1
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Yao X, Gao S, Yan N. Structural biology of voltage-gated calcium channels. Channels (Austin) 2024; 18:2290807. [PMID: 38062897 PMCID: PMC10761187 DOI: 10.1080/19336950.2023.2290807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Voltage-gated calcium (Cav) channels mediate Ca2+ influx in response to membrane depolarization, playing critical roles in diverse physiological processes. Dysfunction or aberrant regulation of Cav channels can lead to life-threatening consequences. Cav-targeting drugs have been clinically used to treat cardiovascular and neuronal disorders for several decades. This review aims to provide an account of recent developments in the structural dissection of Cav channels. High-resolution structures have significantly advanced our understanding of the working and disease mechanisms of Cav channels, shed light on the molecular basis for their modulation, and elucidated the modes of actions (MOAs) of representative drugs and toxins. The progress in structural studies of Cav channels lays the foundation for future drug discovery efforts targeting Cav channelopathies.
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Affiliation(s)
- Xia Yao
- TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Shuai Gao
- TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Shenzhen Medical Academy of Research and Translation, Shenzhen, China
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2
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Li Z, Wu Q, Yan N. A structural atlas of druggable sites on Na v channels. Channels (Austin) 2024; 18:2287832. [PMID: 38033122 PMCID: PMC10732651 DOI: 10.1080/19336950.2023.2287832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
Voltage-gated sodium (Nav) channels govern membrane excitability by initiating and propagating action potentials. Consistent with their physiological significance, dysfunction, or mutations in these channels are associated with various channelopathies. Nav channels are thereby major targets for various clinical and investigational drugs. In addition, a large number of natural toxins, both small molecules and peptides, can bind to Nav channels and modulate their functions. Technological breakthrough in cryo-electron microscopy (cryo-EM) has enabled the determination of high-resolution structures of eukaryotic and eventually human Nav channels, alone or in complex with auxiliary subunits, toxins, and drugs. These studies have not only advanced our comprehension of channel architecture and working mechanisms but also afforded unprecedented clarity to the molecular basis for the binding and mechanism of action (MOA) of prototypical drugs and toxins. In this review, we will provide an overview of the recent advances in structural pharmacology of Nav channels, encompassing the structural map for ligand binding on Nav channels. These findings have established a vital groundwork for future drug development.
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Affiliation(s)
- Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiurong Wu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong Province, China
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3
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Huang J, Fan X, Jin X, Lyu C, Guo Q, Liu T, Chen J, Davakan A, Lory P, Yan N. Structural basis for human Ca v3.2 inhibition by selective antagonists. Cell Res 2024:10.1038/s41422-024-00959-8. [PMID: 38605177 DOI: 10.1038/s41422-024-00959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
The Cav3.2 subtype of T-type calcium channels has been targeted for developing analgesics and anti-epileptics for its role in pain and epilepsy. Here we present the cryo-EM structures of Cav3.2 alone and in complex with four T-type calcium channel selective antagonists with overall resolutions ranging from 2.8 Å to 3.2 Å. The four compounds display two binding poses. ACT-709478 and TTA-A2 both place their cyclopropylphenyl-containing ends in the central cavity to directly obstruct ion flow, meanwhile extending their polar tails into the IV-I fenestration. TTA-P2 and ML218 project their 3,5-dichlorobenzamide groups into the II-III fenestration and place their hydrophobic tails in the cavity to impede ion permeation. The fenestration-penetrating mode immediately affords an explanation for the state-dependent activities of these antagonists. Structure-guided mutational analysis identifies several key residues that determine the T-type preference of these drugs. The structures also suggest the role of an endogenous lipid in stabilizing drug binding in the central cavity.
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Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA.
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chen Lyu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qinmeng Guo
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Tao Liu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaofeng Chen
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Amaël Davakan
- IGF, Université de Montpellier, CNRS, INSERM, LabEx 'Ion Channel Science and Therapeutics', Montpellier, France
| | - Philippe Lory
- IGF, Université de Montpellier, CNRS, INSERM, LabEx 'Ion Channel Science and Therapeutics', Montpellier, France
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China.
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4
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Huang J, Tao H, Chen J, Shen Y, Lei J, Pan J, Yan C, Yan N. Structure-guided discovery of protein and glycan components in native mastigonemes. Cell 2024; 187:1733-1744.e12. [PMID: 38552612 DOI: 10.1016/j.cell.2024.02.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/07/2024] [Accepted: 02/27/2024] [Indexed: 04/02/2024]
Abstract
Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we report the cryo-EM structure of native mastigonemes isolated from Chlamydomonas at 3.0 Å resolution. The long stem assembles as a super spiral, with each helical turn comprising four pairs of anti-parallel mastigoneme-like protein 1 (Mst1). A large array of arabinoglycans, which represents a common class of glycosylation in plants and algae, is resolved surrounding the type II poly-hydroxyproline (Hyp) helix in Mst1. The EM map unveils a mastigoneme axial protein (Mstax) that is rich in heavily glycosylated Hyp and contains a PKD2-like transmembrane domain (TMD). Mstax, with nearly 8,000 residues spanning from the intracellular region to the distal end of the mastigoneme, provides the framework for Mst1 assembly. Our study provides insights into the complexity of protein and glycan interactions in native bio-architectures.
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Affiliation(s)
- Junhao Huang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hui Tao
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jikun Chen
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Shen
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute of Bio-Architecture and Bio-Interactions (IBABI), Shenzhen Medical Academy of Research and Translation (SMART), Shenzhen, Guangdong 518107, China.
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5
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Li Z, Cong Y, Wu T, Wang T, Lou X, Yang X, Yan N. Structural basis for different ω-agatoxin IVA sensitivities of the P-type and Q-type Ca v2.1 channels. Cell Res 2024:10.1038/s41422-024-00940-5. [PMID: 38443561 DOI: 10.1038/s41422-024-00940-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Ye Cong
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Tong Wu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Tongtong Wang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xinyao Lou
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xinyu Yang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong, China.
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6
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Li Z, Wu Q, Huang G, Jin X, Li J, Pan X, Yan N. Dissection of the structure-function relationship of Na v channels. Proc Natl Acad Sci U S A 2024; 121:e2322899121. [PMID: 38381792 PMCID: PMC10907234 DOI: 10.1073/pnas.2322899121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
Voltage-gated sodium channels (Nav) undergo conformational shifts in response to membrane potential changes, a mechanism known as the electromechanical coupling. To delineate the structure-function relationship of human Nav channels, we have performed systematic structural analysis using human Nav1.7 as a prototype. Guided by the structural differences between wild-type (WT) Nav1.7 and an eleven mutation-containing variant, designated Nav1.7-M11, we generated three additional intermediate mutants and solved their structures at overall resolutions of 2.9-3.4 Å. The mutant with nine-point mutations in the pore domain (PD), named Nav1.7-M9, has a reduced cavity volume and a sealed gate, with all voltage-sensing domains (VSDs) remaining up. Structural comparison of WT and Nav1.7-M9 pinpoints two residues that may be critical to the tightening of the PD. However, the variant containing these two mutations, Nav1.7-M2, or even in combination with two additional mutations in the VSDs, named Nav1.7-M4, failed to tighten the PD. Our structural analysis reveals a tendency of PD contraction correlated with the right shift of the static inactivation I-V curves. We predict that the channel in the resting state should have a "tight" PD with down VSDs.
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Affiliation(s)
- Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Qiurong Wu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou310024, China
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Jiaao Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Xiaojing Pan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen518107, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen518107, China
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7
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Gao S, Yao X, Chen J, Huang G, Fan X, Xue L, Li Z, Wu T, Zheng Y, Huang J, Jin X, Wang Y, Wang Z, Yu Y, Liu L, Pan X, Song C, Yan N. Structural basis for human Ca v1.2 inhibition by multiple drugs and the neurotoxin calciseptine. Cell 2023; 186:5363-5374.e16. [PMID: 37972591 DOI: 10.1016/j.cell.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/16/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023]
Abstract
Cav1.2 channels play crucial roles in various neuronal and physiological processes. Here, we present cryo-EM structures of human Cav1.2, both in its apo form and in complex with several drugs, as well as the peptide neurotoxin calciseptine. Most structures, apo or bound to calciseptine, amlodipine, or a combination of amiodarone and sofosbuvir, exhibit a consistent inactivated conformation with a sealed gate, three up voltage-sensing domains (VSDs), and a down VSDII. Calciseptine sits on the shoulder of the pore domain, away from the permeation path. In contrast, when pinaverium bromide, an antispasmodic drug, is inserted into a cavity reminiscent of the IFM-binding site in Nav channels, a series of structural changes occur, including upward movement of VSDII coupled with dilation of the selectivity filter and its surrounding segments in repeat III. Meanwhile, S4-5III merges with S5III to become a single helix, resulting in a widened but still non-conductive intracellular gate.
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Affiliation(s)
- Shuai Gao
- Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Xia Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jiaofeng Chen
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lingfeng Xue
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Wu
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yupeng Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Wang
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Zhifei Wang
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Yong Yu
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaojing Pan
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong 518107, China
| | - Chen Song
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong 518107, China.
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8
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Huang J, Fan X, Jin X, Teng L, Yan N. Dual-pocket inhibition of Na v channels by the antiepileptic drug lamotrigine. Proc Natl Acad Sci U S A 2023; 120:e2309773120. [PMID: 37782796 PMCID: PMC10576118 DOI: 10.1073/pnas.2309773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Voltage-gated sodium (Nav) channels govern membrane excitability, thus setting the foundation for various physiological and neuronal processes. Nav channels serve as the primary targets for several classes of widely used and investigational drugs, including local anesthetics, antiepileptic drugs, antiarrhythmics, and analgesics. In this study, we present cryogenic electron microscopy (cryo-EM) structures of human Nav1.7 bound to two clinical drugs, riluzole (RLZ) and lamotrigine (LTG), at resolutions of 2.9 Å and 2.7 Å, respectively. A 3D EM reconstruction of ligand-free Nav1.7 was also obtained at 2.1 Å resolution. RLZ resides in the central cavity of the pore domain and is coordinated by residues from repeats III and IV. Whereas one LTG molecule also binds to the central cavity, the other is found beneath the intracellular gate, known as site BIG. Therefore, LTG, similar to lacosamide and cannabidiol, blocks Nav channels via a dual-pocket mechanism. These structures, complemented with docking and mutational analyses, also explain the structure-activity relationships of the LTG-related linear 6,6 series that have been developed for improved efficacy and subtype specificity on different Nav channels. Our findings reveal the molecular basis for these drugs' mechanism of action and will aid the development of novel antiepileptic and pain-relieving drugs.
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Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Liming Teng
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
- Shenzhen Medical Academy of Research and Translation, Shenzhen, Guangdong Province518107, China
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9
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Huang J, Fan X, Jin X, Jo S, Zhang HB, Fujita A, Bean BP, Yan N. Cannabidiol inhibits Na v channels through two distinct binding sites. Nat Commun 2023; 14:3613. [PMID: 37330538 PMCID: PMC10276812 DOI: 10.1038/s41467-023-39307-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Cannabidiol (CBD), a major non-psychoactive phytocannabinoid in cannabis, is an effective treatment for some forms of epilepsy and pain. At high concentrations, CBD interacts with a huge variety of proteins, but which targets are most relevant for clinical actions is still unclear. Here we show that CBD interacts with Nav1.7 channels at sub-micromolar concentrations in a state-dependent manner. Electrophysiological experiments show that CBD binds to the inactivated state of Nav1.7 channels with a dissociation constant of about 50 nM. The cryo-EM structure of CBD bound to Nav1.7 channels reveals two distinct binding sites. One is in the IV-I fenestration near the upper pore. The other binding site is directly next to the inactivated "wedged" position of the Ile/Phe/Met (IFM) motif on the short linker between repeats III and IV, which mediates fast inactivation. Consistent with producing a direct stabilization of the inactivated state, mutating residues in this binding site greatly reduced state-dependent binding of CBD. The identification of this binding site may enable design of compounds with improved properties compared to CBD itself.
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Affiliation(s)
- Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sooyeon Jo
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA
| | - Hanxiong Bear Zhang
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA
| | - Akie Fujita
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA
| | - Bruce P Bean
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA, 02115, USA.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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10
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Wu Q, Huang J, Fan X, Wang K, Jin X, Huang G, Li J, Pan X, Yan N. Structural mapping of Na v1.7 antagonists. Nat Commun 2023; 14:3224. [PMID: 37270609 DOI: 10.1038/s41467-023-38942-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
Voltage-gated sodium (Nav) channels are targeted by a number of widely used and investigational drugs for the treatment of epilepsy, arrhythmia, pain, and other disorders. Despite recent advances in structural elucidation of Nav channels, the binding mode of most Nav-targeting drugs remains unknown. Here we report high-resolution cryo-EM structures of human Nav1.7 treated with drugs and lead compounds with representative chemical backbones at resolutions of 2.6-3.2 Å. A binding site beneath the intracellular gate (site BIG) accommodates carbamazepine, bupivacaine, and lacosamide. Unexpectedly, a second molecule of lacosamide plugs into the selectivity filter from the central cavity. Fenestrations are popular sites for various state-dependent drugs. We show that vinpocetine, a synthetic derivative of a vinca alkaloid, and hardwickiic acid, a natural product with antinociceptive effect, bind to the III-IV fenestration, while vixotrigine, an analgesic candidate, penetrates the IV-I fenestration of the pore domain. Our results permit building a 3D structural map for known drug-binding sites on Nav channels summarized from the present and previous structures.
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Affiliation(s)
- Qiurong Wu
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Kan Wang
- Department of Anesthesiology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xueqin Jin
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China
| | - Jiaao Li
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaojing Pan
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Shenzhen Medical Academy of Research and Translation, Guangming District, Shenzhen, 518107, Guangdong Province, China.
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11
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Imamura M, Miyagi A, Gao S, Yan N, Scheuring S. High-speed AFM imaging of voltage gated sodium channel NaChBac and voltage application. Biophys J 2023; 122:175a. [PMID: 36782827 DOI: 10.1016/j.bpj.2022.11.1089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Motonori Imamura
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Atsushi Miyagi
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shuai Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA; Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
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12
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Yao X, Gao S, Wang J, Li Z, Huang J, Wang Y, Wang Z, Chen J, Fan X, Wang W, Jin X, Pan X, Yu Y, Lagrutta A, Yan N. Structural basis for the severe adverse interaction of sofosbuvir and amiodarone on L-type Ca v channels. Cell 2022; 185:4801-4810.e13. [PMID: 36417914 PMCID: PMC9891081 DOI: 10.1016/j.cell.2022.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/24/2022] [Accepted: 10/26/2022] [Indexed: 11/23/2022]
Abstract
Drug-drug interaction of the antiviral sofosbuvir and the antiarrhythmics amiodarone has been reported to cause fatal heartbeat slowing. Sofosbuvir and its analog, MNI-1, were reported to potentiate the inhibition of cardiomyocyte calcium handling by amiodarone, which functions as a multi-channel antagonist, and implicate its inhibitory effect on L-type Cav channels, but the molecular mechanism has remained unclear. Here we present systematic cryo-EM structural analysis of Cav1.1 and Cav1.3 treated with amiodarone or sofosbuvir alone, or sofosbuvir/MNI-1 combined with amiodarone. Whereas amiodarone alone occupies the dihydropyridine binding site, sofosbuvir is not found in the channel when applied on its own. In the presence of amiodarone, sofosbuvir/MNI-1 is anchored in the central cavity of the pore domain through specific interaction with amiodarone and directly obstructs the ion permeation path. Our study reveals the molecular basis for the physical, pharmacodynamic interaction of two drugs on the scaffold of Cav channels.
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Affiliation(s)
- Xia Yao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,These authors contribute equally
| | - Shuai Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,These authors contribute equally.,Present address: School of Pharmaceutical Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China,To whom correspondence should be addressed: N. Yan (); S. Gao ()
| | - Jixin Wang
- Department of Genetic and Cellular Toxicology, ADME & Discovery Toxicology, Preclinical Development, Merck Research Laboratories, Merck & Co., Inc., West Point, PA 19486, USA,These authors contribute equally
| | - Zhangqiang Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China,These authors contribute equally
| | - Jian Huang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yan Wang
- Department of Biological Sciences, St. John’s University, Queens, NY 11439, USA
| | - Zhifei Wang
- Department of Biological Sciences, St. John’s University, Queens, NY 11439, USA
| | - Jiaofeng Chen
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weipeng Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xueqin Jin
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong Yu
- Department of Biological Sciences, St. John’s University, Queens, NY 11439, USA
| | - Armando Lagrutta
- Department of Genetic and Cellular Toxicology, ADME & Discovery Toxicology, Preclinical Development, Merck Research Laboratories, Merck & Co., Inc., West Point, PA 19486, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,Lead contact.,To whom correspondence should be addressed: N. Yan (); S. Gao ()
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13
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Yao X, Wang Y, Wang Z, Fan X, Wu D, Huang J, Mueller A, Gao S, Hu M, Robinson CV, Yu Y, Gao S, Yan N. Structures of the R-type human Ca v2.3 channel reveal conformational crosstalk of the intracellular segments. Nat Commun 2022; 13:7358. [PMID: 36446785 PMCID: PMC9708679 DOI: 10.1038/s41467-022-35026-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
The R-type voltage-gated Ca2+ (Cav) channels Cav2.3, widely expressed in neuronal and neuroendocrine cells, represent potential drug targets for pain, seizures, epilepsy, and Parkinson's disease. Despite their physiological importance, there have lacked selective small-molecule inhibitors targeting these channels. High-resolution structures may aid rational drug design. Here, we report the cryo-EM structure of human Cav2.3 in complex with α2δ-1 and β3 subunits at an overall resolution of 3.1 Å. The structure is nearly identical to that of Cav2.2, with VSDII in the down state and the other three VSDs up. A phosphatidylinositol 4,5-bisphosphate (PIP2) molecule binds to the interface of VSDII and the tightly closed pore domain. We also determined the cryo-EM structure of a Cav2.3 mutant in which a Cav2-unique cytosolic helix in repeat II (designated the CH2II helix) is deleted. This mutant, named ΔCH2, still reserves a down VSDII, but PIP2 is invisible and the juxtamembrane region on the cytosolic side is barely discernible. Our structural and electrophysiological characterizations of the wild type and ΔCH2 Cav2.3 show that the CH2II helix stabilizes the inactivated conformation of the channel by tightening the cytosolic juxtamembrane segments, while CH2II helix is not necessary for locking the down state of VSDII.
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Affiliation(s)
- Xia Yao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Yan Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Zhifei Wang
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Xiao Fan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Di Wu
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Jian Huang
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Alexander Mueller
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Sarah Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Miaohui Hu
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
| | - Carol V. Robinson
- grid.4991.50000 0004 1936 8948Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ UK ,grid.4991.50000 0004 1936 8948Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | - Yong Yu
- grid.264091.80000 0001 1954 7928Department of Biological Sciences, St. John’s University, Queens, NY 11439 USA
| | - Shuai Gao
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA ,grid.49470.3e0000 0001 2331 6153Present Address: Department of Radiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Nieng Yan
- grid.16750.350000 0001 2097 5006Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
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14
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Jiang X, Yan N, Deng D, Yan C. Structural aspects of the glucose and monocarboxylate transporters involved in the Warburg effect. IUBMB Life 2022; 74:1180-1199. [PMID: 36082803 DOI: 10.1002/iub.2668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/02/2022] [Indexed: 11/11/2022]
Abstract
Cancer cells shift their glucose catabolism from aerobic respiration to lactic fermentation even in the presence of oxygen, and this is known as the "Warburg effect". To accommodate the high glucose demands and to avoid lactate accumulation, the expression levels of human glucose transporters (GLUTs) and human monocarboxylate transporters (MCTs) are elevated to maintain metabolic homeostasis. Therefore, inhibition of GLUTs and/or MCTs provides potential therapeutic strategies for cancer treatment. Here, we summarize recent advances in the structural characterization of GLUTs and MCTs, providing a comprehensive understanding of their transport and inhibition mechanisms to facilitate further development of anticancer therapies.
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Affiliation(s)
- Xin Jiang
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
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15
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Lutomski CA, El-Baba TJ, Robinson CV, Riek R, Scheres SHW, Yan N, AlQuraishi M, Gan L. The next decade of protein structure. Cell 2022; 185:2617-2620. [PMID: 35868264 DOI: 10.1016/j.cell.2022.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
Abstract
With recent dramatic advances in various techniques used for protein structure research, we asked researchers to comment on the next exciting questions for the field and about how these techniques will advance our knowledge not only about proteins but also about human health and diseases.
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16
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Liu S, Liao L, Wei W, Liang Y, Xu J, Cao L, Li S, Li L, Meng L, Qian J, Zang Q, Wang L, Xu S, Cai J, Yan N, Ma Q, Zhao N, Chen R, Hu G, Liu J, Liu X, Ming T, Li L, Sun Y, Zeng L, Li G, Yao D, Xu G, Gong X, Gao X. Development and application of limiter Langmuir probe array in EAST. Fusion Engineering and Design 2022. [DOI: 10.1016/j.fusengdes.2022.113162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Liu S, Liao L, Zhong L, Wei W, Li L, Wei W, Yan N, Xing Y, Xu G, Shao L, Chen R, Hu G, Liu J, Liang Y, Han X, Cai J, Zhao N, Liu X, Ming T, Zang Q, Wang L, Zeng L, Li G, Gong X, Gao X. Upgrade and application of the gas puff imaging system in EAST. Fusion Engineering and Design 2022. [DOI: 10.1016/j.fusengdes.2022.113156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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18
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Abstract
GLUT4 is the primary glucose transporter in adipose and skeletal muscle tissues. Its cellular trafficking is regulated by insulin signaling. Failed or reduced plasma membrane localization of GLUT4 is associated with diabetes. Here, we report the cryo-EM structures of human GLUT4 bound to a small molecule inhibitor cytochalasin B (CCB) at resolutions of 3.3 Å in both detergent micelles and lipid nanodiscs. CCB-bound GLUT4 exhibits an inward-open conformation. Despite the nearly identical conformation of the transmembrane domain to GLUT1, the cryo-EM structure reveals an extracellular glycosylation site and an intracellular helix that is invisible in the crystal structure of GLUT1. The structural study presented here lays the foundation for further mechanistic investigation of the modulation of GLUT4 trafficking. Our methods for cryo-EM analysis of GLUT4 will also facilitate structural determination of many other small size solute carriers. Small solute carriers remain difficult to study by single particle cryo-EM. Here, the authors report the cryo-EM structure of human insulin-responsive glucose transporter GLUT4 (55 kDa) without rigid soluble domains or binders.
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Affiliation(s)
- Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fang Kong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hanwen Xu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Angqi Zhu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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19
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Huang G, Liu D, Wang W, Wu Q, Chen J, Pan X, Shen H, Yan N. High-resolution structures of human Na v1.7 reveal gating modulation through α-π helical transition of S6 IV. Cell Rep 2022; 39:110735. [PMID: 35476982 DOI: 10.1016/j.celrep.2022.110735] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 04/02/2022] [Indexed: 11/26/2022] Open
Abstract
Nav1.7 represents a preeminent target for next-generation analgesics for its critical role in pain sensation. Here we report a 2.2-Å resolution cryo-EM structure of wild-type (WT) Nav1.7 complexed with the β1 and β2 subunits that reveals several previously indiscernible cytosolic segments. Reprocessing of the cryo-EM data for our reported structures of Nav1.7(E406K) bound to various toxins identifies two distinct conformations of S6IV, one composed of α helical turns only and the other containing a π helical turn in the middle. The structure of ligand-free Nav1.7(E406K), determined at 3.5-Å resolution, is identical to the WT channel, confirming that binding of Huwentoxin IV or Protoxin II to VSDII allosterically induces the α → π transition of S6IV. The local secondary structural shift leads to contraction of the intracellular gate, closure of the fenestration on the interface of repeats I and IV, and rearrangement of the binding site for the fast inactivation motif.
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Affiliation(s)
- Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China
| | - Dongliang Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China
| | - Weipeng Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiurong Wu
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiaofeng Chen
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huaizong Shen
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China.
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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20
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Wu X, Yan R, Cao P, Qian H, Yan N. Structural advances in sterol-sensing domain-containing proteins. Trends Biochem Sci 2022; 47:289-300. [PMID: 35012873 DOI: 10.1016/j.tibs.2021.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022]
Abstract
The sterol-sensing domain (SSD) is present in several membrane proteins that function in cholesterol metabolism, transport, and signaling. Recent progress in structural studies of SSD-containing proteins, such as sterol regulatory element-binding protein (SREBP)-cleavage activating protein (Scap), Patched, Niemann-Pick disease type C1 (NPC1), and related proteins, reveals a conserved core that is essential for their sterol-dependent functions. This domain, by its name, 'senses' the presence of sterol substrates through interactions and may modulate protein behaviors with changing sterol levels. We summarize recent advances in structural and mechanistic investigations of these proteins and propose to divide them to two classes: M for 'moderator' proteins that regulate sterol metabolism in response to membrane sterol levels, and T for 'transporter' proteins that harbor inner tunnels for cargo trafficking across cellular membranes.
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Affiliation(s)
- Xuelan Wu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Renhong Yan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Pingping Cao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Hongwu Qian
- Ministry of Education (MOE) Key Laboratory of Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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21
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Liu S, Liang Y, Yan N, Liao L, Wei W, Meng L, Chen L, Xu S, Zhao N, Chen R, Hu G, Li Y, Liu X, Ming T, Sun Y, Qian J, Zeng L, Li G, Wang L, Xu G, Gong X, Gao X. Application of a newly developed radial directional electron probe to the edge unidirectional electron current measurement in EAST. Nuclear Materials and Energy 2021. [DOI: 10.1016/j.nme.2021.101080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Yan N, Guo S, Li M, Huang S, Guo Q, Geng D, Zhang H, Li X. 1659P Immune checkpoint inhibitors plus VEGF tyrosine kinase inhibitors as second-line or later therapy for patients with extensive stage small cell lung cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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23
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Zhang SN, Chen LY, Yan N, Chen LH. [Historical changes of a missionary hospital - Shanghai General Hospital (1864-1953)]. Zhonghua Yi Shi Za Zhi 2021; 51:201-207. [PMID: 34645116 DOI: 10.376/cma.j.cn112155-20210119-00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Christian missionaries preached through medicine by combining religious preaching with secularisation and social adaptiveness of medicine in the 19th century. They attempted to avoid the negative influence of culture differences between the West and China. Desjacques Marin, one of the missionaries in China, was entrusted by Benoit Edan, a French consul in Shanghai to establish a hospital in 1864, named the "General Hospital". This hospital was moved to the north bank of Suzhou Creek in 1877 and renamed as the Gongji Hospital. The hospital was designated by the Japanese Army in 1940 as a hospital for sick foreign prisoners in the war. It was taken over as an enemy property by the government of the Republic of China in 1945 and became a public hospital opened formally to Chinese patients. It was renamed as "Shanghai First People's Hospital" in 1953. Review of the historical changes of the missionary hospital is of significance for the study on Chinese medical history and medical communication between China and the West.
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Affiliation(s)
- S N Zhang
- Institute of Science, Technology and Humanity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - L Y Chen
- Institute of Science, Technology and Humanity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - N Yan
- Institute of Science, Technology and Humanity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - L H Chen
- Institute of Science, Technology and Humanity, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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24
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Yan R, Cao P, Song W, Li Y, Wang T, Qian H, Yan C, Yan N. Structural basis for sterol sensing by Scap and Insig. Cell Rep 2021; 35:109299. [PMID: 34192549 DOI: 10.1016/j.celrep.2021.109299] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 11/30/2022] Open
Abstract
The sterol regulatory element-binding protein (SREBP) pathway monitors the cellular cholesterol level through sterol-regulated association between the SREBP cleavage-activating protein (Scap) and the insulin-induced gene (Insig). Despite structural determination of the Scap and Insig-2 complex bound to 25-hydroxycholesterol, the luminal domains of Scap remain unresolved. In this study, combining cryogenic electron microscopy (cryo-EM) analysis and artificial intelligence-facilitated structural prediction, we report the structure of the human Scap/Insig-2 complex purified in digitonin. The luminal domain loop 1 and a co-folded segment in loop 7 of Scap resemble those of the luminal/extracellular domain in NPC1 and related proteins, providing clues to the cholesterol-regulated interaction of loop 1 and loop 7. An additional luminal interface is observed between Scap and Insig. We also show that Scap(D428A), which inhibits SREBP activation even under sterol depletion, exhibits an identical conformation with the wild-type protein when complexed with Insig-2, and its constitutive suppression of the SREBP pathway may also involve a later step in protein trafficking.
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Affiliation(s)
- Renhong Yan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Pingping Cao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenqi Song
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yaning Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tongtong Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongwu Qian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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25
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Abstract
Ryanodine receptors (RyRs) are ion channels responsible for the fast release of Ca2+ from the sarco/endoplasmic reticulum to the cytosol and show a selectivity of Ca2+ over monovalent cations. By utilizing a recently developed multisite Ca2+ model in molecular dynamic simulations, we show that multiple cations accumulate in the upper selectivity filter of RyRs, and the small size and high valence of Ca2+ make it preferable to K+ in competition for space in this confined region of negative electrostatic potential. The presence of Ca2+ in the upper selectivity filter significantly increases the energy barrier of K+ permeation, while the presence of K+ has little impact on the Ca2+ permeation. Our results provide the atomistic details of the charge/space competition mechanism for the ion selectivity of RyRs, which ensures the robustness of their Ca2+ release function. The mechanism could be utilized in protein- and nanoengineering for valence selectivity of ion species.
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Affiliation(s)
- Chunhong Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Aihua Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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26
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Abstract
Voltage-gated sodium (Nav) channels are responsible for the initiation and propagation of action potentials. Their abnormal functions are associated with numerous diseases, such as epilepsy, cardiac arrhythmia, and pain syndromes. Therefore, these channels represent important drug targets. Even in the post-resolution revolution era, a lack of structural information continues to impede structure-based drug discovery. The limiting factor for the structural determination of Nav channels using single particle cryo-electron microscopy (cryo-EM) resides in the generation of sufficient high-quality recombinant proteins. After extensive trials, we have been successful in determining a series of high-resolution structures of Nav channels, including NavPaS from American cockroach, Nav1.4 from electric eel, and human Nav1.1, Nav1.2, Nav1.4, Nav1.5, and Nav1.7, with distinct strategies. These structures established the framework for understanding the electromechanical coupling and disease mechanism of Nav channels, and for facilitating drug discovery. Here, we exemplify these methods with two specific cases, human Nav1.4 and Nav1.7, which may shed light on the structural determination of other membrane proteins.
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Affiliation(s)
- Huaizong Shen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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27
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Li Z, Jin X, Wu T, Huang G, Wu K, Lei J, Pan X, Yan N. Structural Basis for Pore Blockade of the Human Cardiac Sodium Channel Na v 1.5 by the Antiarrhythmic Drug Quinidine*. Angew Chem Int Ed Engl 2021; 60:11474-11480. [PMID: 33684260 DOI: 10.1002/anie.202102196] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Indexed: 12/19/2022]
Abstract
Nav 1.5, the primary voltage-gated Na+ (Nav ) channel in heart, is a major target for class I antiarrhythmic agents. Here we present the cryo-EM structure of full-length human Nav 1.5 bound to quinidine, a class Ia antiarrhythmic drug, at 3.3 Å resolution. Quinidine is positioned right beneath the selectivity filter in the pore domain and coordinated by residues from repeats I, III, and IV. Pore blockade by quinidine is achieved through both direct obstruction of the ion permeation path and induced rotation of an invariant Tyr residue that tightens the intracellular gate. Structural comparison with a truncated rat Nav 1.5 in the presence of flecainide, a class Ic agent, reveals distinct binding poses for the two antiarrhythmics within the pore domain. Our work reported here, along with previous studies, reveals the molecular basis for the mechanism of action of class I antiarrhythmic drugs.
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Affiliation(s)
- Zhangqiang Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqin Jin
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tong Wu
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province, Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang Province, China
| | - Kun Wu
- Medical Research Center, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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28
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Li Z, Jin X, Wu T, Huang G, Wu K, Lei J, Pan X, Yan N. Structural Basis for Pore Blockade of the Human Cardiac Sodium Channel Na
v
1.5 by the Antiarrhythmic Drug Quinidine**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhangqiang Li
- State Key Laboratory of Membrane Biology Beijing Advanced Innovation Center for Structural Biology Tsinghua-Peking Joint Center for Life Science School of Life Sciences Tsinghua University Beijing 100084 China
| | - Xueqin Jin
- State Key Laboratory of Membrane Biology Beijing Advanced Innovation Center for Structural Biology Tsinghua-Peking Joint Center for Life Science School of Life Sciences Tsinghua University Beijing 100084 China
| | - Tong Wu
- State Key Laboratory of Membrane Biology Beijing Advanced Innovation Center for Structural Biology Tsinghua-Peking Joint Center for Life Science School of Life Sciences Tsinghua University Beijing 100084 China
| | - Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province Institute of Biology, Westlake Institute for Advanced Study School of Life Sciences Westlake University Hangzhou 310024 Zhejiang Province China
| | - Kun Wu
- Medical Research Center Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation Beijing Chao-Yang Hospital Capital Medical University Beijing 100020 China
| | - Jianlin Lei
- Technology Center for Protein Sciences Ministry of Education Key Laboratory of Protein Sciences School of Life Sciences Tsinghua University Beijing 100084 China
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology Beijing Advanced Innovation Center for Structural Biology Tsinghua-Peking Joint Center for Life Science School of Life Sciences Tsinghua University Beijing 100084 China
| | - Nieng Yan
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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29
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Gao S, Yan N. Structural Basis of the Modulation of the Voltage‐Gated Calcium Ion Channel Ca
v
1.1 by Dihydropyridine Compounds**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shuai Gao
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
| | - Nieng Yan
- Department of Molecular Biology Princeton University Princeton NJ 08544 USA
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30
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Gao S, Yan N. Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca v 1.1 by Dihydropyridine Compounds*. Angew Chem Int Ed Engl 2021; 60:3131-3137. [PMID: 33125829 PMCID: PMC7898392 DOI: 10.1002/anie.202011793] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Indexed: 12/29/2022]
Abstract
1,4-Dihydropyridines (DHP), the most commonly used antihypertensives, function by inhibiting the L-type voltage-gated Ca2+ (Cav ) channels. DHP compounds exhibit chirality-specific antagonistic or agonistic effects. The structure of rabbit Cav 1.1 bound to an achiral drug nifedipine reveals the general binding mode for DHP drugs, but the molecular basis for chiral specificity remained elusive. Herein, we report five cryo-EM structures of nanodisc-embedded Cav 1.1 in the presence of the bestselling drug amlodipine, a DHP antagonist (R)-(+)-Bay K8644, and a titration of its agonistic enantiomer (S)-(-)-Bay K8644 at resolutions of 2.9-3.4 Å. The amlodipine-bound structure reveals the molecular basis for the high efficacy of the drug. All structures with the addition of the Bay K8644 enantiomers exhibit similar inactivated conformations, suggesting that (S)-(-)-Bay K8644, when acting as an agonist, is insufficient to lock the activated state of the channel for a prolonged duration.
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MESH Headings
- 3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethyl-5-nitro-4-(2-(trifluoromethyl)phenyl)-, Methyl ester/chemistry
- 3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethyl-5-nitro-4-(2-(trifluoromethyl)phenyl)-, Methyl ester/metabolism
- Amlodipine/chemistry
- Amlodipine/metabolism
- Binding Sites
- Calcium Channel Agonists/chemistry
- Calcium Channel Agonists/metabolism
- Calcium Channel Blockers/chemistry
- Calcium Channel Blockers/metabolism
- Calcium Channels, L-Type/chemistry
- Calcium Channels, L-Type/metabolism
- Cryoelectron Microscopy
- Dihydropyridines/chemistry
- Dihydropyridines/metabolism
- Molecular Dynamics Simulation
- Nanostructures/chemistry
- Protein Structure, Tertiary
- Stereoisomerism
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Affiliation(s)
- Shuai Gao
- Department of Molecular BiologyPrinceton UniversityPrincetonNJ08544USA
| | - Nieng Yan
- Department of Molecular BiologyPrinceton UniversityPrincetonNJ08544USA
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31
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Wang L, Chen K, Gao S, Yan N, Zhou M. Mechanism of Sulfate Selectivity and Transport in A SLC26 Family of Sulfate Transporter. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Pan Y, Ren Z, Gao S, Shen J, Fan X, Yan N, Zhou M. Structural Basis of Ion Transport and Inhibition in Ferroportin. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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33
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Yan R, Cao P, Song W, Qian H, Du X, Coates HW, Zhao X, Li Y, Gao S, Gong X, Liu X, Sui J, Lei J, Yang H, Brown AJ, Zhou Q, Yan C, Yan N. A structure of human Scap bound to Insig-2 suggests how their interaction is regulated by sterols. Science 2021; 371:science.abb2224. [PMID: 33446483 DOI: 10.1126/science.abb2224] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/31/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
The sterol regulatory element-binding protein (SREBP) pathway controls cellular homeostasis of sterols. The key players in this pathway, Scap and Insig-1 and -2, are membrane-embedded sterol sensors. The 25-hydroxycholesterol (25HC)-dependent association of Scap and Insig acts as the master switch for the SREBP pathway. Here, we present cryo-electron microscopy analysis of the human Scap and Insig-2 complex in the presence of 25HC, with the transmembrane (TM) domains determined at an average resolution of 3.7 angstrom. The sterol-sensing domain in Scap and all six TMs in Insig-2 were resolved. A 25HC molecule is sandwiched between the S4 to S6 segments in Scap and TMs 3 and 4 in Insig-2 in the luminal leaflet of the membrane. Unwinding of the middle of the Scap-S4 segment is crucial for 25HC binding and Insig association.
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Affiliation(s)
- Renhong Yan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Pingping Cao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenqi Song
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongwu Qian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ximing Du
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hudson W Coates
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xin Zhao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yaning Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ximing Liu
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Jianhua Sui
- National Institute of Biological Sciences (NIBS), Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Qiang Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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34
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Gong D, Yan N, Ledford HA. Structural Basis for the Modulation of Ryanodine Receptors. Trends Biochem Sci 2020; 46:489-501. [PMID: 33353849 DOI: 10.1016/j.tibs.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Historically, ryanodine receptors (RyRs) have presented unique challenges for high-resolution structural determination despite long-standing interest in their role in excitation-contraction coupling. Owing to their large size (nearly 2.2 MDa), high-resolution structures remained elusive until the advent of cryogenic electron microscopy (cryo-EM) techniques. In recent years, structures for both RyR1 and RyR2 have been solved at near-atomic resolution. Furthermore, recent reports have delved into their more complex structural associations with key modulators - proteins such as the dihydropyridine receptor (DHPR), FKBP12/12.6, and calmodulin (CaM), as well as ions and small molecules including Ca2+, ATP, caffeine, and PCB95. This review addresses the modulation of RyR1 and RyR2, in addition to the impact of such discoveries on intracellular Ca2+ dynamics and biophysical properties.
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Affiliation(s)
- Deshun Gong
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province/Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Hannah A Ledford
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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35
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Thomas C, Aller SG, Beis K, Carpenter EP, Chang G, Chen L, Dassa E, Dean M, Duong Van Hoa F, Ekiert D, Ford R, Gaudet R, Gong X, Holland IB, Huang Y, Kahne DK, Kato H, Koronakis V, Koth CM, Lee Y, Lewinson O, Lill R, Martinoia E, Murakami S, Pinkett HW, Poolman B, Rosenbaum D, Sarkadi B, Schmitt L, Schneider E, Shi Y, Shyng SL, Slotboom DJ, Tajkhorshid E, Tieleman DP, Ueda K, Váradi A, Wen PC, Yan N, Zhang P, Zheng H, Zimmer J, Tampé R. Structural and functional diversity calls for a new classification of ABC transporters. FEBS Lett 2020; 594:3767-3775. [PMID: 32978974 PMCID: PMC8386196 DOI: 10.1002/1873-3468.13935] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/19/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Germany
| | - Stephen G Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, AL, USA
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London South Kensington, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | | | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lei Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Elie Dassa
- Institut Pasteur, Paris Cedex 15, France
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Franck Duong Van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Damian Ekiert
- Department of Cell Biology and Department of Microbiology, New York University School of Medicine, NY, USA
| | - Robert Ford
- Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - I Barry Holland
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Sud, Orsay, France
| | - Yihua Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Daniel K Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hiroaki Kato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Japan
| | | | | | - Youngsook Lee
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, Korea
| | - Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University Zurich, Switzerland
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Satoshi Murakami
- Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Balazs Sarkadi
- Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Erwin Schneider
- Department of Biology/Microbial Physiology, Humboldt-University of Berlin, Germany
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, China
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Dirk J Slotboom
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, AB, Canada
| | - Kazumitsu Ueda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Japan
| | - András Váradi
- Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary
| | - Po-Chao Wen
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, NJ, USA
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Germany
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36
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Jiang X, Yuan Y, Huang J, Zhang S, Luo S, Wang N, Pu D, Zhao N, Tang Q, Hirata K, Yang X, Jiao Y, Sakata-Kato T, Wu JW, Yan C, Kato N, Yin H, Yan N. Structural Basis for Blocking Sugar Uptake into the Malaria Parasite Plasmodium falciparum. Cell 2020; 183:258-268.e12. [PMID: 32860739 DOI: 10.1016/j.cell.2020.08.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/08/2020] [Accepted: 08/07/2020] [Indexed: 11/25/2022]
Abstract
Plasmodium species, the causative agent of malaria, rely on glucose for energy supply during blood stage. Inhibition of glucose uptake thus represents a potential strategy for the development of antimalarial drugs. Here, we present the crystal structures of PfHT1, the sole hexose transporter in the genome of Plasmodium species, at resolutions of 2.6 Å in complex with D-glucose and 3.7 Å with a moderately selective inhibitor, C3361. Although both structures exhibit occluded conformations, binding of C3361 induces marked rearrangements that result in an additional pocket. This inhibitor-binding-induced pocket presents an opportunity for the rational design of PfHT1-specific inhibitors. Among our designed C3361 derivatives, several exhibited improved inhibition of PfHT1 and cellular potency against P. falciparum, with excellent selectivity to human GLUT1. These findings serve as a proof of concept for the development of the next-generation antimalarial chemotherapeutics by simultaneously targeting the orthosteric and allosteric sites of PfHT1.
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Affiliation(s)
- Xin Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jian Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Shuo Zhang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuchen Luo
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Nan Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Debing Pu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Na Zhao
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Qingxuan Tang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan
| | - Xikang Yang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yaqing Jiao
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Tomoyo Sakata-Kato
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Jia-Wei Wu
- Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu 215123, China
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Nobutaka Kato
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Hang Yin
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
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37
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Abstract
Membrane proteins (MPs) used to be the most difficult targets for structural biology when X-ray crystallography was the mainstream approach. With the resolution revolution of single-particle electron cryo-microscopy (cryo-EM), rapid progress has been made for structural elucidation of isolated MPs. The next challenge is to preserve the electrochemical gradients and membrane curvature for a comprehensive structural elucidation of MPs that rely on these chemical and physical properties for their biological functions. Toward this goal, here we present a convenient workflow for cryo-EM structural analysis of MPs embedded in liposomes, using the well-characterized AcrB as a prototype. Combining optimized proteoliposome isolation, cryo-sample preparation on graphene grids, and an efficient particle selection strategy, the three-dimensional (3D) reconstruction of AcrB embedded in liposomes was obtained at 3.9 Å resolution. The conformation of the homotrimeric AcrB remains the same when the surrounding membranes display different curvatures. Our approach, which can be widely applied to cryo-EM analysis of MPs with distinctive soluble domains, lays out the foundation for cryo-EM analysis of integral or peripheral MPs whose functions are affected by transmembrane electrochemical gradients or/and membrane curvatures.
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Affiliation(s)
- Xia Yao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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38
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Qian H, Zhao X, Yan R, Yao X, Gao S, Sun X, Du X, Yang H, Wong CCL, Yan N. Structural basis for catalysis and substrate specificity of human ACAT1. Nature 2020; 581:333-338. [DOI: 10.1038/s41586-020-2290-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 03/17/2020] [Indexed: 02/03/2023]
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39
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Wang L, Qian H, Nian Y, Han Y, Ren Z, Zhang H, Hu L, Prasad BVV, Laganowsky A, Yan N, Zhou M. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature 2020; 581:329-332. [PMID: 32433610 PMCID: PMC7255049 DOI: 10.1038/s41586-020-2280-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 03/17/2020] [Indexed: 12/27/2022]
Abstract
Diacylglycerol O-acyltransferase-1 (DGAT1) synthesizes triacylglycerides and is required for dietary fat absorption and fat storage in humans1. DGAT1 belongs to the superfamily of membrane-bound O-acyltransferases (MBOAT) that are found in all kingdoms of life and involved in acylation of lipids and proteins2,3. It remains unclear how human DGAT1 (hDGAT1) or other mammalian members of the MBOAT family recognize their substrates and catalyze their reactions. The absence of three-dimensional structures also hampers rational targeting of hDGAT1 for therapeutic purposes. Here we present the structure of hDGAT1 in complex with a substrate oleoyl Coenzyme A solved by cryo-electron microscopy. Each hDGAT1 protomer has nine transmembrane helices and eight of which form a conserved structural fold that we define as the MBOAT fold. The MBOAT fold in hDGAT1 carves out a hollow chamber in the membrane that encloses highly conserved catalytic residues. The chamber has separate entrances for the two substrates fatty acyl Coenzyme A and diacylglycerol. hDGAT1 can exist as either a homodimer or homotetramer and the two forms have similar enzymatic activity. The N-terminus of hDGAT1 interacts with the neighboring protomer and these interactions are required for the enzymatic activity.
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Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hongwu Qian
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yin Nian
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yimo Han
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.,Department of Material Science and Nanoengineering, Rice University, Houston, TX, USA
| | - Zhenning Ren
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hanzhi Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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40
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Zhao Y, Huang G, Wu J, Wu Q, Gao S, Yan Z, Lei J, Yan N. Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca 2+ Channel. Cell 2020; 177:1495-1506.e12. [PMID: 31150622 DOI: 10.1016/j.cell.2019.04.043] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/23/2019] [Accepted: 04/25/2019] [Indexed: 10/26/2022]
Abstract
The L-type voltage-gated Ca2+ (Cav) channels are modulated by various compounds exemplified by 1,4-dihydropyridines (DHP), benzothiazepines (BTZ), and phenylalkylamines (PAA), many of which have been used for characterizing channel properties and for treatment of hypertension and other disorders. Here, we report the cryoelectron microscopy (cryo-EM) structures of Cav1.1 in complex with archetypal antagonistic drugs, nifedipine, diltiazem, and verapamil, at resolutions of 2.9 Å, 3.0 Å, and 2.7 Å, respectively, and with a DHP agonist Bay K 8644 at 2.8 Å. Diltiazem and verapamil traverse the central cavity of the pore domain, directly blocking ion permeation. Although nifedipine and Bay K 8644 occupy the same fenestration site at the interface of repeats III and IV, the coordination details support previous functional observations that Bay K 8644 is less favored in the inactivated state. These structures elucidate the modes of action of different Cav ligands and establish a framework for structure-guided drug discovery.
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Affiliation(s)
- Yanyu Zhao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianping Wu
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Qiurong Wu
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zhen Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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41
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Liu Y, Hu H, Wang J, Zhou Q, Wu P, Yan N, Wang HW, Wu JW, Sun L. Cryo-EM structure of L-fucokinase/GDP-fucose pyrophosphorylase (FKP) in Bacteroides fragilis. Protein Cell 2020; 10:365-369. [PMID: 30242642 PMCID: PMC6468028 DOI: 10.1007/s13238-018-0576-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ying Liu
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huifang Hu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiang Zhou
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nieng Yan
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hong-Wei Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jia-Wei Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Linfeng Sun
- CAS Center for Excellence in Molecular Cell Science, Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
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42
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Han Y, Fan X, Wang H, Zhao F, Tully CG, Kong J, Yao N, Yan N. High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy. Proc Natl Acad Sci U S A 2020; 117:1009-1014. [PMID: 31879346 PMCID: PMC6969529 DOI: 10.1073/pnas.1919114117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) has become one of the most powerful techniques to reveal the atomic structures and working mechanisms of biological macromolecules. New designs of the cryo-EM grids-aimed at preserving thin, uniform vitrified ice and improving protein adsorption-have been considered a promising approach to achieving higher resolution with the minimal amount of materials and data. Here, we describe a method for preparing graphene cryo-EM grids with up to 99% monolayer graphene coverage that allows for more than 70% grid squares for effective data acquisition with improved image quality and protein density. Using our graphene grids, we have achieved 2.6-Å resolution for streptavidin, with a molecular weight of 52 kDa, from 11,000 particles. Our graphene grids increase the density of examined soluble, membrane, and lipoproteins by at least 5-fold, affording the opportunity for structural investigation of challenging proteins which cannot be produced in large quantity. In addition, our method employs only simple tools that most structural biology laboratories can access. Moreover, this approach supports customized grid designs targeting specific proteins, owing to its broad compatibility with a variety of nanomaterials.
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Affiliation(s)
- Yimo Han
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544;
| | - Xiao Fan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Haozhe Wang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Fang Zhao
- Department of Physics, Princeton University, Princeton, NJ 08544
| | | | - Jing Kong
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Nan Yao
- PRISM Imaging and Analysis Center, Princeton University, Princeton, NJ 08544
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544;
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43
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Ripani P, Delp J, Bode K, Delgado ME, Dietrich L, Betzler VM, Yan N, von Scheven G, Mayer TU, Leist M, Brunner T. Thiazolides promote G1 cell cycle arrest in colorectal cancer cells by targeting the mitochondrial respiratory chain. Oncogene 2019; 39:2345-2357. [PMID: 31844249 DOI: 10.1038/s41388-019-1142-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 01/10/2023]
Abstract
Systemic toxicity and tumor cell resistance still limit the efficacy of chemotherapy in colorectal cancer. Therefore, alternative treatments are desperately needed. The thiazolide Nitazoxanide (NTZ) is an FDA-approved drug for the treatment of parasite-mediated infectious diarrhea with a favorable safety profile. Interestingly, NTZ and the thiazolide RM4819-its bromo-derivative lacking antibiotic activity-are also promising candidates for cancer treatment. Yet the exact anticancer mechanism(s) of these compounds still remains unclear. In this study, we systematically investigated RM4819 and NTZ in 2D and 3D colorectal cancer culture systems. Both compounds strongly inhibited proliferation of colon carcinoma cell lines by promoting G1 phase cell cycle arrest. Thiazolide-induced cell cycle arrest was independent of the p53/p21 axis, but was mediated by inhibition of protein translation via the mTOR/c-Myc/p27 pathway, likely caused by inhibition of mitochondrial respiration. While both thiazolides demonstrated mitochondrial uncoupling activity, only RM4819 inhibited the mitochondrial respiratory chain complex III. Interestingly, thiazolides also potently inhibited the growth of murine colonic tumoroids in a comparable manner with cisplatin, while in contrast to cisplatin thiazolides did not affect the growth of primary intestinal organoids. Thus, thiazolides appear to have a tumor-selective antiproliferative activity, which offers new perspectives in the treatment of colorectal cancer.
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Affiliation(s)
- P Ripani
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology KORS-CB, University of Konstanz, Konstanz, Germany
| | - J Delp
- Konstanz Research School Chemical Biology KORS-CB, University of Konstanz, Konstanz, Germany.,Chair for In Vitro Toxicology and Biomedicine, inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - K Bode
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany
| | - M E Delgado
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany
| | - L Dietrich
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany
| | - V M Betzler
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany.,Biotechnology Institute Thurgau, University of Konstanz, Konstanz, Germany
| | - N Yan
- Department of Medicinal Chemistry, Peking University Health Science Centre, Beijing, China
| | - G von Scheven
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - T U Mayer
- Konstanz Research School Chemical Biology KORS-CB, University of Konstanz, Konstanz, Germany.,Department of Biology, Molecular Genetics, University of Konstanz, Konstanz, Germany
| | - M Leist
- Konstanz Research School Chemical Biology KORS-CB, University of Konstanz, Konstanz, Germany.,Chair for In Vitro Toxicology and Biomedicine, inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - T Brunner
- Department of Biology, Biochemical Pharmacology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology KORS-CB, University of Konstanz, Konstanz, Germany.
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44
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Zhao Y, Huang G, Wu Q, Wu K, Li R, Lei J, Pan X, Yan N. Cryo-EM structures of apo and antagonist-bound human Ca v3.1. Nature 2019; 576:492-497. [PMID: 31766050 DOI: 10.1038/s41586-019-1801-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/01/2019] [Indexed: 01/02/2023]
Abstract
Among the ten subtypes of mammalian voltage-gated calcium (Cav) channels, Cav3.1-Cav3.3 constitute the T-type, or the low-voltage-activated, subfamily, the abnormal activities of which are associated with epilepsy, psychiatric disorders and pain1-5. Here we report the cryo-electron microscopy structures of human Cav3.1 alone and in complex with a highly Cav3-selective blocker, Z9446,7, at resolutions of 3.3 Å and 3.1 Å, respectively. The arch-shaped Z944 molecule reclines in the central cavity of the pore domain, with the wide end inserting into the fenestration on the interface between repeats II and III, and the narrow end hanging above the intracellular gate like a plug. The structures provide the framework for comparative investigation of the distinct channel properties of different Cav subfamilies.
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Affiliation(s)
- Yanyu Zhao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Gaoxingyu Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiurong Wu
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kun Wu
- Medical Research Center, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ruiqi Li
- Medical Research Center, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaojing Pan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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45
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Xu GS, Yang QQ, Yan N, Wang YF, Xu XQ, Guo HY, Maingi R, Wang L, Qian JP, Gong XZ, Chan VS, Zhang T, Zang Q, Li YY, Zhang L, Hu GH, Wan BN. Promising High-Confinement Regime for Steady-State Fusion. Phys Rev Lett 2019; 122:255001. [PMID: 31347864 DOI: 10.1103/physrevlett.122.255001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 05/18/2019] [Indexed: 06/10/2023]
Abstract
A reproducible stationary high-confinement regime with small "edge-localized modes" (ELMs) has been achieved recently in the Experimental Advanced Superconducting Tokamak, which has a metal wall and low plasma rotation as projected for a fusion reactor. We have uncovered that this small ELM regime is enabled by a wide edge transport barrier (pedestal) with a low density gradient and a high density ratio between the pedestal foot and top. Nonlinear simulations reveal, for the first time, that the underlying mechanism for the observed small ELM crashes is the upper movement of the peeling boundary induced by an initial radially localized collapse in the pedestal, which stops the growth of instabilities and further collapse of the pedestal, thus providing a physics basis for mitigating ELMs in future steady-state fusion reactors.
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Affiliation(s)
- G S Xu
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Q Q Yang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - N Yan
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Y F Wang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - X Q Xu
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - H Y Guo
- General Atomics, P.O. Box 85608, San Diego, California 92186-5608, USA
| | - R Maingi
- Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543, USA
| | - L Wang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - J P Qian
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - X Z Gong
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - V S Chan
- University of Science and Technology of China, Hefei 230026, China
- General Atomics, P.O. Box 85608, San Diego, California 92186-5608, USA
| | - T Zhang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Q Zang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - Y Y Li
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - L Zhang
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - G H Hu
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
| | - B N Wan
- Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
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46
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Bai JY, Meng FH, Shao XX, Wang JF, Zhang L, Luo J, Yan N, Chen FH, Zhang YM. [Research on feasibility and effectiveness of the bone-implant contact evaluation in dogs by micro-CT]. Zhonghua Kou Qiang Yi Xue Za Zhi 2019; 54:250-256. [PMID: 30955297 DOI: 10.3760/cma.j.issn.1002-0098.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To discuss the feasibility and effectiveness of using micro-CT in bone-implant contact (BIC) evaluation in dogs, and to provide reference for clinical and scientific research. Methods: Bilateral mandibular second premolar and first molar of six male Beagle dogs were extracted. After 3 months' healing, eight implants were placed in bilateral mandible of each dog, four on each side. Dogs were sacrificed at 2 weeks, 4 weeks and 8 weeks after implant placement, two on each time point. Samples were scanned with micro-CT and digitally reconstructed. Bone-implant interface was analyzed at different analysis regions (25, 50 and 100 μm from implants' surface), different detection range models were obtained (each time point consists 48 models), and BIC was evaluated, and the results were counted as micro-CT(25), micro-CT(50), and micro-CT(100) groups. Then undecalcified slides were made (three slides for each sample) and stained with toluidine blue for observation and analysis of BIC using an optical microscope, and the results were counted as optical microscope groups. The advantages and disadvantages, evaluation efficiency and BIC of different methods were analyzed. Results: To evaluate BIC of single sample, it took about 90 minutes by micro-CT, which was much lower than the time of 14 days by optical microscope. The success rates of modeling of micro-CT(25), micro-CT(50), and micro-CT(100) groups all were 100.0% (48/48), and total success rate of micro-CT group was 100.0% (144/144). For optical microscope groups, the success rates of making slides 2, 4, 8 weeks were 89.6% (43/48), 93.8% (45/48) and 93.8% (45/48), respectively, and total success rates of optical microscope group was 92.4% (133/144). At 2, 4,8 weeks after implantation, BIC in micro-CT(25) group was significantly smaller than that in optical microscope group at the same time point (P<0.05). However, at 2, 4,8 weeks after implantation, BIC of the micro-CT(50) and micro-CT(100) groups showed no significant difference with optical microscope groups at the same time point (P>0.05). A significant correlation (P<0.001, each) was seen between slides and micro-CT (25, 50, 100 μm groups) concerning BIC (r=0.680, r=0.892, r=0.713), and error bias was -19.4%, -0.9%, 3.0%, respectively. The probability within the 95% limits of agreement were 97.9%. Conclusions: Micro-CT is a faster, simpler and more efficient way to analyze BIC at the implant-bone interface than optical microscope observation. BIC analysis by selecting 50 μm from implants' surface as analysis region using micro-CT is in consistent with that using the optical microscope.
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Affiliation(s)
- J Y Bai
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - F H Meng
- Department of Dental Materials, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases, Xi'an 710032, China
| | - X X Shao
- Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Clinical Research Center for Oral Diseases, Xi'an 710032, China
| | - J F Wang
- Department of Oral and Maxillofacial Surgery, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Clinical Research Center for Oral Diseases, Xi'an 710032, China
| | - L Zhang
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - J Luo
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - N Yan
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - F H Chen
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
| | - Y M Zhang
- Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University & State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Xi'an 710032, China
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47
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Affiliation(s)
- Juanrong Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Wenzhi Mao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Yanhui Ren
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Rui-Ning Sun
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Nieng Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
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48
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Pan X, Li Z, Huang X, Huang G, Gao S, Shen H, Liu L, Lei J, Yan N. Molecular basis for pore blockade of human Na + channel Na v1.2 by the μ-conotoxin KIIIA. Science 2019; 363:1309-1313. [PMID: 30765605 DOI: 10.1126/science.aaw2999] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022]
Abstract
The voltage-gated sodium channel Nav1.2 is responsible for the initiation and propagation of action potentials in the central nervous system. We report the cryo-electron microscopy structure of human Nav1.2 bound to a peptidic pore blocker, the μ-conotoxin KIIIA, in the presence of an auxiliary subunit, β2, to an overall resolution of 3.0 angstroms. The immunoglobulin domain of β2 interacts with the shoulder of the pore domain through a disulfide bond. The 16-residue KIIIA interacts with the extracellular segments in repeats I to III, placing Lys7 at the entrance to the selectivity filter. Many interacting residues are specific to Nav1.2, revealing a molecular basis for KIIIA specificity. The structure establishes a framework for the rational design of subtype-specific blockers for Nav channels.
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Affiliation(s)
- Xiaojing Pan
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhangqiang Li
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaoshuang Huang
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shuai Gao
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huaizong Shen
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. .,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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49
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Shen H, Liu D, Wu K, Lei J, Yan N. Structures of human Na v1.7 channel in complex with auxiliary subunits and animal toxins. Science 2019; 363:1303-1308. [PMID: 30765606 DOI: 10.1126/science.aaw2493] [Citation(s) in RCA: 260] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 01/29/2019] [Indexed: 12/18/2022]
Abstract
Voltage-gated sodium channel Nav1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Nav1.7-β1-β2 complex bound to two combinations of pore blockers and gating modifier toxins (GMTs), tetrodotoxin with protoxin-II and saxitoxin with huwentoxin-IV, both determined at overall resolutions of 3.2 angstroms. The two structures are nearly identical except for minor shifts of voltage-sensing domain II (VSDII), whose S3-S4 linker accommodates the two GMTs in a similar manner. One additional protoxin-II sits on top of the S3-S4 linker in VSDIV The structures may represent an inactivated state with all four VSDs "up" and the intracellular gate closed. The structures illuminate the path toward mechanistic understanding of the function and disease of Nav1.7 and establish the foundation for structure-aided development of analgesics.
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Affiliation(s)
- Huaizong Shen
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dongliang Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kun Wu
- Medical Research Center, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Nieng Yan
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China. .,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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50
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Yan R, Qian H, Lukmantara I, Gao M, Du X, Yan N, Yang H. Human SEIPIN Binds Anionic Phospholipids. Dev Cell 2018; 47:248-256.e4. [PMID: 30293840 DOI: 10.1016/j.devcel.2018.09.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/05/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
The biogenesis of lipid droplets (LDs) and the development of adipocytes are two key aspects of mammalian fat storage. SEIPIN, an integral membrane protein of the endoplasmic reticulum (ER), plays a critical role in both LD formation and adipogenesis. The molecular function of SEIPIN, however, has yet to be elucidated. Here, we report the cryogenic electron microscopy structure of human SEIPIN at 3.8 Å resolution. SEIPIN exists as an undecamer, and this oligomerization state is critical for its physiological function. The evolutionarily conserved lumenal domain of SEIPIN forms an eight-stranded β sandwich fold. Both full-length SEIPIN and its lumenal domain can bind anionic phospholipids including phosphatidic acid. Our results suggest that SEIPIN forms a scaffold that helps maintain phospholipid homeostasis and surface tension of the ER.
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Affiliation(s)
- Renhong Yan
- Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hongwu Qian
- Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ivan Lukmantara
- School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW 2052, Australia
| | - Mingming Gao
- Laboratory of Lipid Metabolism, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Ximing Du
- School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW 2052, Australia
| | - Nieng Yan
- Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA.
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW 2052, Australia.
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