to be solved from a single molecule, and an inward-facing state, IFSopen-1, to be determined as a kinetic dead-end in the conformational landscape. The approaches presented on GltPh are generally applicable and open possibilities for time-resolved dynamic single-molecule structural biology.
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Affiliation(s)
- Yining Jiang
- Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology Program, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Atsushi Miyagi
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Xiaoyu Wang
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
| | - Biao Qiu
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Olga Boudker
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA.
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2
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Takahashi K, Sato K. The Conventional and Breakthrough Tool for the Study of L-Glutamate Transporters. MEMBRANES 2024; 14:77. [PMID: 38668105 PMCID: PMC11052088 DOI: 10.3390/membranes14040077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/26/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
In our recent report, we clarified the direct interaction between the excitatory amino acid transporter (EAAT) 1/2 and polyunsaturated fatty acids (PUFAs) by applying electrophysiological and molecular biological techniques to Xenopus oocytes. Xenopus oocytes have a long history of use in the scientific field, but they are still attractive experimental systems for neuropharmacological studies. We will therefore summarize the pharmacological significance, advantages (especially in the study of EAAT2), and experimental techniques that can be applied to Xenopus oocytes; our new findings concerning L-glutamate (L-Glu) transporters and PUFAs; and the significant outcomes of our data. The data obtained from electrophysiological and molecular biological studies of Xenopus oocytes have provided us with further important questions, such as whether or not some PUFAs can modulate EAATs as allosteric modulators and to what extent docosahexaenoic acid (DHA) affects neurotransmission and thereby affects brain functions. Xenopus oocytes have great advantages in the studies about the interactions between molecules and functional proteins, especially in the case when the expression levels of the proteins are small in cell culture systems without transfections. These are also proper to study the mechanisms underlying the interactions. Based on the data collected in Xenopus oocyte experiments, we can proceed to the next step, i.e., the physiological roles of the compounds and their significances. In the case of EAAT2, the effects on the neurotransmission should be examined by electrophysiological approach using acute brain slices. For new drug development, pharmacokinetics pharmacodynamics (PKPD) data and blood brain barrier (BBB) penetration data are also necessary. In order not to miss the promising candidate compounds at the primary stages of drug development, we should reconsider using Xenopus oocytes in the early phase of drug development.
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Grants
- a Research Grant on Regulatory Harmonization and Evaluation of Pharmaceuticals, Medical Devices, Regenerative and Cellular Therapy Products, Gene Therapy Products, and Cosmetics from AMED, Japan Japan Agency for Medical Research and Development
- KAKENHI 18700373, 21700422, 17K08330 Ministry of Education, Culture, Sports, Science and Technology
- a Grant for the Program for Promotion of Fundamental Studies in Health Sciences of NIBIO National Institute of Biomedical Innovation, Health and Nutrition
- a grant for Research on Risks of Chemicals, a Labor Science Research Grant for Research on New Drug Development MHLW
- a Grant-in-Aid from Hoansha Foundation Hoansha Foundation
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Affiliation(s)
| | - Kaoru Sato
- Laboratory of Neuropharmacology, Division of Pharmacology, National Institute of Health Sciences, Kanagawa 210-9501, Japan;
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3
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Drew D, Boudker O. Ion and lipid orchestration of secondary active transport. Nature 2024; 626:963-974. [PMID: 38418916 DOI: 10.1038/s41586-024-07062-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024]
Abstract
Transporting small molecules across cell membranes is an essential process in cell physiology. Many structurally diverse, secondary active transporters harness transmembrane electrochemical gradients of ions to power the uptake or efflux of nutrients, signalling molecules, drugs and other ions across cell membranes. Transporters reside in lipid bilayers on the interface between two aqueous compartments, where they are energized and regulated by symported, antiported and allosteric ions on both sides of the membrane and the membrane bilayer itself. Here we outline the mechanisms by which transporters couple ion and solute fluxes and discuss how structural and mechanistic variations enable them to meet specific physiological needs and adapt to environmental conditions. We then consider how general bilayer properties and specific lipid binding modulate transporter activity. Together, ion gradients and lipid properties ensure the effective transport, regulation and distribution of small molecules across cell membranes.
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Affiliation(s)
- David Drew
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY, USA.
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4
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Geertsma ER, Oliver D. SLC26 Anion Transporters. Handb Exp Pharmacol 2024; 283:319-360. [PMID: 37947907 DOI: 10.1007/164_2023_698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Solute carrier family 26 (SLC26) is a family of functionally diverse anion transporters found in all kingdoms of life. Anions transported by SLC26 proteins include chloride, bicarbonate, and sulfate, but also small organic dicarboxylates such as fumarate and oxalate. The human genome encodes ten functional homologs, several of which are causally associated with severe human diseases, highlighting their physiological importance. Here, we review novel insights into the structure and function of SLC26 proteins and summarize the physiological relevance of human members.
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Affiliation(s)
- Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Dominik Oliver
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps University Marburg, Marburg, Germany.
- Center for Mind, Brain and Behavior (CMBB), Universities of Marburg and Giessen, Marburg, Giessen, Germany.
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5
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Xu L, Jia W, Tao X, Ye F, Zhang Y, Ding ZJ, Zheng SJ, Qiao S, Su N, Zhang Y, Wu S, Guo J. Structures and mechanisms of the Arabidopsis cytokinin transporter AZG1. NATURE PLANTS 2024; 10:180-191. [PMID: 38172575 DOI: 10.1038/s41477-023-01590-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/10/2023] [Indexed: 01/05/2024]
Abstract
Cytokinins are essential for plant growth and development, and their tissue distributions are regulated by transmembrane transport. Recent studies have revealed that members of the 'Aza-Guanine Resistant' (AZG) protein family from Arabidopsis thaliana can mediate cytokinin uptake in roots. Here we present 2.7 to 3.3 Å cryo-electron microscopy structures of Arabidopsis AZG1 in the apo state and in complex with its substrates trans-zeatin (tZ), 6-benzyleaminopurine (6-BAP) or kinetin. AZG1 forms a homodimer and each subunit shares a similar topology and domain arrangement with the proteins of the nucleobase/ascorbate transporter (NAT) family. These structures, along with functional analyses, reveal the molecular basis for cytokinin recognition. Comparison of the AZG1 structures determined in inward-facing conformations and predicted by AlphaFold2 in the occluded conformation allowed us to propose that AZG1 may carry cytokinins across the membrane through an elevator mechanism.
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Affiliation(s)
- Lingyi Xu
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Nanhu Brain-computer Interface Institute, Hangzhou, China.
| | - Wei Jia
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
- Calibra Lab at DIAN Diagnostics, Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Provinces, Hangzhou, Zhejiang, China
| | - Xin Tao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Fan Ye
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Nanhu Brain-computer Interface Institute, Hangzhou, China
| | - Yan Zhang
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Nanhu Brain-computer Interface Institute, Hangzhou, China
| | - Zhong Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuai Qiao
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Nannan Su
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Zhang
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Nanhu Brain-computer Interface Institute, Hangzhou, China.
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
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6
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Guo J, Mei H, Zhang Y, Che C, Guo L, Zhang Y, Li H, Sun S. Glutamate-aspartate transporter dysfunction enhances aminoglycoside-induced cochlear hair cell death via NMDA receptor activation. Neurochem Int 2023; 169:105587. [PMID: 37495172 DOI: 10.1016/j.neuint.2023.105587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/02/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Glutamate is a crucial neurotransmitter for hearing transduction in the cochlea, but excess glutamate is detrimental to the survival of cochlear sensory cells. Glutamate-aspartate transporter (GLAST) is the major transporter for glutamate removal; however, its role in aminoglycoside-induced hair cell loss is not well studied. In the present study, we first investigated the localization and expression of GLAST over the course of development of the mouse cochlea, and we found that inhibition of GLAST increased hair cell death. However, when the glutamate receptor NMDAR was inhibited by D-AP5, hair cell death was no longer increased by the GLAST inhibitor. Our results indicate that GLAST inhibition aggravates damage to cochlear hair cells, which may occur via NMDAR, and this suggests new clinical strategies for ameliorating the ototoxicity associated with the dysfunction of glutamate metabolism.
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Affiliation(s)
- Jin Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Honglin Mei
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Yanping Zhang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Chenhao Che
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Luo Guo
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Yunzhong Zhang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Huawei Li
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200032, China.
| | - Shan Sun
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China; NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China.
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7
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Suslova M, Kortzak D, Machtens JP, Kovermann P, Fahlke C. Apo state pore opening as functional basis of increased EAAT anion channel activity in episodic ataxia 6. Front Physiol 2023; 14:1147216. [PMID: 37538371 PMCID: PMC10394623 DOI: 10.3389/fphys.2023.1147216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023] Open
Abstract
SLC1A2 and SLC1A3 encode the glial glutamate transporters EAAT2 and EAAT1, which are not only the predominant glutamate uptake carriers in our brain, but also function as anion channels. Two homologous mutations, which predict substitutions of prolines in the center of the fifth transmembrane helix by arginine (P289R EAAT2, P290R EAAT1), have been identified in patients with epileptic encephalopathy (SLC1A2) or with episodic ataxia type 6 (SLC1A3). Both mutations have been shown to impair glutamate uptake and to increase anion conduction. The molecular processes that link the disease-causing mutations to two major alterations of glutamate transporter function remain insufficiently understood. The mutated proline is conserved in every EAAT. Since the pathogenic changes mainly affect the anion channel function, we here study the functional consequences of the homologous P312R mutation in the neuronal glutamate transporter EAAT4, a low capacity glutamate transporter with predominant anion channel function. To assess the impact of charge and structure of the inserted amino acid for the observed functional changes, we generated and functionally evaluated not only P312R, but also substitutions of P312 with all other amino acids. However, only exchange of proline by arginine, lysine, histidine and asparagine were functionally tolerated. We compared WT, P312R and P312N EAAT4 using a combination of cellular electrophysiology, fast substrate application and kinetic modelling. We found that WT and mutant EAAT4 anion currents can be described with a 11-state model of the transport cycle, in which several states are connected to branching anion channel states to account for the EAAT anion channel function. Substitutions of P312 modify various transitions describing substrate binding/unbinding, translocation or anion channel opening. Most importantly, P312R generates a new anion conducting state that is accessible in the outward facing apo state and that is the main determinant of the increased anion conduction of EAAT transporters carrying this mutation. Our work provides a quantitative description how a naturally occurring mutation changes glutamate uptake and anion currents in two genetic diseases.
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8
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Zhao C, Wang C, Zhang H, Yan W. A mini-review of the role of vesicular glutamate transporters in Parkinson's disease. Front Mol Neurosci 2023; 16:1118078. [PMID: 37251642 PMCID: PMC10211467 DOI: 10.3389/fnmol.2023.1118078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/06/2023] [Indexed: 05/31/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease implicated in multiple interacting neurotransmitter pathways. Glutamate is the central excitatory neurotransmitter in the brain and plays critical influence in the control of neuronal activity. Impaired Glutamate homeostasis has been shown to be closely associated with PD. Glutamate is synthesized in the cytoplasm and stored in synaptic vesicles by vesicular glutamate transporters (VGLUTs). Following its exocytotic release, Glutamate activates Glutamate receptors (GluRs) and mediates excitatory neurotransmission. While Glutamate is quickly removed by excitatory amino acid transporters (EAATs) to maintain its relatively low extracellular concentration and prevent excitotoxicity. The involvement of GluRs and EAATs in the pathophysiology of PD has been widely studied, but little is known about the role of VGLUTs in the PD. In this review, we highlight the role of VGLUTs in neurotransmitter and synaptic communication, as well as the massive alterations in Glutamate transmission and VGLUTs levels in PD. Among them, adaptive changes in the expression level and function of VGLUTs may exert a crucial role in excitatory damage in PD, and VGLUTs are considered as novel potential therapeutic targets for PD.
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Affiliation(s)
- Cheng Zhao
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Chunyu Wang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hainan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Weiqian Yan
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
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9
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Qiu B, Boudker O. Symport and antiport mechanisms of human glutamate transporters. Nat Commun 2023; 14:2579. [PMID: 37142617 PMCID: PMC10160106 DOI: 10.1038/s41467-023-38120-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/17/2023] [Indexed: 05/06/2023] Open
Abstract
Excitatory amino acid transporters (EAATs) uptake glutamate into glial cells and neurons. EAATs achieve million-fold transmitter gradients by symporting it with three sodium ions and a proton, and countertransporting a potassium ion via an elevator mechanism. Despite the availability of structures, the symport and antiport mechanisms still need to be clarified. We report high-resolution cryo-EM structures of human EAAT3 bound to the neurotransmitter glutamate with symported ions, potassium ions, sodium ions alone, or without ligands. We show that an evolutionarily conserved occluded translocation intermediate has a dramatically higher affinity for the neurotransmitter and the countertransported potassium ion than outward- or inward-facing transporters and plays a crucial role in ion coupling. We propose a comprehensive ion coupling mechanism involving a choreographed interplay between bound solutes, conformations of conserved amino acid motifs, and movements of the gating hairpin and the substrate-binding domain.
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Affiliation(s)
- Biao Qiu
- Department of Physiology & Biophysics, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10021, USA.
| | - Olga Boudker
- Department of Physiology & Biophysics, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10021, USA.
- Howard Hughes Medical Institute, Weill Cornell Medicine, 1300 York Ave, New York, NY, 10021, USA.
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10
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Colucci E, Anshari ZR, Patiño-Ruiz MF, Nemchinova M, Whittaker J, Slotboom DJ, Guskov A. Mutation in glutamate transporter homologue GltTk provides insights into pathologic mechanism of episodic ataxia 6. Nat Commun 2023; 14:1799. [PMID: 37002226 PMCID: PMC10066184 DOI: 10.1038/s41467-023-37503-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Episodic ataxias (EAs) are rare neurological conditions affecting the nervous system and typically leading to motor impairment. EA6 is linked to the mutation of a highly conserved proline into an arginine in the glutamate transporter EAAT1. In vitro studies showed that this mutation leads to a reduction in the substrates transport and an increase in the anion conductance. It was hypothesised that the structural basis of these opposed functional effects might be the straightening of transmembrane helix 5, which is kinked in the wild-type protein. In this study, we present the functional and structural implications of the mutation P208R in the archaeal homologue of glutamate transporters GltTk. We show that also in GltTk the P208R mutation leads to reduced aspartate transport activity and increased anion conductance, however a cryo-EM structure reveals that the kink is preserved. The arginine side chain of the mutant points towards the lipidic environment, where it may engage in interactions with the phospholipids, thereby potentially interfering with the transport cycle and contributing to stabilisation of an anion conducting state.
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Affiliation(s)
- Emanuela Colucci
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Zaid R Anshari
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Miyer F Patiño-Ruiz
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Mariia Nemchinova
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Jacob Whittaker
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Dirk J Slotboom
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands.
| | - Albert Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands.
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11
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Seiferth D, Biggin PC, Tucker SJ. When is a hydrophobic gate not a hydrophobic gate? J Gen Physiol 2022; 154:213612. [PMID: 36287215 PMCID: PMC9614698 DOI: 10.1085/jgp.202213210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The flux of ions through a channel is most commonly regulated by changes that result in steric occlusion of its pore. However, ion permeation can also be prevented by formation of a desolvation barrier created by hydrophobic residues that line the pore. As a result of relatively minor structural changes, confined hydrophobic regions in channels may undergo transitions between wet and dry states to gate the pore closed without physical constriction of the permeation pathway. This concept is referred to as hydrophobic gating, and many examples of this process have been demonstrated. However, the term is also now being used in a much broader context that often deviates from its original meaning. In this Viewpoint, we explore the formal definition of a hydrophobic gate, discuss examples of this process compared with other gating mechanisms that simply exploit hydrophobic residues and/or lipids in steric closure of the pore, and describe the best practice for identification of a hydrophobic gate.
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Affiliation(s)
- David Seiferth
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen J Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK.,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
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12
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Dastvan R, Rasouli A, Dehghani-Ghahnaviyeh S, Gies S, Tajkhorshid E. Proton-driven alternating access in a spinster lipid transporter. Nat Commun 2022; 13:5161. [PMID: 36055994 PMCID: PMC9440201 DOI: 10.1038/s41467-022-32759-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange. The Spns lipid transporters use ion gradients to drive substrate transport, including bioactive sphingolipids. Here, Dastvan et al. investigated how binding of protons powers the conformational changes that enable broad transport by a bacterial Spns.
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Affiliation(s)
- Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha Gies
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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13
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Kato T, Kusakizako T, Jin C, Zhou X, Ohgaki R, Quan L, Xu M, Okuda S, Kobayashi K, Yamashita K, Nishizawa T, Kanai Y, Nureki O. Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2. Nat Commun 2022; 13:4714. [PMID: 35953475 PMCID: PMC9372063 DOI: 10.1038/s41467-022-32442-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Glutamate is a pivotal excitatory neurotransmitter in mammalian brains, but excessive glutamate causes numerous neural disorders. Almost all extracellular glutamate is retrieved by the glial transporter, Excitatory Amino Acid Transporter 2 (EAAT2), belonging to the SLC1A family. However, in some cancers, EAAT2 expression is enhanced and causes resistance to therapies by metabolic disturbance. Despite its crucial roles, the detailed structural information about EAAT2 has not been available. Here, we report cryo-EM structures of human EAAT2 in substrate-free and selective inhibitor WAY213613-bound states at 3.2 Å and 2.8 Å, respectively. EAAT2 forms a trimer, with each protomer consisting of transport and scaffold domains. Along with a glutamate-binding site, the transport domain possesses a cavity that could be disrupted during the transport cycle. WAY213613 occupies both the glutamate-binding site and cavity of EAAT2 to interfere with its alternating access, where the sensitivity is defined by the inner environment of the cavity. We provide the characterization of the molecular features of EAAT2 and its selective inhibition mechanism that may facilitate structure-based drug design for EAAT2. EAAT2 is an amino acid transporter implicated in glutamate homeostasis in brain and therapy resistance of cancer cells. Here, the authors report cryo-EM structures and reveal inhibitory mechanisms via selective inhibitor WAY213613.
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Affiliation(s)
- Takafumi Kato
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biochemistry, The University of Oxford, Oxford, UK
| | - Tsukasa Kusakizako
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Chunhuan Jin
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Xinyu Zhou
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryuichi Ohgaki
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI), Osaka University, Osaka, Japan
| | - LiLi Quan
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Molecular Pharmacology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Minhui Xu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Suguru Okuda
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kan Kobayashi
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Peptidream Inc, Kawasaki, Japan
| | - Keitaro Yamashita
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tomohiro Nishizawa
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan. .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI), Osaka University, Osaka, Japan.
| | - Osamu Nureki
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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14
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Guo D, Luo L, Kong Y, Kuang Z, Wen S, Zhao M, Zhang W, Fan J. Enantioselective neurotoxicity and oxidative stress effects of paclobutrazol in zebrafish (Danio rerio). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 185:105136. [PMID: 35772839 DOI: 10.1016/j.pestbp.2022.105136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/07/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Paclobutrazol is a widely used chiral plant growth regulator and its enantioselective toxicity in aquatic organisms is less explored till now. Herein, the enantioselective neurotoxicity of paclobutrazol mediated by oxidative stress in zebrafish were investigated. The oxidative stress parameters and neurotoxic biomarkers changed significantly in each exposure group, and paclobutrazol showed enantioselective toxicity in zebrafish. Firstly, (2R, 3R)-paclobutrazol exhibited a stronger oxidative stress in zebrafish than (2S, 3S)-enantiomer (P < 0.05). Then, activities of acetylcholinesterase, calcineurin, and total nitric oxide synthase in (2R, 3R)-paclobutrazol treatments were 0.61-0.89, 1.24-1.53, and 1.21-1.35-fold stronger (P < 0.05) than those in (2S, 3S)-enantiomer treatments, respectively. Next, the content variations of four neurotransmitters in zebrafish exposed to (2R, 3R)-paclobutrazol were significantly larger than those in (2S, 3S)-enantiomer treatments (P < 0.05). Moreover, (2R, 3R)-paclobutrazol had stronger binding with the receptors than (2S, 3S)-enantiomer through molecular docking. The integrated biomarker response values further demonstrated that (2R, 3R)-paclobutrazol showed stronger toxicity to zebrafish than (2S, 3S)-enantiomer. Furthermore, the neurotoxicity of paclobutrazol can be interpreted as the mediating effect of oxidative stress in zebrafish through correlation analysis, and an adverse outcome pathway for the nervous system in zebrafish induced by paclobutrazol was proposed. This work will greatly extend our understanding on the enantioselective toxic effects of paclobutrazol in aquatic organisms.
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Affiliation(s)
- Dong Guo
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China
| | - Lulu Luo
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China
| | - Yuan Kong
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhiyang Kuang
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China
| | - Siyi Wen
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Weiguang Zhang
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China; GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou 510006, China.
| | - Jun Fan
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou 510006, China; GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou 510006, China.
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15
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Freidman N, Briot C, Ryan R. Characterizing unexpected interactions of a glutamine transporter inhibitor with members of the SLC1A transporter family. J Biol Chem 2022; 298:102178. [PMID: 35752361 PMCID: PMC9293768 DOI: 10.1016/j.jbc.2022.102178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 11/29/2022] Open
Abstract
The solute carrier 1A family comprises a group of membrane proteins that act as dual-function amino acid transporters and chloride (Cl−) channels and includes the alanine serine cysteine transporters (ASCTs) as well as the excitatory amino acid transporters. ASCT2 is regarded as a promising target for cancer therapy, as it can transport glutamine and other neutral amino acids into cells and is upregulated in a range of solid tumors. The compound L-γ-glutamyl-p-nitroanilide (GPNA) is widely used in studies probing the role of ASCT2 in cancer biology; however, the mechanism by which GPNA inhibits ASCT2 is not entirely clear. Here, we used electrophysiology and radiolabelled flux assays to demonstrate that GPNA activates the Cl− conductance of ASCT2 to the same extent as a transported substrate, whilst not undergoing the full transport cycle. This is a previously unreported phenomenon for inhibitors of the solute carrier 1A family but corroborates a body of literature suggesting that the structural requirements for transport are distinct from those for Cl− channel formation. We also show that in addition to its currently known targets, GPNA inhibits several of the excitatory amino acid transporters. Together, these findings raise questions about the true mechanisms of its anticancer effects.
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Affiliation(s)
- Natasha Freidman
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Chelsea Briot
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Renae Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia.
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16
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Khera R, Mehdipour AR, Bolla JR, Kahnt J, Welsch S, Ermler U, Muenke C, Robinson CV, Hummer G, Xie H, Michel H. Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. EMBO J 2022; 41:e109990. [PMID: 35698912 PMCID: PMC9475539 DOI: 10.15252/embj.2021109990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022] Open
Abstract
Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.
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Affiliation(s)
- Radhika Khera
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Centre for molecular modelling, Ghent University, Zwijnaarde, Belgium
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Joerg Kahnt
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ulrich Ermler
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Cornelia Muenke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
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17
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Chen I, Wu Q, Font J, Ryan RM. The twisting elevator mechanism of glutamate transporters reveals the structural basis for the dual transport-channel functions. Curr Opin Struct Biol 2022; 75:102405. [PMID: 35709614 DOI: 10.1016/j.sbi.2022.102405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
Abstract
Glutamate transporters facilitate the removal of this excitatory neurotransmitter from the synapse. Increasing evidence indicates that this process is linked to intrinsic chloride channel activity that is thermodynamically uncoupled from substrate transport. A recent cryo-EM structure of GltPh - an archaeal homolog of the glutamate transporters - in an open channel state has shed light on the structural basis for channel opening formed at the interface of two domains within the transporter which is gated by two clusters of hydrophobic residues. These transporters cycle through several conformational states during the transport process, including the chloride conducting state, which appears to be stabilised by protein-membrane interactions and membrane deformation. Several point mutations that perturb the chloride conductance can have detrimental effects and are linked to the pathogenesis of the neurological disorder, episodic ataxia type 6.
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Affiliation(s)
- Ichia Chen
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Qianyi Wu
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Josep Font
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Renae M Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia.
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18
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Zhang Z, Chen H, Geng Z, Yu Z, Li H, Dong Y, Zhang H, Huang Z, Jiang J, Zhao Y. Structural basis of ligand binding modes of human EAAT2. Nat Commun 2022; 13:3329. [PMID: 35680945 PMCID: PMC9184463 DOI: 10.1038/s41467-022-31031-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 05/31/2022] [Indexed: 01/07/2023] Open
Abstract
In the central nervous system (CNS), excitatory amino acid transporters (EAATs) mediate the uptake of excitatory neurotransmitter glutamate and maintain its low concentrations in the synaptic cleft for avoiding neuronal cytotoxicity. Dysfunction of EAATs can lead to many psychiatric diseases. Here we report cryo-EM structures of human EAAT2 in an inward-facing conformation, in the presence of substrate glutamate or selective inhibitor WAY-213613. The glutamate is coordinated by extensive hydrogen bonds and further stabilized by HP2. The inhibitor WAY-213613 occupies a similar binding pocket to that of the substrate glutamate. Upon association with the WAY-213613, the HP2 undergoes a substantial conformational change, and in turn stabilizes the inhibitor binding by forming hydrophobic interactions. Electrophysiological experiments elucidate that the unique S441 plays pivotal roles in the binding of hEAAT2 with glutamate or WAY-213613, and the I464-L467-V468 cluster acts as a key structural determinant for the selective inhibition of this transporter by WAY-213613.
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Affiliation(s)
- Zhenglai Zhang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huiwen Chen
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ze Geng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, China.,IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China
| | - Zhuoya Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanli Dong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, China. .,IDG/McGovern Institute for Brain Research, Peking University, Beijing, 100871, China.
| | - Juquan Jiang
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin, 150030, China.
| | - Yan Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Kapoor K, Thangapandian S, Tajkhorshid E. Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem Sci 2022; 13:4150-4169. [PMID: 35440993 PMCID: PMC8985516 DOI: 10.1039/d2sc00841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 11/21/2022] Open
Abstract
Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of a protein is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables are first used to describe the transition cycle of the transporter. An extended set of conformations (extended ensemble) representing the full transition cycle between the inward- and the outward-facing states is then used to seed high-throughput docking calculations of known substrates, non-substrates, and modulators of the transporter. Large differences are predicted in the binding affinities to different conformations, with compounds showing stronger binding affinities to intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the binding modes shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present within the individual TMD leaflets. Based on the results, the central cavity is further divided into two major subsites, first preferably binding smaller substrates and high-affinity inhibitors, whereas the second one shows preference for larger substrates and low-affinity modulators. These central subsites along with the low-affinity interaction sites present within the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further an optimization strategy for developing more potent inhibitors of Pgp, based on increasing its specificity to the extended ensemble of the protein, instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in silico studies using single static structures of Pgp, our results show better agreement with experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.
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Affiliation(s)
- Karan Kapoor
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Sundar Thangapandian
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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20
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Pant S, Wu Q, Ryan R, Tajkhorshid E. Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1 (EAAT1). ACS Chem Neurosci 2022; 13:776-785. [PMID: 35192345 PMCID: PMC9725111 DOI: 10.1021/acschemneuro.1c00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Excitatory amino acid transporters (EAATs) are glutamate transporters that belong to the solute carrier 1A (SLC1A) family. They couple glutamate transport to the cotransport of three sodium (Na+) ions and one proton (H+) and the counter-transport of one potassium (K+) ion. In addition to this coupled transport, binding of cotransported species to EAATs activates a thermodynamically uncoupled chloride (Cl-) conductance. Structures of SLC1A family members have revealed that these transporters use a twisting elevator mechanism of transport, where a mobile transport domain carries substrate and coupled ions across the membrane, while a static scaffold domain anchors the transporter in the membrane. We recently demonstrated that the uncoupled Cl- conductance is activated by the formation of an aqueous pore at the domain interface during the transport cycle in archaeal GltPh. However, a pathway for the uncoupled Cl- conductance has not been reported for the EAATs, and it is unclear if such a pathway is conserved. Here, we employ all-atom molecular dynamics (MD) simulations combined with enhanced sampling, free-energy calculations, and experimental mutagenesis to approximate large-scale conformational changes during the transport process and identified a Cl--conducting conformation in human EAAT1 (hEAAT1). Sampling the large-scale structural transitions in hEAAT1 allowed us to capture an intermediate conformation formed during the transport cycle with a continuous aqueous pore at the domain interface. The free-energy calculations performed for the conduction of Cl- and Na+ ions through the captured conformation highlight the presence of two hydrophobic gates that control low-barrier movement of Cl- through the aqueous pathway. Overall, our findings provide insights into the mechanism by which a human neurotransmitter transporter supports functional duality of active transport and passive Cl- permeation and confirm the commonality of this mechanism in different members of the SLC1A family.
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Affiliation(s)
- Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Qianyi Wu
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Renae Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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21
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Beckstein O, Naughton F. General principles of secondary active transporter function. BIOPHYSICS REVIEWS 2022; 3:011307. [PMID: 35434715 PMCID: PMC8984959 DOI: 10.1063/5.0047967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/23/2022] [Indexed: 04/13/2023]
Abstract
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.
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Affiliation(s)
- Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
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22
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Puthenveetil R, Christenson ET, Vinogradova O. New Horizons in Structural Biology of Membrane Proteins: Experimental Evaluation of the Role of Conformational Dynamics and Intrinsic Flexibility. MEMBRANES 2022; 12:227. [PMID: 35207148 PMCID: PMC8877495 DOI: 10.3390/membranes12020227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
A plethora of membrane proteins are found along the cell surface and on the convoluted labyrinth of membranes surrounding organelles. Since the advent of various structural biology techniques, a sub-population of these proteins has become accessible to investigation at near-atomic resolutions. The predominant bona fide methods for structure solution, X-ray crystallography and cryo-EM, provide high resolution in three-dimensional space at the cost of neglecting protein motions through time. Though structures provide various rigid snapshots, only an amorphous mechanistic understanding can be inferred from interpolations between these different static states. In this review, we discuss various techniques that have been utilized in observing dynamic conformational intermediaries that remain elusive from rigid structures. More specifically we discuss the application of structural techniques such as NMR, cryo-EM and X-ray crystallography in studying protein dynamics along with complementation by conformational trapping by specific binders such as antibodies. We finally showcase the strength of various biophysical techniques including FRET, EPR and computational approaches using a multitude of succinct examples from GPCRs, transporters and ion channels.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Dr., Bethesda, MD 20892, USA
| | | | - Olga Vinogradova
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA
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23
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Wu Q, Akhter A, Pant S, Cho E, Zhu JX, Garner AR, Ohyama T, Tajkhorshid E, van Meyel DJ, Ryan RM. Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. J Clin Invest 2022; 132:154891. [PMID: 35167492 PMCID: PMC8970671 DOI: 10.1172/jci154891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate is the predominant excitatory neurotransmitter in the mammalian central nervous system (CNS). Excitatory Amino Acid Transporters (EAATs) regulate extracellular glutamate by transporting it into cells, mostly glia, to terminate neurotransmission and to avoid neurotoxicity. EAATs are also chloride (Cl-) channels, but the physiological role of Cl- conductance through EAATs is poorly understood. Mutations of human EAAT1 (hEAAT1) have been identified in patients with episodic ataxia type 6 (EA6). One mutation showed increased Cl- channel activity and decreased glutamate transport, but the relative contributions of each function of hEAAT1 to mechanisms underlying the pathology of EA6 remain unclear. Here we investigated the effects of five additional EA6-related mutations on hEAAT1 function in Xenopus laevis oocytes, and on CNS function in a Drosophila melanogaster model of locomotor behavior. Our results indicate that mutations resulting in decreased hEAAT1 Cl- channel activity but with functional glutamate transport can also contribute to the pathology of EA6, highlighting the importance of Cl- homeostasis in glial cells for proper CNS function. We also identified a novel mechanism involving an ectopic sodium (Na+) leak conductance in glial cells. Together, these results strongly support the idea that EA6 is primarily an ion channelopathy of CNS glia.
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Affiliation(s)
- Qianyi Wu
- School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Azman Akhter
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Eunjoo Cho
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Jin Xin Zhu
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | | | - Tomoko Ohyama
- Department of Biology, McGill University, Montreal, Canada
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Donald J van Meyel
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Renae M Ryan
- School of Medical Sciences, University of Sydney, Sydney, Australia
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24
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Guo R, Goudeli E, Xu W, Richardson JJ, Xu W, Pan S. Exploiting Molecular Dynamics in Composite Coatings to Design Robust Super-Repellent Surfaces. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104331. [PMID: 34997692 PMCID: PMC8867138 DOI: 10.1002/advs.202104331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Fluorinated motifs are promising for the engineering of repellent coatings, however, a fundamental understanding of how to effectively bind these motifs to various substrates is required to improve their stability in different use scenarios. Herein, the binding of fluorinated polyhedral oligomeric silsesquioxanes (POSS) using a cyanoacrylate glue (binder) is computationally and experimentally evaluated. The composite POSS-binder coatings display ultralow surface energy (≈10 mJ m-2 ), while still having large surface adhesions to substrates (300-400 nN), highlighting that super-repellent coatings (contact angles >150°) can be readily generated with this composite approach. Importantly, the coatings show super-repellency to both corrosive liquids (e.g., 98 wt% H2 SO4 ) and ultralow surface tension liquids (e.g., alcohols), with ultralow roll-off angles (<5°), and tunable resistance to liquid penetration. Additionally, these coatings demonstrate the potential in effective cargo loading and robust self-cleaning properties, where experimental datasets are correlated with both relevant theoretical predictions and systematic all-atom molecular dynamics simulations of the repellent coatings. This work not only holds promise for chemical shielding, heat transfer, and liquid manipulations but offers a facile yet robust pathway for engineering advanced coatings by effectively combining components for their mutually desired properties.
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Affiliation(s)
- Rui Guo
- State Key Laboratory of Chemo/Biosensing and Chemometricsand College of Chemistry and Chemical EngineeringHunan UniversityChangsha410082China
| | - Eirini Goudeli
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Wanjun Xu
- State Key Laboratory of Chemo/Biosensing and Chemometricsand College of Chemistry and Chemical EngineeringHunan UniversityChangsha410082China
| | - Joseph J. Richardson
- Department of Materials EngineeringThe University of Tokyo7‐3‐1 Hongo, BunkyoTokyo113‐8656Japan
| | - Weijian Xu
- Department of Chemical EngineeringThe University of MelbourneParkvilleVictoria3010Australia
| | - Shuaijun Pan
- State Key Laboratory of Chemo/Biosensing and Chemometricsand College of Chemistry and Chemical EngineeringHunan UniversityChangsha410082China
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25
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Functional and Kinetic Comparison of Alanine Cysteine Serine Transporters ASCT1 and ASCT2. Biomolecules 2022; 12:biom12010113. [PMID: 35053261 PMCID: PMC8773628 DOI: 10.3390/biom12010113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Neutral amino acid transporters ASCT1 and ASCT2 are two SLC1 (solute carrier 1) family subtypes, which are specific for neutral amino acids. The other members of the SLC1 family are acidic amino acid transporters (EAATs 1–5). While the functional similarities and differences between the EAATs have been well studied, less is known about how the subtypes ASCT1 and 2 differ in kinetics and function. Here, by performing comprehensive electrophysiological analysis, we identified similarities and differences between these subtypes, as well as novel functional properties, such as apparent substrate affinities of the inward-facing conformation (in the range of 70 μM for L-serine as the substrate). Key findings were: ASCT1 has a higher apparent affinity for Na+, as well as a larger [Na+] dependence of substrate affinity compared to ASCT2. However, the general sequential Na+/substrate binding mechanism with at least one Na+ binding first, followed by amino acid substrate, followed by at least one more Na+ ion, appears to be conserved between the two subtypes. In addition, the first Na+ binding step, presumably to the Na3 site, occurs with high apparent affinity (<1 mM) in both transporters. In addition, ASCT1 and 2 show different substrate selectivities, where ASCT1 does not respond to extracellular glutamine. Finally, in both transporters, we measured rapid, capacitive charge movements upon application and removal of amino acid, due to rearrangement of the translocation equilibrium. This charge movement decays rapidly, with a time constant of 4–5 ms and recovers with a time constant in the 15 ms range after substrate removal. This places a lower limit on the turnover rate of amino acid exchange by these two transporters of 60–80 s−1.
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26
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Kovermann P, Engels M, Müller F, Fahlke C. Cellular Physiology and Pathophysiology of EAAT Anion Channels. Front Cell Neurosci 2022; 15:815279. [PMID: 35087380 PMCID: PMC8787812 DOI: 10.3389/fncel.2021.815279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Excitatory amino acid transporters (EAATs) optimize the temporal resolution and energy demand of mammalian excitatory synapses by quickly removing glutamate from the synaptic cleft into surrounding neuronal and glial cells and ensuring low resting glutamate concentrations. In addition to secondary active glutamate transport, EAATs also function as anion channels. The channel function of these transporters is conserved in all homologs ranging from archaebacteria to mammals; however, its physiological roles are insufficiently understood. There are five human EAATs, which differ in their glutamate transport rates. Until recently the high-capacity transporters EAAT1, EAAT2, and EAAT3 were believed to conduct only negligible anion currents, with no obvious function in cell physiology. In contrast, the low-capacity glutamate transporters EAAT4 and EAAT5 are thought to regulate neuronal signaling as glutamate-gated channels. In recent years, new experimental approaches and novel animal models, together with the discovery of a human genetic disease caused by gain-of-function mutations in EAAT anion channels have enabled identification of the first physiological and pathophysiological roles of EAAT anion channels.
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27
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Kovermann P, Kolobkova Y, Franzen A, Fahlke C. Mutations associated with epileptic encephalopathy modify EAAT2 anion channel function. Epilepsia 2021; 63:388-401. [PMID: 34961934 DOI: 10.1111/epi.17154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Mutations in the gene solute carrier family member 1A2 (SLC1A2) encoding the excitatory amino acid transporter 2 (EAAT2) are associated with severe forms of epileptic encephalopathy. EAAT2 is expressed in glial cells and presynaptic nerve terminals and represents the main l-glutamate uptake carrier in the mammalian brain. It does not only function as a secondary active glutamate transporter, but also as an anion channel. How naturally occurring mutations affect these two transport functions of EAAT2 and how such alterations cause epilepsy is insufficiently understood. METHODS Here we studied the functional consequences of three disease-associated mutations, which predict amino acid exchanges p.Gly82Arg (G82R), p.Leu85Pro (L85P), and p.Pro289Arg (P289R), by heterologous expression in mammalian cells, biochemistry, confocal imaging, and whole-cell patch-clamp recordings of EAAT2 l-glutamate transport and anion current. RESULTS G82R and L85P exchange amino acid residues contribute to the formation of the EAAT anion pore. They enlarge the pore diameter sufficiently to permit the passage of l-glutamate and thus function as l-glutamate efflux pathways. The mutation P289R decreases l-glutamate uptake, but increases anion currents despite a lower membrane expression. SIGNIFICANCE l-glutamate permeability of the EAAT anion pore is an unexpected functional consequence of naturally occurring single amino acid substitutions. l-glutamate efflux through mutant EAAT2 anion channels will cause glutamate excitotoxicity and neuronal hyperexcitability in affected patients. Antagonists that selectively suppress the EAAT anion channel function could serve as therapeutic agents in the future.
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Affiliation(s)
- Peter Kovermann
- Molekular- und Zellphysiologie (IBI-1) Forschungszentrum Jülich, Institute of Biological Information Processing, Jülich, Germany
| | - Yulia Kolobkova
- Molekular- und Zellphysiologie (IBI-1) Forschungszentrum Jülich, Institute of Biological Information Processing, Jülich, Germany
| | - Arne Franzen
- Molekular- und Zellphysiologie (IBI-1) Forschungszentrum Jülich, Institute of Biological Information Processing, Jülich, Germany
| | - Christoph Fahlke
- Molekular- und Zellphysiologie (IBI-1) Forschungszentrum Jülich, Institute of Biological Information Processing, Jülich, Germany
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28
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Ciftci D, Martens C, Ghani VG, Blanchard SC, Politis A, Huysmans GHM, Boudker O. Linking function to global and local dynamics in an elevator-type transporter. Proc Natl Acad Sci U S A 2021; 118:e2025520118. [PMID: 34873050 PMCID: PMC8670510 DOI: 10.1073/pnas.2025520118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/24/2022] Open
Abstract
Transporters cycle through large structural changes to translocate molecules across biological membranes. The temporal relationships between these changes and function, and the molecular properties setting their rates, determine transport efficiency-yet remain mostly unknown. Using single-molecule fluorescence microscopy, we compare the timing of conformational transitions and substrate uptake in the elevator-type transporter GltPh We show that the elevator-like movements of the substrate-loaded transport domain across membranes and substrate release are kinetically heterogeneous, with rates varying by orders of magnitude between individual molecules. Mutations increasing the frequency of elevator transitions and reducing substrate affinity diminish transport rate heterogeneities and boost transport efficiency. Hydrogen deuterium exchange coupled to mass spectrometry reveals destabilization of secondary structure around the substrate-binding site, suggesting that increased local dynamics leads to faster rates of global conformational changes and confers gain-of-function properties that set transport rates.
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Affiliation(s)
- Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065
| | - Chloe Martens
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Vishnu G Ghani
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Argyris Politis
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Gerard H M Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- Tri-Institutional Training Program in Chemical Biology, New York, NY 10065
- Howard Hughes Medical Institute, Weill Cornell Medicine, New York, NY 10065
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29
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IUPAB 2021 Symposium 13: ion channels and membrane transporters. Biophys Rev 2021; 13:871-873. [DOI: 10.1007/s12551-021-00874-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022] Open
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30
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Conquer by cryo-EM without physically dividing. Biochem Soc Trans 2021; 49:2287-2298. [PMID: 34709401 DOI: 10.1042/bst20210360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022]
Abstract
This mini-review provides an update regarding the substantial progress that has been made in using single-particle cryo-EM to obtain high-resolution structures for proteins and other macromolecules whose particle sizes are smaller than 100 kDa. We point out that establishing the limits of what can be accomplished, both in terms of particle size and attainable resolution, serves as a guide for what might be expected when attempting to improve the resolution of small flexible portions of a larger structure using focused refinement approaches. These approaches, which involve computationally ignoring all but a specific, targeted region of interest on the macromolecules, is known as 'masking and refining,' and it thus is the computational equivalent of the 'divide and conquer' approach that has been used so successfully in X-ray crystallography. The benefit of masked refinement, however, is that one is able to determine structures in their native architectural context, without physically separating them from the biological connections that they require for their function. This mini-review also compares where experimental achievements currently stand relative to various theoretical estimates for the smallest particle size that can be successfully reconstructed to high resolution. Since it is clear that a substantial gap still remains between the two, we briefly recap the areas in which further improvement seems possible, both in equipment and in methods.
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31
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Multiscale simulations of large complexes in conjunction with cryo-EM analysis. Curr Opin Struct Biol 2021; 72:27-32. [PMID: 34399155 DOI: 10.1016/j.sbi.2021.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022]
Abstract
The cellular environment is highly crowded with most proteins and RNA/DNA forming homomeric and heteromeric complexes. Essential questions regarding how these complexes switch between functional, rest, and abnormal states with regulators or modifications remain challenging and complicated. Here, we review the recent progress integrating cryoelectron microscopy and multiscale molecular modeling to understand the dynamics and function-related mechanism in protein-RNA/DNA complexes, protein-protein complexes/assemblies, and membrane protein complexes. One future direction of multiscale simulations will be to interpret the large complex multibody regulation in assembly-induced function enhancement in conjunction with advanced atomic resolution structural-biology techniques and specialized computing architectures.
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Elucidating the Mechanism Behind Sodium-Coupled Neurotransmitter Transporters by Reconstitution. Neurochem Res 2021; 47:127-137. [PMID: 34347265 DOI: 10.1007/s11064-021-03413-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
Sodium-coupled neurotransmitter transporters play a fundamental role in the termination of synaptic neurotransmission, which makes them a major drug target. The reconstitution of these secondary active transporters into liposomes has shed light on their molecular transport mechanisms. From the earliest days of the reconstitution technique up to today's single-molecule studies, insights from live functioning transporters have been indispensable for our understanding of their physiological impact. The two classes of sodium-coupled neurotransmitter transporters, the neurotransmitter: sodium symporters and the excitatory amino acid transporters, have vastly different molecular structures, but complementary proteoliposome studies have sought to unravel their ion-dependence and transport kinetics. Furthermore, reconstitution experiments have been used on both protein classes to investigate the role of e.g. the lipid environment, of posttranslational modifications, and of specific amino acid residues in transport. Techniques that allow the detection of transport at a single-vesicle resolution have been developed, and single-molecule studies have started to reveal single transporter kinetics, which will expand our understanding of how transport across the membrane is facilitated at protein level. Here, we review a selection of the results and applications where the reconstitution of the two classes of neurotransmitter transporters has been instrumental.
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Scalise M, Console L, Cosco J, Pochini L, Galluccio M, Indiveri C. ASCT1 and ASCT2: Brother and Sister? SLAS DISCOVERY 2021; 26:1148-1163. [PMID: 34269129 DOI: 10.1177/24725552211030288] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The SLC1 family includes seven members divided into two groups, namely, EAATs and ASCTs, that share similar 3D architecture; the first one includes high-affinity glutamate transporters, and the second one includes SLC1A4 and SLC1A5, known as ASCT1 and ASCT2, respectively, responsible for the traffic of neutral amino acids across the cell plasma membrane. The physiological role of ASCT1 and ASCT2 has been investigated over the years, revealing different properties in terms of substrate specificities, affinities, and regulation by physiological effectors and posttranslational modifications. Furthermore, ASCT1 and ASCT2 are involved in pathological conditions, such as neurodegenerative disorders and cancer. This has driven research in the pharmaceutical field aimed to find drugs able to target the two proteins.This review focuses on structural, functional, and regulatory aspects of ASCT1 and ASCT2, highlighting similarities and differences.
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Affiliation(s)
- Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Lara Console
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Jessica Cosco
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Lorena Pochini
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Michele Galluccio
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia e Scienze della Terra), Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Arcavacata di Rende, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), Bari, Italy
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CryoEM reconstructions of membrane proteins solved in several amphipathic solvents, nanodisc, amphipol and detergents, yield amphipathic belts of similar sizes corresponding to a common ordered solvent layer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183693. [PMID: 34271006 DOI: 10.1016/j.bbamem.2021.183693] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
To maintain membrane proteins soluble in aqueous solution, amphipathic compounds are used to shield the hydrophobic patch of their membrane insertion, which forms a belt around the protein. This amphipathic belt is seldom looked at due to the difficulty to visualize it. Cryo-EM is now offering this possibility, where belts are visible in 3D reconstructions. We investigated membrane proteins solved in nanodiscs, amphipols or detergents to analyze whether the nature of the amphipathic compound influences the belt size in 3D reconstructions. We identified belt boundaries in map-density distributions and measured distances for every reconstruction. We showed that all the belts create on average similar reconstructions, whether they originate from the same protein, or from protein from different shapes and structures. There is no difference among detergents or types of nanodisc used. These observations illustrate that the belt observed in 3D reconstructions corresponds to the minimum ordered layer around membrane proteins.
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