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Zhekova HR, Ramirez Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. Biophys J 2024:S0006-3495(24)00327-8. [PMID: 38760929 DOI: 10.1016/j.bpj.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 04/09/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024] Open
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3-, CO32-, Cl-, Na+, K+, NH3, and H+, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl-/HCO3- exchanger) and NBCe1 (Na+-CO32-cotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na+-CO32-/Cl- exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Daniel P Ramirez Echemendía
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Brain Research Institute, University of California, Los Angeles, Los Angeles, California.
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2
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Hu W, Song A, Zheng H. Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2. Nat Commun 2024; 15:3616. [PMID: 38684689 PMCID: PMC11059360 DOI: 10.1038/s41467-024-48028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.
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Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Alex Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US.
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3
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Zhang C, Wei G, Zhou N, Wang Y, Feng J, Wang X, Zhang A, Chen K. Systematic Engineering of Escherichia coli for Efficient Production of Pseudouridine from Glucose and Uracil. ACS Synth Biol 2024; 13:1303-1311. [PMID: 38529630 DOI: 10.1021/acssynbio.4c00028] [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: 03/27/2024]
Abstract
In this study, we proposed a biological approach to efficiently produce pseudouridine (Ψ) from glucose and uracil in vivo using engineered Escherichia coli. By screening host strains and core enzymes, E. coli MG1655 overexpressing Ψ monophosphate (ΨMP) glycosidase and ΨMP phosphatase was obtained, which displayed the highest Ψ concentration. Then, optimization of the RBS sequences, enhancement of ribose 5-phosphate supply in the cells, and overexpression of the membrane transport protein UraA were investigated. Finally, fed-batch fermentation of Ψ in a 5 L fermentor can reach 27.5 g/L with a yield of 89.2 mol % toward uracil and 25.6 mol % toward glucose within 48 h, both of which are the highest to date. In addition, the Ψ product with a high purity of 99.8% can be purified from the fermentation broth after crystallization. This work provides an efficient and environmentally friendly protocol for allowing for the possibility of Ψ bioproduction on an industrial scale.
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Affiliation(s)
- Chi Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jia Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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4
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577062. [PMID: 38352416 PMCID: PMC10862720 DOI: 10.1101/2024.01.24.577062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A. Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Samuel P. Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael A. Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Novartis Biomedical Research, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Lead contact
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5
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Wang L, Hoang A, Gil-Iturbe E, Laganowsky A, Quick M, Zhou M. Mechanism of anion exchange and small-molecule inhibition of pendrin. Nat Commun 2024; 15:346. [PMID: 38184688 PMCID: PMC10771415 DOI: 10.1038/s41467-023-44612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pendrin (SLC26A4) is an anion exchanger that mediates bicarbonate (HCO3-) exchange for chloride (Cl-) and is crucial for maintaining pH and salt homeostasis in the kidney, lung, and cochlea. Pendrin also exports iodide (I-) in the thyroid gland. Pendrin mutations in humans lead to Pendred syndrome, causing hearing loss and goiter. Inhibition of pendrin is a validated approach for attenuating airway hyperresponsiveness in asthma and for treating hypertension. However, the mechanism of anion exchange and its inhibition by drugs remains poorly understood. We applied cryo-electron microscopy to determine structures of pendrin from Sus scrofa in the presence of either Cl-, I-, HCO3- or in the apo-state. The structures reveal two anion-binding sites in each protomer, and functional analyses show both sites are involved in anion exchange. The structures also show interactions between the Sulfate Transporter and Anti-Sigma factor antagonist (STAS) and transmembrane domains, and mutational studies suggest a regulatory role. We also determine the structure of pendrin in a complex with niflumic acid (NFA), which uncovers a mechanism of inhibition by competing with anion binding and impeding the structural changes necessary for anion exchange. These results reveal directions for understanding the mechanisms of anion selectivity and exchange and their regulations by the STAS domain. This work also establishes a foundation for analyzing the pathophysiology of mutations associated with Pendred syndrome.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony Hoang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Eva Gil-Iturbe
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Matthias Quick
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
- Area Neuroscience - Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
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6
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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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7
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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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8
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Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D. Substrate binding and inhibition of the anion exchanger 1 transporter. Nat Struct Mol Biol 2023; 30:1495-1504. [PMID: 37679563 PMCID: PMC11008770 DOI: 10.1038/s41594-023-01085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-bound and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying an AE1 inhibitor. Together, our findings provide insight into mechanisms of solute carrier transport and inhibition.
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Affiliation(s)
- Michael J Capper
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander C Stone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yamuna Kalyani Mathiharan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raul Habib
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yihan Zhao
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Wacker
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Li L, Zhou L, Jiang C, Liu Z, Meng D, Luo F, He Q, Yin H. AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia. Front Microbiol 2023; 14:1243987. [PMID: 37744906 PMCID: PMC10512742 DOI: 10.3389/fmicb.2023.1243987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Microorganism-mediated biohydrometallurgy, a sustainable approach for metal recovery from ores, relies on the metabolic activity of acidophilic bacteria. Acidithiobacillia with sulfur/iron-oxidizing capacities are extensively studied and applied in biohydrometallurgy-related processes. However, only 14 distinct proteins from Acidithiobacillia have experimentally determined structures currently available. This significantly hampers in-depth investigations of Acidithiobacillia's structure-based biological mechanisms pertaining to its relevant biohydrometallurgical processes. To address this issue, we employed a state-of-the-art artificial intelligence (AI)-driven approach, with a median model confidence of 0.80, to perform high-quality full-chain structure predictions on the pan-proteome (10,458 proteins) of the type strain Acidithiobacillia. Additionally, we conducted various case studies on de novo protein structural prediction, including sulfate transporter and iron oxidase, to demonstrate how accurate structure predictions and gene co-occurrence networks can contribute to the development of mechanistic insights and hypotheses regarding sulfur and iron utilization proteins. Furthermore, for the unannotated proteins that constitute 35.8% of the Acidithiobacillia proteome, we employed the deep-learning algorithm DeepFRI to make structure-based functional predictions. As a result, we successfully obtained gene ontology (GO) terms for 93.6% of these previously unknown proteins. This study has a significant impact on improving protein structure and function predictions, as well as developing state-of-the-art techniques for high-throughput analysis of large proteomic data.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC, United States
| | - Qiang He
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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10
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Zhekova HR, Ramirez-Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Coarse-grained molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546592. [PMID: 37425774 PMCID: PMC10327080 DOI: 10.1101/2023.06.26.546592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO 3 -, CO 3 2- , Cl - , Na + , K + , NH 3 and H + necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl - /HCO 3 - exchanger) and NBCe1 (Na + -CO 3 2- cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed multiple 50 µs coarse-grained molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na + -CO 3 2- /Cl - exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed. Statement of significance The SLC4 protein family is involved in critical physiological processes like pH and blood pressure regulation and maintenance of ion homeostasis. Its members can be found in various tissues. A number of studies suggest possible lipid regulation of the SLC4 function. However, the protein-lipid interactions in the SLC4 family are still poorly understood. Here we make use of long coarse-grained molecular dynamics simulations to assess the protein-lipid interactions in three SLC4 proteins with different transport modes, AE1, NBCe1, and NDCBE. We identify putative lipid binding sites for several lipid types of potential mechanistic importance, discuss them in the framework of the known experimental data and provide a necessary basis for further studies on lipid regulation of SLC4 function.
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11
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Liu Q, Zhang X, Huang H, Chen Y, Wang F, Hao A, Zhan W, Mao Q, Hu Y, Han L, Sun Y, Zhang M, Liu Z, Li GL, Zhang W, Shu Y, Sun L, Chen Z. Asymmetric pendrin homodimer reveals its molecular mechanism as anion exchanger. Nat Commun 2023; 14:3012. [PMID: 37230976 DOI: 10.1038/s41467-023-38303-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/23/2023] [Indexed: 05/27/2023] Open
Abstract
Pendrin (SLC26A4) is an anion exchanger expressed in the apical membranes of selected epithelia. Pendrin ablation causes Pendred syndrome, a genetic disorder associated with sensorineural hearing loss, hypothyroid goiter, and reduced blood pressure. However its molecular structure has remained unknown, limiting our understanding of the structural basis of transport. Here, we determine the cryo-electron microscopy structures of mouse pendrin with symmetric and asymmetric homodimer conformations. The asymmetric homodimer consists of one inward-facing protomer and the other outward-facing protomer, representing coincident uptake and secretion- a unique state of pendrin as an electroneutral exchanger. The multiple conformations presented here provide an inverted alternate-access mechanism for anion exchange. The structural and functional data presented here disclose the properties of an anion exchange cleft and help understand the importance of disease-associated variants, which will shed light on the pendrin exchange mechanism.
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Affiliation(s)
- Qianying Liu
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiang Zhang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Hui Huang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxin Chen
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200031, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Fang Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200031, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Aihua Hao
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Wuqiang Zhan
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiyu Mao
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxia Hu
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lin Han
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yifang Sun
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Meng Zhang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhimin Liu
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Geng-Lin Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200031, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200031, China
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, 200031, China
| | - Weijia Zhang
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yilai Shu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital and State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200031, China.
- 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.
| | - Lei Sun
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, China.
| | - Zhenguo Chen
- The Fifth People's Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Epigenetics, Shanghai, 200032, China.
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12
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Sauve S, Williamson J, Polasa A, Moradi M. Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters. MEMBRANES 2023; 13:membranes13050462. [PMID: 37233523 DOI: 10.3390/membranes13050462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
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Affiliation(s)
- Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Williamson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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13
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Zhang Q, Jian L, Yao D, Rao B, Xia Y, Hu K, Li S, Shen Y, Cao M, Qin A, Zhao J, Cao Y. The structural basis of the pH-homeostasis mediated by the Cl -/HCO 3- exchanger, AE2. Nat Commun 2023; 14:1812. [PMID: 37002221 PMCID: PMC10066210 DOI: 10.1038/s41467-023-37557-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
The cell maintains its intracellular pH in a narrow physiological range and disrupting the pH-homeostasis could cause dysfunctional metabolic states. Anion exchanger 2 (AE2) works at high cellular pH to catalyze the exchange between the intracellular HCO3- and extracellular Cl-, thereby maintaining the pH-homeostasis. Here, we determine the cryo-EM structures of human AE2 in five major operating states and one transitional hybrid state. Among those states, the AE2 shows the inward-facing, outward-facing, and intermediate conformations, as well as the substrate-binding pockets at two sides of the cell membrane. Furthermore, critical structural features were identified showing an interlock mechanism for interactions among the cytoplasmic N-terminal domain and the transmembrane domain and the self-inhibitory effect of the C-terminal loop. The structural and cell-based functional assay collectively demonstrate the dynamic process of the anion exchange across membranes and provide the structural basis for the pH-sensitive pH-rebalancing activity of AE2.
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Affiliation(s)
- Qing Zhang
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Liyan Jian
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Deqiang Yao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, 200127, Shanghai, China
| | - Bing Rao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Ying Xia
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Kexin Hu
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Shaobai Li
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Yafeng Shen
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - Mi Cao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China
| | - An Qin
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
- Department of Orthopaedics, Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Yu Cao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 115 Jinzun Road, 200125, Shanghai, China.
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14
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Wang M, He J, Li S, Cai Q, Zhang K, She J. Structural basis of vitamin C recognition and transport by mammalian SVCT1 transporter. Nat Commun 2023; 14:1361. [PMID: 36914666 PMCID: PMC10011568 DOI: 10.1038/s41467-023-37037-3] [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: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 03/15/2023] Open
Abstract
Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for vitamin C uptake and tissue distribution in mammals. Here, we present cryogenic electron microscopy structures of mouse SVCT1 in both the apo and substrate-bound states. Mouse SVCT1 forms a homodimer with each protomer containing a core domain and a gate domain. The tightly packed extracellular interfaces between the core domain and gate domain stabilize the protein in an inward-open conformation for both the apo and substrate-bound structures. Vitamin C binds at the core domain of each subunit, and two potential sodium ions are identified near the binding site. The coordination of sodium ions by vitamin C explains their coupling transport. SVCTs probably deliver substrate through an elevator mechanism in combination with local structural arrangements. Altogether, our results reveal the molecular mechanism by which SVCTs recognize vitamin C and lay a foundation for further mechanistic studies on SVCT substrate transport.
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Affiliation(s)
- Mingxing Wang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Jin He
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Qianwen Cai
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China.
| | - Ji She
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China.
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15
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Beltran JL, McGrath LG, Caruso S, Bain RK, Hendrix CE, Kamran H, Johnston HG, Collings RM, Henry MCN, Abera TAL, Donoso VA, Carriker EC, Thurtle-Schmidt BH. Borate Transporters and SLC4 Bicarbonate Transporters Share Key Functional Properties. MEMBRANES 2023; 13:membranes13020235. [PMID: 36837738 PMCID: PMC9959716 DOI: 10.3390/membranes13020235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/03/2023]
Abstract
Borate transporters are membrane transport proteins that regulate intracellular borate levels. In plants, borate is a micronutrient essential for growth but is toxic in excess, while in yeast, borate is unnecessary for growth and borate export confers tolerance. Borate transporters share structural homology with human bicarbonate transporters in the SLC4 family despite low sequence identity and differences in transported solutes. Here, we characterize the S. cerevisiae borate transporter Bor1p and examine whether key biochemical features of SLC4 transporters extend to borate transporters. We show that borate transporters and SLC4 transporters share multiple properties, including lipid-promoted dimerization, sensitivity to stilbene disulfonate-derived inhibitors, and a requirement for an acidic residue at the solute binding site. We also identify several amino acids critical for Bor1p function and show that disease-causing mutations in human SLC4A1 will eliminate in vivo function when their homologous mutations are introduced in Bor1p. Our data help elucidate mechanistic features of Bor1p and reveal significant functional properties shared between borate transporters and SLC4 transporters.
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16
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CryoEM structures of anion exchanger 1 capture multiple states of inward- and outward-facing conformations. Commun Biol 2022; 5:1372. [PMID: 36517642 PMCID: PMC9751308 DOI: 10.1038/s42003-022-04306-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Anion exchanger 1 (AE1, band 3) is a major membrane protein of red blood cells and plays a key role in acid-base homeostasis, urine acidification, red blood cell shape regulation, and removal of carbon dioxide during respiration. Though structures of the transmembrane domain (TMD) of three SLC4 transporters, including AE1, have been resolved previously in their outward-facing (OF) state, no mammalian SLC4 structure has been reported in the inward-facing (IF) conformation. Here we present the cryoEM structures of full-length bovine AE1 with its TMD captured in both IF and OF conformations. Remarkably, both IF-IF homodimers and IF-OF heterodimers were detected. The IF structures feature downward movement in the core domain with significant unexpected elongation of TM11. Molecular modeling and structure guided mutagenesis confirmed the functional significance of residues involved in TM11 elongation. Our data provide direct evidence for an elevator-like mechanism of ion transport by an SLC4 family member.
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17
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Dobson L, Szekeres LI, Gerdán C, Langó T, Zeke A, Tusnády GE. TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures. Nucleic Acids Res 2022; 51:D517-D522. [PMID: 36318239 PMCID: PMC9825488 DOI: 10.1093/nar/gkac928] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 12/12/2022] Open
Abstract
AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https://tmalphafold.ttk.hu/.
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Affiliation(s)
- Laszlo Dobson
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Levente I Szekeres
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Csongor Gerdán
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - András Zeke
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gábor E Tusnády
- To whom correspondence should be addressed. Tel: +36 1 382 6709;
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18
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Futamata H, Fukuda M, Umeda R, Yamashita K, Tomita A, Takahashi S, Shikakura T, Hayashi S, Kusakizako T, Nishizawa T, Homma K, Nureki O. Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility. Nat Commun 2022; 13:6208. [PMID: 36266333 PMCID: PMC9584906 DOI: 10.1038/s41467-022-34017-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/11/2022] [Indexed: 01/11/2023] Open
Abstract
Outer hair cell elecromotility, driven by prestin, is essential for mammalian cochlear amplification. Here, we report the cryo-EM structures of thermostabilized prestin (PresTS), complexed with chloride, sulfate, or salicylate at 3.52-3.63 Å resolutions. The central positively-charged cavity allows flexible binding of various anion species, which likely accounts for the known distinct modulations of nonlinear capacitance (NLC) by different anions. Comparisons of these PresTS structures with recent prestin structures suggest rigid-body movement between the core and gate domains, and provide mechanistic insights into prestin inhibition by salicylate. Mutations at the dimeric interface severely diminished NLC, suggesting that stabilization of the gate domain facilitates core domain movement, thereby contributing to the expression of NLC. These findings advance our understanding of the molecular mechanism underlying mammalian cochlear amplification.
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Affiliation(s)
- Haon Futamata
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiro Fukuda
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.26999.3d0000 0001 2151 536XPresent Address: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo; Meguro-ku, Tokyo, 153-8503 Japan
| | - Rie Umeda
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Keitaro Yamashita
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.42475.300000 0004 0605 769XPresent Address: MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Atsuhiro Tomita
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Satoe Takahashi
- grid.16753.360000 0001 2299 3507Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Takafumi Shikakura
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Shigehiko Hayashi
- grid.258799.80000 0004 0372 2033Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Tsukasa Kusakizako
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Tomohiro Nishizawa
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan ,grid.268441.d0000 0001 1033 6139Present Address: Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kazuaki Homma
- grid.16753.360000 0001 2299 3507Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA ,grid.16753.360000 0001 2299 3507The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL 60608 USA
| | - Osamu Nureki
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
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19
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M S, N RP, Chakraborty A, Rajendrasozhan S. Proteomic profiling of Deinococcus radiodurans with response to thioredoxin reductase inhibitor and ionizing radiation treatment. J Proteomics 2022; 267:104697. [PMID: 35995383 DOI: 10.1016/j.jprot.2022.104697] [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: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022]
Abstract
This study explains the importance of cellular redox system in preserving the proteome of the radioresistant Deinococcus radiodurans. The thioredoxin reductase (TrxR) redox system was inhibited by ebselen (10 μM), and then the bacterium was exposed to 4 kGy of ionizing radiation. The differentially expressed proteins were analyzed using label-free quantitative (LFQ) proteomics. The 4 kGy radiation treatment increases the expression of stress response proteins like osmotically inducible protein OsmC, catalase, and metallophosphoesterase compared to control. Ebselen plus radiation treatment augments oxidoreductases proteins in D. radiodurans. Further, the proteins involved in glycolysis, tricarboxylic acetic acid (TCA) and proteins like proteases, peptidase, and peptide transporters were significantly decreased in the ebselen plus radiation group compared to radiation treated group. Further, ebselen plus radiation treatment increases the ATP-binding cassette (ABC) transporters involved in the efflux of toxic chemicals and nutrient uptake and the stress response related membrane protein like S-layer homology domain-containing protein in D. radiodurans. Thus, the results show that the altered redox status via inhibition of TrxR redox system significantly affects the expression of essential cellular proteins for the survival. The cellular content of D. radiodurans may be used to handle redox imbalances in the normal cells during cancer radiotherapy. SIGNIFICANCE: Deinococcus radiodurans is a popular radioresistance organism with efficient antioxidant systems and DNA repair mechanisms. There are many antioxidant systems and small molecules that responsible for its resistance. The importance of thiol based antioxidant systems in its resistance property has not fully studied yet. Thioredoxin reductase is an important disulfide containing protein that involved in maintaining redox homeostasis. The TrxR inhibition affects the cell survival and synthesis of molecules against ionizing radiation. In this study we are reporting the effects of TrxR inhibitor on proteome of D. radiodurans upon ionizing radiation. This study reveals the significance of TrxR antioxidant system on the proteome of D. radiodurans. The inhibition of TrxR antioxidant system and the subsequent disturbances in the proteome content makes the organism vulnerable to oxidative stress.
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Affiliation(s)
- Sudharsan M
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, 608 002, Tamilnadu, India
| | - Rajendra Prasad N
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar, 608 002, Tamilnadu, India
| | - Anindita Chakraborty
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, 700098, West Bengal, India
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20
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TTYH family members form tetrameric complexes at the cell membrane. Commun Biol 2022; 5:886. [PMID: 36042377 PMCID: PMC9427776 DOI: 10.1038/s42003-022-03862-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
The conserved Tweety homolog (TTYH) family consists of three paralogs in vertebrates, displaying a ubiquitous expression pattern. Although considered as ion channels for almost two decades, recent structural and functional analyses refuted this role. Intriguingly, while all paralogs shared a dimeric stoichiometry following detergent solubilization, their structures revealed divergence in their relative subunit orientation. Here, we determined the stoichiometry of intact mouse TTYH (mTTYH) complexes in cells. Using cross-linking and single-molecule fluorescence microscopy, we demonstrate that mTTYH1 and mTTYH3 form tetramers at the plasma membrane, stabilized by interactions between their extracellular domains. Using blue-native PAGE, fluorescence-detection size-exclusion chromatography, and hydrogen/deuterium exchange mass spectrometry (HDX-MS), we reveal that detergent solubilization results in tetramers destabilization, leading to their dissolution into dimers. Moreover, HDX-MS demonstrates that the extracellular domains are stabilized in the context of the tetrameric mTTYH complex. Together, our results expose the innate tetrameric organization of TTYH complexes at the cell membrane. Future structural analyses of these assemblies in native membranes are required to illuminate their long-sought cellular function.
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21
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Kalli AC, Reithmeier RAF. Organization and Dynamics of the Red Blood Cell Band 3 Anion Exchanger SLC4A1: Insights From Molecular Dynamics Simulations. Front Physiol 2022; 13:817945. [PMID: 35283786 PMCID: PMC8914234 DOI: 10.3389/fphys.2022.817945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/27/2022] [Indexed: 01/16/2023] Open
Abstract
Molecular dynamics (MD) simulations have provided new insights into the organization and dynamics of the red blood cell Band 3 anion exchanger (AE1, SLC4A1). Band 3, like many solute carriers, works by an alternating access mode of transport where the protein rapidly (104/s) changes its conformation between outward and inward-facing states via a transient occluded anion-bound intermediate. While structural studies of membrane proteins usually reveal valuable structural information, these studies provide a static view often in the presence of detergents. Membrane transporters are embedded in a lipid bilayer and associated lipids play a role in their folding and function. In this review, we highlight MD simulations of Band 3 in realistic lipid bilayers that revealed specific lipid and protein interactions and were used to re-create a model of the Wright (Wr) blood group antigen complex of Band 3 and Glycophorin A. Current MD studies of Band 3 and related transporters are focused on describing the trajectory of substrate binding and translocation in real time. A structure of the intact Band 3 protein has yet to be achieved experimentally, but cryo-electron microscopy in combination with MD simulations holds promise to capture the conformational changes associated with anion transport in exquisite molecular detail.
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Affiliation(s)
- Antreas C. Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Reinhart A. F. Reithmeier
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- *Correspondence: Reinhart A. F. Reithmeier,
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22
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Wu H, Liu S, Su P, Xie Z, Gui T, Zhao L, Liu Y, Chen L. Molecular insight into coordination sites for substrates and their coupling kinetics in Na
+
/HCO
3
−
cotransporter NBCe1. J Physiol 2022; 600:3083-3111. [DOI: 10.1113/jp282034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/03/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Han Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Shiyong Liu
- School of Physics Huazhong University of Science and Technology Wuhan 430074 China
| | - Pan Su
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Zhang‐Dong Xie
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Tian‐Xiang Gui
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Lei Zhao
- Department of Obstetrics Maternal and Child Health Hospital of Hubei Province Wuhan 430070 China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
| | - Li‐Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education School of Life Science & Technology Huazhong University of Science & Technology Wuhan 430074 China
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23
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Butan C, Song Q, Bai JP, Tan WJT, Navaratnam D, Santos-Sacchi J. Single particle cryo-EM structure of the outer hair cell motor protein prestin. Nat Commun 2022; 13:290. [PMID: 35022426 PMCID: PMC8755724 DOI: 10.1038/s41467-021-27915-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
The mammalian outer hair cell (OHC) protein prestin (Slc26a5) differs from other Slc26 family members due to its unique piezoelectric-like property that drives OHC electromotility, the putative mechanism for cochlear amplification. Here, we use cryo-electron microscopy to determine prestin’s structure at 3.6 Å resolution. Prestin is structurally similar to the anion transporter Slc26a9. It is captured in an inward-open state which may reflect prestin’s contracted state. Two well-separated transmembrane (TM) domains and two cytoplasmic sulfate transporter and anti-sigma factor antagonist (STAS) domains form a swapped dimer. The transmembrane domains consist of 14 transmembrane segments organized in two 7+7 inverted repeats, an architecture first observed in the bacterial symporter UraA. Mutation of prestin’s chloride binding site removes salicylate competition with anions while retaining the prestin characteristic displacement currents (Nonlinear Capacitance), undermining the extrinsic voltage sensor hypothesis for prestin function. Prestin, expressed in outer hair cell (OHC), belongs to the Slc26 transporter family and functions as a voltage-driven motor that drives OHC electromotility. Here, the authors report cryo-EM structure and characterization of gerbil prestin, with insights into its mechanism of action.
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Affiliation(s)
- Carmen Butan
- Department of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, CT, USA
| | - Qiang Song
- Department of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, CT, USA
| | - Jun-Ping Bai
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - Winston J T Tan
- Department of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, CT, USA
| | - Dhasakumar Navaratnam
- Department of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, CT, USA. .,Department of Neurology, Yale University School of Medicine, New Haven, CT, USA. .,Neuroscience, Yale University School of Medicine, New Haven, CT, USA.
| | - Joseph Santos-Sacchi
- Department of Surgery (Otolaryngology), Yale University School of Medicine, New Haven, CT, USA. .,Neuroscience, Yale University School of Medicine, New Haven, CT, USA. .,Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA.
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24
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Progress in understanding the structural mechanism underlying prestin's electromotile activity. Hear Res 2021; 423:108423. [PMID: 34987017 DOI: 10.1016/j.heares.2021.108423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
Prestin (SLC26A5), a member of the SLC26 transporter family, is the molecular actuator that drives OHC electromotility (eM). A wealth of biophysical data indicates that eM is mediated by an area motor mechanism, in which prestin molecules act as elementary actuators by changing their area in the membrane in response to changes in membrane potential. The area changes of a large and densely packed population of prestin molecules sum up, resulting in macroscopic cellular movement. At the single protein level, this model implies major voltage-driven conformational rearrangements. However, the nature of these structural dynamics remained unknown. A main obstacle in elucidating the eM mechanism has been the lack of structural information about SLC26 transporters. The recent emergence of several high-resolution cryo-EM structures of prestin as well as other SLC26 transporter family members now provides a reliable picture of prestin's molecular architecture. Thus, SLC26 transporters including prestin generally are dimers, and each protomer is folded according to a 7+7 transmembrane domain inverted repeat (7TMIR) architecture. Here, we review these structural findings and discuss insights into a potential molecular mechanism. Most important, distinct conformations were observed when purifying and imaging prestin bound to either its physiological ligand, chloride, or to competitively inhibitory anions, sulfate or salicylate. Despite differences in detail, these structural snapshots indicate that the conformational landscape of prestin includes rearrangements between the two major domains of prestin's transmembrane region (TMD), core and scaffold ('gate') domains. Notably, distinct conformations differ in the area the TMD occupies in the membrane and in their impact on the immediate lipid environment. Both effects can contribute to generate membrane deformation and thus may underly electromotility. Further functional studies will be necessary to determine whether these or similar structural rearrangements are driven by membrane potential to mediate piezoelectric activity. This article is part of the Special Issue Outer hair cell Edited by Joseph Santos-Sacchi and Kumar Navaratnam.
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25
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Holzhüter K, Geertsma ER. Uniport, Not Proton-Symport, in a Non-Mammalian SLC23 Transporter. J Mol Biol 2021; 434:167393. [PMID: 34896363 DOI: 10.1016/j.jmb.2021.167393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/17/2021] [Accepted: 12/01/2021] [Indexed: 10/25/2022]
Abstract
SLC23 family members are transporters of either nucleobases or ascorbate. While the mammalian SLC23 ascorbate transporters are sodium-coupled, the non-mammalian nucleobase transporters have been proposed, but not formally shown, to be proton-coupled symporters. This assignment is exclusively based on in vivo transport assays using protonophores. Here, by establishing the first in vitro transport assay for this protein family, we demonstrate that a representative member of the SLC23 nucleobase transporters operates as a uniporter instead. We explain these conflicting assignments by identifying a critical role of uracil phosphoribosyltransferase, the enzyme converting uracil to UMP, in driving uracil uptake in vivo. Detailed characterization of uracil phosphoribosyltransferase reveals that the sharp reduction of uracil uptake in whole cells in presence of protonophores is caused by acidification-induced enzyme inactivation. The SLC23 family therefore consists of both uniporters and symporters in line with the structurally related SLC4 and SLC26 families that have previously been demonstrated to accommodate both transport modes as well.
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Affiliation(s)
- Katharina Holzhüter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt am Main, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
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26
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Tatsaki E, Anagnostopoulou E, Zantza I, Lazou P, Mikros E, Frillingos S. Identification of New Specificity Determinants in Bacterial Purine Nucleobase Transporters based on an Ancestral Sequence Reconstruction Approach. J Mol Biol 2021; 433:167329. [PMID: 34710398 DOI: 10.1016/j.jmb.2021.167329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022]
Abstract
The relation of sequence with specificity in membrane transporters is challenging to explore. Most relevant studies until now rely on comparisons of present-day homologs. In this work, we study a set of closely related transporters by employing an evolutionary, ancestral-reconstruction approach and reveal unexpected new specificity determinants. We analyze a monophyletic group represented by the xanthine-specific XanQ of Escherichia coli in the Nucleobase-Ascorbate Transporter/Nucleobase-Cation Symporter-2 (NAT/NCS2) family. We reconstructed AncXanQ, the putative common ancestor of this clade, expressed it in E. coli K-12, and found that, in contrast to XanQ, it encodes a high-affinity permease for both xanthine and guanine, which also recognizes adenine, hypoxanthine, and a range of analogs. AncXanQ conserves all binding-site residues of XanQ and differs substantially in only five intramembrane residues outside the binding site. We subjected both homologs to rationally designed mutagenesis and present evidence that these five residues are linked with the specificity change. In particular, we reveal Ser377 of XanQ (Gly in AncXanQ) as a major determinant. Replacement of this Ser with Gly enlarges the specificity of XanQ towards an AncXanQ-phenotype. The ortholog from Neisseria meningitidis retaining Gly at this position is also a xanthine/guanine transporter with extended substrate profile like AncXanQ. Molecular Dynamics shows that the S377G replacement tilts transmembrane helix 12 resulting in rearrangement of Phe376 relative to Phe94 in the XanQ binding pocket. This effect may rationalize the enlarged specificity. On the other hand, the specificity effect of S377G can be masked by G27S or other mutations through epistatic interactions.
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Affiliation(s)
- Ekaterini Tatsaki
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Eleni Anagnostopoulou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece. https://twitter.com/EleniAnagn
| | - Iliana Zantza
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece; Institute of Biosciences, University Research Center of Ioannina, Ioannina, Greece.
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27
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Alanazi SA, Harisa GI, Badran MM, Alanazi FK, Elzayat E, Alomrani AH, Al Meanazel OT, Al Meanazel AT. Crosstalk of low density lipoprotein and liposome as a paradigm for targeting of 5-fluorouracil into hepatic cells: cytotoxicity and liver deposition. Bioengineered 2021; 12:914-926. [PMID: 33678142 PMCID: PMC8806320 DOI: 10.1080/21655979.2021.1896202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/19/2021] [Indexed: 11/20/2022] Open
Abstract
This study aimed to utilize cholesterol conjugation of 5-fluorouracil (5-FUC) and liposomal formulas to enhance the partitioning of 5-FU into low density lipoprotein (LDL) to target hepatocellular carcinoma (HCC). Thus, 5-FU and 5-FUCwere loaded into liposomes. Later, the direct loading and transfer of 5-FU, and 5-FUC from liposomes into LDL were attained. The preparations were characterized in terms of particle size, zeta potential, morphology, entrapment efficiency, and cytotoxicity using the HepG2 cell line. Moreover, the drug deposition into the LDL and liver tissues was investigated. The present results revealed that liposomal preparations have a nanosize range (155 - 194 nm), negative zeta potential (- 0.82 to - 16 mV), entrapment efficiency of 69% for 5-FU, and 66% for 5-FUC. Moreover, LDL particles have a nanosize range (28-49 nm), negative zeta potential (- 17 to -27 mV), and the entrapment efficiency is 11% for 5-FU and 85% for 5-FUC. Furthermore, 5-FUC loaded liposomes displayed a sustained release profile (57%) at 24 h compared to fast release (92%) of 5-FU loaded liposomes. 5-FUC and liposomal formulas enhanced the transfer of 5-FUC into LDL compared to 5-FU. 5-FUC loaded liposomes and LDL have greater cytotoxicity against HepG2 cell lines compared to 5-FU and 5-FUC solutions. Moreover, the deposition of 5-FUC in LDL (26.87ng/mg) and liver tissues (534 ng/gm tissue) was significantly increased 5-FUC liposomes compared to 5-FU (11.7 ng/g tissue) liposomal formulation. In conclusion, 5-FUC is a promising strategy for hepatic targeting of 5-FU through LDL-mediated gateway.
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Affiliation(s)
- Saleh A. Alanazi
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmaceutical Care Services, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Gamaleldin I. Harisa
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Biochemistry, College of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed M. Badran
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, Al-Azhar University, Nasr City Cairo, Egypt
| | - Fars K. Alanazi
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ehab Elzayat
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah H. Alomrani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Nanobiotechnology Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Osaid T. Al Meanazel
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Michael Sayegh Faculty of Pharmacy, Aqaba University of Technology, Aqaba, Jordan
| | - Ahmed T. Al Meanazel
- Prince Naif for the Health Research Center, King Saud University, Riyadh, Saudi Arabia
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28
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Jennings ML. Cell Physiology and Molecular Mechanism of Anion Transport by Erythrocyte Band 3/AE1. Am J Physiol Cell Physiol 2021; 321:C1028-C1059. [PMID: 34669510 PMCID: PMC8714990 DOI: 10.1152/ajpcell.00275.2021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The major transmembrane protein of the red blood cell, known as band 3, AE1, and SLC4A1, has two main functions: 1) catalysis of Cl-/HCO3- exchange, one of the steps in CO2 excretion; 2) anchoring the membrane skeleton. This review summarizes the 150 year history of research on red cell anion transport and band 3 as an experimental system for studying membrane protein structure and ion transport mechanisms. Important early findings were that red cell Cl- transport is a tightly coupled 1:1 exchange and band 3 is labeled by stilbenesulfonate derivatives that inhibit anion transport. Biochemical studies showed that the protein is dimeric or tetrameric (paired dimers) and that there is one stilbenedisulfonate binding site per subunit of the dimer. Transport kinetics and inhibitor characteristics supported the idea that the transporter acts by an alternating access mechanism with intrinsic asymmetry. The sequence of band 3 cDNA provided a framework for detailed study of protein topology and amino acid residues important for transport. The identification of genetic variants produced insights into the roles of band 3 in red cell abnormalities and distal renal tubular acidosis. The publication of the membrane domain crystal structure made it possible to propose concrete molecular models of transport. Future research directions include improving our understanding of the transport mechanism at the molecular level and of the integrative relationships among band 3, hemoglobin, carbonic anhydrase, and gradients (both transmembrane and subcellular) of HCO3-, Cl-, O2, CO2, pH, and NO metabolites during pulmonary and systemic capillary gas exchange.
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Affiliation(s)
- Michael L Jennings
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States
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29
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Wang W, Tsirulnikov K, Zhekova HR, Kayık G, Khan HM, Azimov R, Abuladze N, Kao L, Newman D, Noskov SY, Zhou ZH, Pushkin A, Kurtz I. Cryo-EM structure of the sodium-driven chloride/bicarbonate exchanger NDCBE. Nat Commun 2021; 12:5690. [PMID: 34584093 PMCID: PMC8478935 DOI: 10.1038/s41467-021-25998-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
SLC4 transporters play significant roles in pH regulation and cellular sodium transport. The previously solved structures of the outward facing (OF) conformation for AE1 (SLC4A1) and NBCe1 (SLC4A4) transporters revealed an identical overall fold despite their different transport modes (chloride/bicarbonate exchange versus sodium-carbonate cotransport). However, the exact mechanism determining the different transport modes in the SLC4 family remains unknown. In this work, we report the cryo-EM 3.4 Å structure of the OF conformation of NDCBE (SLC4A8), which shares transport properties with both AE1 and NBCe1 by mediating the electroneutral exchange of sodium-carbonate with chloride. This structure features a fully resolved extracellular loop 3 and well-defined densities corresponding to sodium and carbonate ions in the tentative substrate binding pocket. Further, we combine computational modeling with functional studies to unravel the molecular determinants involved in NDCBE and SLC4 transport.
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Affiliation(s)
- Weiguang Wang
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA
| | - Kirill Tsirulnikov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Hristina R. Zhekova
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Gülru Kayık
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Hanif Muhammad Khan
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Rustam Azimov
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Natalia Abuladze
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Liyo Kao
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Debbie Newman
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Sergei Yu. Noskov
- grid.22072.350000 0004 1936 7697Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Z. Hong Zhou
- grid.509979.b0000 0004 7666 6191Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA USA
| | - Alexander Pushkin
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Ira Kurtz
- grid.19006.3e0000 0000 9632 6718Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Brain Research Institute, University of California, Los Angeles, CA USA
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30
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Molecular mechanism of prestin electromotive signal amplification. Cell 2021; 184:4669-4679.e13. [PMID: 34390643 PMCID: PMC8674105 DOI: 10.1016/j.cell.2021.07.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/26/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022]
Abstract
Hearing involves two fundamental processes: mechano-electrical transduction and signal amplification. Despite decades of studies, the molecular bases for both remain elusive. Here, we show how prestin, the electromotive molecule of outer hair cells (OHCs) that senses both voltage and membrane tension, mediates signal amplification by coupling conformational changes to alterations in membrane surface area. Cryoelectron microscopy (cryo-EM) structures of human prestin bound with chloride or salicylate at a common "anion site" adopt contracted or expanded states, respectively. Prestin is ensconced within a perimeter of well-ordered lipids, through which it induces dramatic deformation in the membrane and couples protein conformational changes to the bulk membrane. Together with computational studies, we illustrate how the anion site is allosterically coupled to changes in the transmembrane domain cross-sectional area and the surrounding membrane. These studies provide insight into OHC electromotility by providing a structure-based mechanism of the membrane motor prestin.
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31
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Comparative Molecular Dynamics Investigation of the Electromotile Hearing Protein Prestin. Int J Mol Sci 2021; 22:ijms22158318. [PMID: 34361083 PMCID: PMC8347359 DOI: 10.3390/ijms22158318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/05/2023] Open
Abstract
The mammalian protein prestin is expressed in the lateral membrane wall of the cochlear hair outer cells and is responsible for the electromotile response of the basolateral membrane, following hyperpolarisation or depolarisation of the cells. Its impairment marks the onset of severe diseases, like non-syndromic deafness. Several studies have pointed out possible key roles of residues located in the Transmembrane Domain (TMD) that differentiate mammalian prestins as incomplete transporters from the other proteins belonging to the same solute-carrier (SLC) superfamily, which are classified as complete transporters. Here, we exploit the homology of a prototypical incomplete transporter (rat prestin, rPres) and a complete transporter (zebrafish prestin, zPres) with target structures in the outward open and inward open conformations. The resulting models are then embedded in a model membrane and investigated via a rigorous molecular dynamics simulation protocol. The resulting trajectories are analyzed to obtain quantitative descriptors of the equilibration phase and to assess a structural comparison between proteins in different states, and between different proteins in the same state. Our study clearly identifies a network of key residues at the interface between the gate and the core domains of prestin that might be responsible for the conformational change observed in complete transporters and hindered in incomplete transporters. In addition, we study the pathway of Cl− ions in the presence of an applied electric field towards their putative binding site in the gate domain. Based on our simulations, we propose a tilt and shift mechanism of the helices surrounding the ion binding cavity as the working principle of the reported conformational changes in complete transporters.
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32
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Structure and function of an Arabidopsis thaliana sulfate transporter. Nat Commun 2021; 12:4455. [PMID: 34294705 PMCID: PMC8298490 DOI: 10.1038/s41467-021-24778-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Plant sulfate transporters (SULTR) mediate absorption and distribution of sulfate (SO42-) and are essential for plant growth; however, our understanding of their structures and functions remains inadequate. Here we present the structure of a SULTR from Arabidopsis thaliana, AtSULTR4;1, in complex with SO42- at an overall resolution of 2.8 Å. AtSULTR4;1 forms a homodimer and has a structural fold typical of the SLC26 family of anion transporters. The bound SO42- is coordinated by side-chain hydroxyls and backbone amides, and further stabilized electrostatically by the conserved Arg393 and two helix dipoles. Proton and SO42- are co-transported by AtSULTR4;1 and a proton gradient significantly enhances SO42- transport. Glu347, which is ~7 Å from the bound SO42-, is required for H+-driven transport. The cytosolic STAS domain interacts with transmembrane domains, and deletion of the STAS domain or mutations to the interface compromises dimer formation and reduces SO42- transport, suggesting a regulatory function of the STAS domain.
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Alexander CR, Huntley RB, Schultes NP, Mourad GS. Functional characterization of the adenine transporter EaAdeP from the fire blight pathogen Erwinia amylovora and its effect on disease establishment in apples and pears. FEMS Microbiol Lett 2021; 367:5932216. [PMID: 33152083 DOI: 10.1093/femsle/fnaa173] [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: 03/31/2020] [Accepted: 10/18/2020] [Indexed: 11/13/2022] Open
Abstract
Erwinia amylovora is the causal agent of fire blight, an economically important disease of apples and pears. As part of the infection process, Er. amylovora propagates on different plant tissues each with distinct nutrient environments. Here, the biochemical properties of the Er. amylovora adenine permease (EaAdeP) are investigated. Heterologous expression of EaAdeP in nucleobase transporter-deficient Escherichia coli strains, coupled with radiolabel uptake studies, revealed that EaAdeP is a high affinity adenine transporter with a Km of 0.43 ± 0.09 μM. Both Es. coli and Er. amylovora carrying extra copies of EaAdeP are sensitive to growth on the toxic analog 8-azaadenine. EaAdeP is expressed during immature pear fruit infection. Immature pear and apple fruit virulence assays reveal that an E. amylovora ΔadeP::Camr mutant is still able to cause disease symptoms, however, with growth at a lower level, indicating that external adenine is utilized in disease establishment.
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Affiliation(s)
- Candace R Alexander
- Department of Biology, Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Regan B Huntley
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA
| | - Neil P Schultes
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA
| | - George S Mourad
- Department of Biology, Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
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Muñoz-Montesino C, Peña E, Roa FJ, Sotomayor K, Escobar E, Rivas CI. Transport of Vitamin C in Cancer. Antioxid Redox Signal 2021; 35:61-74. [PMID: 33607936 DOI: 10.1089/ars.2020.8166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Significance: Vitamin C is a powerful antioxidant that has an intricate relationship with cancer and has been studied for more than 60 years. However, the specific mechanisms that allow malignant cells to uptake, metabolize, and compartmentalize vitamin C remain unclear. In normal human cells, two different transporter systems are responsible for its acquisition: glucose transporters (GLUTs) transport the oxidized form of vitamin C (dehydroascorbic acid) and sodium-coupled ascorbic acid transporters (SVCTs) transport the reduced form (ascorbic acid [AA]). In this study, we review the mechanisms described for vitamin C uptake and metabolization in cancer. Recent Advances: Several studies performed recently in vivo and in vitro have provided the scientific community a better understanding of the differential capacities of cancer cells to acquire vitamin C: tumors from different origins do not express SVCTs in the plasma membrane and are only able to acquire vitamin C in its oxidized form. Interestingly, cancer cells differentially express a mitochondrial form of SVCT2. Critical Issues: Why tumors have reduced AA uptake capacity at the plasma membrane, but develop the capacity of AA transport within mitochondria, remains a mystery. However, it shows that understanding vitamin C physiology in tumor survival might be key to decipher the controversies in its relationship with cancer. Future Directions: A comprehensive analysis of the mechanisms by which cancer cells acquire, compartmentalize, and use vitamin C will allow the design of new therapeutic approaches in human cancer. Antioxid. Redox Signal. 35, 61-74.
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Affiliation(s)
- Carola Muñoz-Montesino
- Departamento de Fisiología and Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Eduardo Peña
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Francisco J Roa
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Kirsty Sotomayor
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Elizabeth Escobar
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Coralia I Rivas
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
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Plant transporters involved in combating boron toxicity: beyond 3D structures. Biochem Soc Trans 2021; 48:1683-1696. [PMID: 32779723 PMCID: PMC7458394 DOI: 10.1042/bst20200164] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Membrane transporters control the movement and distribution of solutes, including the disposal or compartmentation of toxic substances that accumulate in plants under adverse environmental conditions. In this minireview, in the light of the approaching 100th anniversary of unveiling the significance of boron to plants (K. Warington, 1923; Ann. Bot.37, 629) we discuss the current state of the knowledge on boron transport systems that plants utilise to combat boron toxicity. These transport proteins include: (i) nodulin-26-like intrinsic protein-types of aquaporins, and (ii) anionic efflux (borate) solute carriers. We describe the recent progress made on the structure–function relationships of these transport proteins and point out that this progress is integral to quantitative considerations of the transporter's roles in tissue boron homeostasis. Newly acquired knowledge at the molecular level has informed on the transport mechanics and conformational states of boron transport systems that can explain their impact on cell biology and whole plant physiology. We expect that this information will form the basis for engineering transporters with optimised features to alleviate boron toxicity tolerance in plants exposed to suboptimal soil conditions for sustained food production.
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Identification of multiple substrate binding sites in SLC4 transporters in the outward-facing conformation: Insights into the transport mechanism. J Biol Chem 2021; 296:100724. [PMID: 33932403 PMCID: PMC8191340 DOI: 10.1016/j.jbc.2021.100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 01/17/2023] Open
Abstract
Solute carrier family 4 (SLC4) transporters mediate the transmembrane transport of HCO3-, CO32-, and Cl- necessary for pH regulation, transepithelial H+/base transport, and ion homeostasis. Substrate transport with varying stoichiometry and specificity is achieved through an exchange mechanism and/or through coupling of the uptake of anionic substrates to typically co-transported Na+. Recently solved outward-facing structures of two SLC4 members (human anion exchanger 1 [hAE1] and human electrogenic sodium bicarbonate cotransporter 1 [hNBCe1]) with different transport modes (Cl-/HCO3- exchange versus Na+-CO32- symport) revealed highly conserved three-dimensional organization of their transmembrane domains. However, the exact location of the ion binding sites and their protein-ion coordination motifs are still unclear. In the present work, we combined site identification by ligand competitive saturation mapping and extensive molecular dynamics sampling with functional mutagenesis studies which led to the identification of two substrate binding sites (entry and central) in the outward-facing states of hAE1 and hNBCe1. Mutation of residues in the identified binding sites led to impaired transport in both proteins. We also showed that R730 in hAE1 is crucial for anion binding in both entry and central sites, whereas in hNBCe1, a Na+ acts as an anchor for CO32- binding to the central site. Additionally, protonation of the central acidic residues (E681 in hAE1 and D754 in hNBCe1) alters the ion dynamics in the permeation cavity and may contribute to the transport mode differences in SLC4 proteins. These results provide a basis for understanding the functional differences between hAE1 and hNBCe1 and may facilitate potential drug development for diseases such as proximal and distal renal tubular acidosis.
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Fairweather SJ, Shah N, Brӧer S. Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 21:13-127. [PMID: 33052588 DOI: 10.1007/5584_2020_584] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H+ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b0,+AT-rBAT and the SLC6 family heteromer B0AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.
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Affiliation(s)
- Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, ACT, Australia. .,Resarch School of Chemistry, Australian National University, Canberra, ACT, Australia.
| | - Nishank Shah
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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Qin QL, Wang ZB, Su HN, Chen XL, Miao J, Wang XJ, Li CY, Zhang XY, Li PY, Wang M, Fang J, Lidbury I, Zhang W, Zhang XH, Yang GP, Chen Y, Zhang YZ. Oxidation of trimethylamine to trimethylamine N-oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage. SCIENCE ADVANCES 2021; 7:7/13/eabf9941. [PMID: 33771875 PMCID: PMC7997507 DOI: 10.1126/sciadv.abf9941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/05/2021] [Indexed: 06/01/2023]
Abstract
High hydrostatic pressure (HHP) is a characteristic environmental factor of the deep ocean. However, it remains unclear how piezotolerant bacteria adapt to HHP. Here, we identify a two-step metabolic pathway to cope with HHP stress in a piezotolerant bacterium. Myroides profundi D25T, obtained from a deep-sea sediment, can take up trimethylamine (TMA) through a previously unidentified TMA transporter, TmaT, and oxidize intracellular TMA into trimethylamine N-oxide (TMAO) by a TMA monooxygenase, MpTmm. The produced TMAO is accumulated in the cell, functioning as a piezolyte, improving both growth and survival at HHP. The function of the TmaT-MpTmm pathway was further confirmed by introducing it into Escherichia coli and Bacillus subtilis Encoded TmaT-like and MpTmm-like sequences extensively exist in marine metagenomes, and other marine Bacteroidetes bacteria containing genes encoding TmaT-like and MpTmm-like proteins also have improved HHP tolerance in the presence of TMA, implying the universality of this HHP tolerance strategy in marine Bacteroidetes.
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Affiliation(s)
- Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Zhi-Bin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Miao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Weipeng Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Elevator-type mechanisms of membrane transport. Biochem Soc Trans 2021; 48:1227-1241. [PMID: 32369548 PMCID: PMC7329351 DOI: 10.1042/bst20200290] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
Membrane transporters are integral membrane proteins that mediate the passage of solutes across lipid bilayers. These proteins undergo conformational transitions between outward- and inward-facing states, which lead to alternating access of the substrate-binding site to the aqueous environment on either side of the membrane. Dozens of different transporter families have evolved, providing a wide variety of structural solutions to achieve alternating access. A sub-set of structurally diverse transporters operate by mechanisms that are collectively named 'elevator-type'. These transporters have one common characteristic: they contain a distinct protein domain that slides across the membrane as a rigid body, and in doing so it 'drags" the transported substrate along. Analysis of the global conformational changes that take place in membrane transporters using elevator-type mechanisms reveals that elevator-type movements can be achieved in more than one way. Molecular dynamics simulations and experimental data help to understand how lipid bilayer properties may affect elevator movements and vice versa.
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Context-dependent Cryptic Roles of Specific Residues in Substrate Selectivity of the UapA Purine Transporter. J Mol Biol 2021; 433:166814. [PMID: 33497644 DOI: 10.1016/j.jmb.2021.166814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
Members of the ubiquitous Nucleobase Ascorbate Transporter (NAT) family are H+ or Na+ symporters specific for the cellular uptake of either purines and pyrimidines or L-ascorbic acid. Despite the fact that several bacterial and fungal members have been extensively characterised at a genetic, biochemical or cellular level, and crystal structures of NAT members from Escherichia coli and Aspergillus nidulans have been determined pointing to a mechanism of transport, we have little insight on how substrate selectivity is determined. Here, we present systematic mutational analyses, rational combination of mutations, and novel genetic screens that reveal cryptic context-dependent roles of partially conserved residues in the so-called NAT signature motif in determining the specificity of the UapA transporter of A. nidulans. We show that specific NAT signature motif substitutions, alone and in combinations with each other or with distant mutations in residues known to affect substrate selectivity, lead to novel UapA versions possessing variable transport capacities and specificities for nucleobases. In particular, we show that a UapA version including the quadruple mutation T405S/F406Y/A407S/Q408E in the NAT signature motif (UapA-SYSE) becomes incapable of purine transport, but gains a novel pyrimidine-related profile, which can be further altered to a more promiscuous purine/pyrimidine profile when combined with replacements at distantly located residues, especially at F528. Our results reveal that UapA specificity is genetically highly modifiable and allow us to speculate on how the elevator-type mechanism of transport might account for this flexibility.
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Dissecting the Conformational Dynamics of the Bile Acid Transporter Homologue ASBT NM. J Mol Biol 2021; 433:166764. [PMID: 33359100 DOI: 10.1016/j.jmb.2020.166764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/21/2022]
Abstract
Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na+ as the driving force. The crystal structures of two bacterial homologues ASBTNM and ASBTYf have previously been determined, with the former showing an inward-facing conformation, and the latter adopting an outward-facing conformation accomplished by the substitution of the critical Na+-binding residue glutamate-254 with an alanine residue. While the two crystal structures suggested an elevator-like movement to afford alternating access to the substrate binding site, the mechanistic role of Na+ and substrate in the conformational isomerization remains unclear. In this study, we utilized site-directed alkylation monitored by in-gel fluorescence (SDAF) to probe the solvent accessibility of the residues lining the substrate permeation pathway of ASBTNM under different Na+ and substrate conditions, and interpreted the conformational states inferred from the crystal structures. Unexpectedly, the crosslinking experiments demonstrated that ASBTNM is a monomer protein, unlike the other elevator-type transporters, usually forming a homodimer or a homotrimer. The conformational dynamics observed by the biochemical experiments were further validated using DEER measuring the distance between the spin-labelled pairs. Our results revealed that Na+ ions shift the conformational equilibrium of ASBTNM toward the inward-facing state thereby facilitating cytoplasmic uptake of substrate. The current findings provide a novel perspective on the conformational equilibrium of secondary active transporters.
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Chorev DS, Robinson CV. The importance of the membrane for biophysical measurements. Nat Chem Biol 2020; 16:1285-1292. [PMID: 33199903 PMCID: PMC7116504 DOI: 10.1038/s41589-020-0574-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/22/2020] [Indexed: 11/09/2022]
Abstract
Within cell membranes numerous protein assemblies reside. Among their many functions, these assemblies regulate the movement of molecules between membranes, facilitate signaling into and out of cells, allow movement of cells by cell-matrix attachment, and regulate the electric potential of the membrane. With such critical roles, membrane protein complexes are of considerable interest for human health, yet they pose an enduring challenge for structural biologists because it is difficult to study these protein structures at atomic resolution in in situ environments. To advance structural and functional insights for these protein assemblies, membrane mimetics are typically employed to recapitulate some of the physical and chemical properties of the lipid bilayer membrane. However, extraction from native membranes can sometimes change the structure and lipid-binding properties of these complexes, leading to conflicting results and fueling a drive to study complexes directly from native membranes. Here we consider the co-development of membrane mimetics with technological breakthroughs in both cryo-electron microscopy (cryo-EM) and native mass spectrometry (nMS). Together, these developments are leading to a plethora of high-resolution protein structures, as well as new knowledge of their lipid interactions, from different membrane-like environments.
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Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
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Su P, Wu H, Wang M, Cai L, Liu Y, Chen LM. IRBIT activates NBCe1-B by releasing the auto-inhibition module from the transmembrane domain. J Physiol 2020; 599:1151-1172. [PMID: 33237573 PMCID: PMC7898672 DOI: 10.1113/jp280578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Key points The electrogenic Na+/HCO3−cotransporter NBCe1‐B is widely expressed in many tissues, including pancreas, submandibular gland, brain, heart, etc. NBCe1‐B has very low activity under basal condition due to auto‐inhibition, but can be fully activated by protein interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). The structural components of the auto‐inhibition domain and the IRBIT‐binding domain of NBCe1‐B are finely characterized based on systematic mutations in the present study and data from previous studies. Reducing negative charges on the cytosol side of the transmembrane domain greatly decreases the magnitude of the auto‐inhibition of NBCe1‐B. We propose that the auto‐inhibition domain functions as a brake module that inactivates NBCe1‐B by binding to, via electrostatic attraction, the transmembrane domain; IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain via competitive binding to the auto‐inhibition domain.
Abstract The electrogenic Na+/HCO3− cotransporter NBCe1‐B is widely expressed in many tissues in the body. NBCe1‐B exhibits only basal activity due to the action of the auto‐inhibition domain (AID) in its unique amino‐terminus. However, NBCe1‐B can be activated by interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). Here, we investigate the molecular mechanism underlying the auto‐inhibition of NBCe1‐B and its activation by IRBIT. The IRBIT‐binding domain (IBD) of NBCe1‐B spans residues 1−52, essentially consisting of two arms, one negatively charged (residues 1−24) and the other positively charged (residues 40−52). The AID mainly spans residues 40−85, overlapping with the IBD in the positively charged arm. The magnitude of auto‐inhibition of NBCe1‐B is greatly decreased by manipulating the positively charged residues in the AID or by replacing a set of negatively charged residues with neutral ones in the transmembrane domain. The interaction between IRBIT and NBCe1‐B is abolished by mutating a set of negatively charged Asp/Glu residues (to Asn/Gln) plus a set of Ser/Thr residues (to Ala) in the PEST domain of IRBIT. However, this interaction is not affected by replacing the same set of Ser/Thr residues in the PEST domain with Asp. We propose that: (1) the AID, acting as a brake, binds to the transmembrane domain via electrostatic interaction to slow down NBCe1‐B; (2) IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain. The electrogenic Na+/HCO3−cotransporter NBCe1‐B is widely expressed in many tissues, including pancreas, submandibular gland, brain, heart, etc. NBCe1‐B has very low activity under basal condition due to auto‐inhibition, but can be fully activated by protein interaction with the IP3R‐binding protein released with inositol 1,4,5‐trisphosphate (IRBIT). The structural components of the auto‐inhibition domain and the IRBIT‐binding domain of NBCe1‐B are finely characterized based on systematic mutations in the present study and data from previous studies. Reducing negative charges on the cytosol side of the transmembrane domain greatly decreases the magnitude of the auto‐inhibition of NBCe1‐B. We propose that the auto‐inhibition domain functions as a brake module that inactivates NBCe1‐B by binding to, via electrostatic attraction, the transmembrane domain; IRBIT activates NBCe1‐B by releasing the brake from the transmembrane domain via competitive binding to the auto‐inhibition domain.
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Affiliation(s)
- Pan Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Han Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Meng Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Lu Cai
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
| | - Li-Ming Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, School of Life Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
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Gatchell IT, Huntley RB, Schultes NP, Mourad GS. The guanine-hypoxanthine permease GhxP of Erwinia amylovora facilitates the influx of the toxic guanine derivative 6-thioguanine. J Appl Microbiol 2020; 130:2018-2028. [PMID: 33152175 DOI: 10.1111/jam.14925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
AIM Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. This study determines whether the E. amylovora guanine-hypoxanthine transporter (EaGhxP) is required for virulence and if it can import the E. amylovora produced toxic analogue 6-thioguanine (6TG) into cells. METHODS AND RESULTS Characterization of EaGhxP in guanine transport deficient Escherichia coli reveals that it can transport guanine, hypoxanthine and the toxic analogues 8-azaguanine (8AG) and 6TG. Similarly, EaGhxP transports 8AG and 6TG into E. amylovora cells. EaGhxP has a high affinity for 6TG with a Ki of 3·7 µmol l-1 . An E. amylovora ⊿ghxP::Camr strain shows resistance to growth on 8AG and 6TG. Although EaGhxP is expressed during active disease propagation, it is not necessary for virulence as determined on immature apple and pear assays. CONCLUSIONS EaGhxP is not required for virulence, but it does import 6TG into E. amylovora cells. SIGNIFICANCE AND IMPACT OF THE STUDY As part of the disease establishment process, E. amylovora synthesizes and exports a toxic guanine derivative 6TG. Our results are counter intuitive and show that EaGhxP, an influx transporter, can move 6TG into cells raising questions regarding the role of 6TG in disease establishment.
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Affiliation(s)
- I T Gatchell
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
| | - R B Huntley
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - N P Schultes
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - G S Mourad
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
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45
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Characterization of two sugar transporters responsible for efficient xylose uptake in an oleaginous yeast Candida tropicalis SY005. Arch Biochem Biophys 2020; 695:108645. [PMID: 33122161 DOI: 10.1016/j.abb.2020.108645] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/02/2020] [Accepted: 10/17/2020] [Indexed: 01/01/2023]
Abstract
Microbial conversion of lignocellulosic feedstock to the target bioproduct requires efficient assimilation of its constituent sugars, a large part of which comprises of glucose and xylose. This study aims to identify and characterize sugar transporters capable of xylose uptake in an oleaginous strain of the industrially relevant yeast Candida tropicalis. In silico database mining resulted in two sugar transporter proteins- CtStp1 and CtStp2, containing conserved amino acid residues and motifs that have been previously reported to be involved in xylose transport in other organisms. Several softwares predicted the likelihood of 10-12 transmembrane (TM) helices to be present in both the Stps, while molecular modelling showed 12 TM helices that were organized into a typical structure found in the major facilitator superfamily of transporters. Docking with different sugars also predicted favorable interactions. Heterologous expression in a Saccharomyces cerevisiae strain harboring functional xylose metabolic genes validated the broad substrate specificity of the two Stps. Each transporter supported prominent growth of recombinant S. cerevisiae strains on six sugars including xylose at various concentrations. Expression of CtSTP1 and CtSTP2 along with the xylose metabolic genes in yeast transformants grown in presence of xylose was confirmed by transcript detection. Growth curve and sugar consumption profiles revealed uptake of both glucose and xylose simultaneously by the recombinant yeast strains, though CtStp1 showed relatively less effect of glucose repression in mixed sugars and was a better transporter of xylose than CtStp2. Such glucose-xylose utilizing efficient transporters can be effective tools for developing co-fermenting yeasts through genetic engineering in future, with noteworthy applications in renewable biomass utilization.
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46
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Functional (un)cooperativity in elevator transport proteins. Biochem Soc Trans 2020; 48:1047-1055. [PMID: 32573703 DOI: 10.1042/bst20190970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/17/2022]
Abstract
The activity of enzymes is subject to regulation at multiple levels. Cooperativity, the interconnected behavior of active sites within a protein complex, directly affects protein activity. Cooperativity is a mode of regulation that requires neither extrinsic factors nor protein modifications. Instead, it allows enzymes themselves to modulate reaction rates. Cooperativity is an important regulatory mechanism in soluble proteins, but also examples of cooperative membrane proteins have been described. In this review, we summarize the current knowledge on interprotomer cooperativity in elevator-type proteins, a class of membrane transporters characterized by large rigid-body movements perpendicular to the membrane, and highlight well-studied examples and experimental approaches.
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47
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An Erwinia amylovora uracil transporter mutant retains virulence on immature apple and pear fruit. Microb Pathog 2020; 147:104363. [PMID: 32615243 DOI: 10.1016/j.micpath.2020.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. A previous study revealed that an E. amylovora uracil auxotroph was still virulent and can cause disease, suggesting that uracil can be obtained from the host environment. The E. amylovora genome contains a locus encoding for a uracil transporter belonging to the nucleobase cation symporter 2 family, displaying a high level of amino acid sequence similarity to the Escherichia coli UraA. Expression of E. amylovora UraA in nucleobase transporter-deficient E. coli strains, coupled with radiolabeled uptake studies reveal that E. amylovora UraA is a high affinity uracil transporter with a Km of 0.57 μM. Both E. coli and E. amylovora carrying extra copies of E. amylovora UraA are sensitive to growth on the toxic analog 5-fluorouracil. An E. amylovora ΔuraA::Camr mutant is still able to grow and cause disease symptoms on immature pears and apples.
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48
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Wang YH, Chen HH, Huang Z, Li XJ, Zhou N, Liu C, Jiang CY, Li DF, Liu SJ. PapA, a peptidoglycan-associated protein, interacts with OmpC and maintains cell envelope integrity. Environ Microbiol 2020; 23:600-612. [PMID: 32329167 DOI: 10.1111/1462-2920.15038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 01/26/2023]
Abstract
The bacterial cell envelope is critical to support and maintain cellular life. In Gram-negative bacterial cells, the outer membrane and the peptidoglycan layer are two important parts of the cell envelope and they harbour abundant proteins. Here, we report the identification and characterization of a previously unknown peptidoglycan-associated protein, PapA, from the Gram-negative Comamonas testosteroni. PapA bound peptidoglycan with its C-terminal domain and interacted with the outer-membrane porin OmpC. The PapA-OmpC complex riveted the outer membrane and the peptidoglycan layer, and played a role in maintaining cell envelope integrity. When papA was disrupted, the mutant CNB-1ΔpapA apparently had an outer membrane partly separated from the peptidoglycan layer. Phenotypically, the mutant CNB-1ΔpapA lost chemotactic responses and had longer lag-phase of growth, less flagellation and higher sensitivity to harsh environments. Totally, 1093 functionally unknown PapA homologues were identified from the public NR protein database and they were mainly distributed in Burkholderiales of Betaproteobacteria. Our finding provides a clue that the PapA homologous proteins might function as a rivet to maintain cell envelope integrity in those Gram-negative bacteria.
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Affiliation(s)
- Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hong-He Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao-Jing Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Chang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.,Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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49
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Botou M, Yalelis V, Lazou P, Zantza I, Papakostas K, Charalambous V, Mikros E, Flemetakis E, Frillingos S. Specificity profile of NAT/NCS2 purine transporters in
Sinorhizobium
(
Ensifer
)
meliloti. Mol Microbiol 2020; 114:151-171. [DOI: 10.1111/mmi.14503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/16/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Botou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Vassilis Yalelis
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Iliana Zantza
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences National and Kapodistrian University of Athens Athens Greece
| | - Konstantinos Papakostas
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Vassiliki Charalambous
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences National and Kapodistrian University of Athens Athens Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology Department of Biotechnology Agricultural University of Athens Athens Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
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50
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Zimmermann I, Egloff P, Hutter CAJ, Kuhn BT, Bräuer P, Newstead S, Dawson RJP, Geertsma ER, Seeger MA. Generation of synthetic nanobodies against delicate proteins. Nat Protoc 2020; 15:1707-1741. [PMID: 32269381 DOI: 10.1038/s41596-020-0304-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Here, we provide a protocol to generate synthetic nanobodies, known as sybodies, against any purified protein or protein complex within a 3-week period. Unlike methods that require animals for antibody generation, sybody selections are carried out entirely in vitro under controlled experimental conditions. This is particularly relevant for the generation of conformation-specific binders against labile membrane proteins or protein complexes and allows selections in the presence of non-covalent ligands. Sybodies are especially suited for cases where binder generation via immune libraries fails due to high sequence conservation, toxicity or insufficient stability of the target protein. The procedure entails a single round of ribosome display using the sybody libraries encoded by mRNA, followed by two rounds of phage display and binder identification by ELISA. The protocol is optimized to avoid undesired reduction in binder diversity and enrichment of non-specific binders to ensure the best possible selection outcome. Using the efficient fragment exchange (FX) cloning method, the sybody sequences are transferred from the phagemid to different expression vectors without the need to amplify them by PCR, which avoids unintentional shuffling of complementary determining regions. Using quantitative PCR (qPCR), the efficiency of each selection round is monitored to provide immediate feedback and guide troubleshooting. Our protocol can be carried out by any trained biochemist or molecular biologist using commercially available reagents and typically gives rise to 10-30 unique sybodies exhibiting binding affinities in the range of 500 pM-500 nM.
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Affiliation(s)
- Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics AG, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Benedikt T Kuhn
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Roger J P Dawson
- Linkster Therapeutics AG, Zurich, Switzerland.,Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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