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van Bergen W, Žuna K, Fiala J, Pohl EE, Heck AJ, Baggelaar MP. Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs. ACS Chem Biol 2024; 19:1705-1718. [PMID: 39052621 PMCID: PMC11334109 DOI: 10.1021/acschembio.3c00637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 06/24/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Comparative, dose-dependent analysis of interactions between small molecule drugs and their targets, as well as off-target interactions, in complex proteomes is crucial for selecting optimal drug candidates. The affinity of small molecules for targeted proteins is largely dictated by interactions between amino acid side chains and these drugs. Thus, studying drug-protein interactions at an amino acid resolution provides a comprehensive understanding of the drug selectivity and efficacy. In this study, we further refined the site-specific activity-based protein profiling strategy (ABPP), PhosID-ABPP, on a timsTOF HT mass spectrometer. This refinement enables dual dose-dependent competition of inhibitors within a single cellular proteome. Here, a comparative analysis of two activity-based probes (ABPs), developed to selectively target the epidermal growth factor receptor (EGFR), namely, PF-06672131 (PF131) and PF-6422899 (PF899), facilitated the simultaneous identification of ABP-specific binding sites at a proteome-wide scale within a cellular proteome. Dose-dependent probe-binding preferences for proteinaceous cysteines, even at low nanomolar ABP concentrations, could be revealed. Notably, in addition to the intrinsic affinity of the electrophilic probes for specific sites in targeted proteins, the observed labeling intensity is influenced by several other factors. These include the efficiency of cellular uptake, the stability of the probes, and their intracellular distribution. While both ABPs showed comparable labeling efficiency for EGFR, PF131 had a broader off-target reactivity profile. In contrast, PF899 exhibited a higher labeling efficiency for the ERBB2 receptor and bound to catalytic cysteines in several other enzymes, which is likely to disrupt their catalytic activity. Notably, PF131 effectively labeled ADP/ATP translocase proteins at a concentration of just 1 nm, and we found this affected ATP transport. Analysis of the effect of PF131 and its parent inhibitor Afatinib on murine translocase SLC25A4 (ANT1)-mediated ATP transport strongly indicated that PF131 (10 μM) partially blocked ATP transport. Afatinib was less efficient at inhibiting ATP transport by SLC25A4 than PF131, and the reduction of ATP transport by Afatinib was not significant. Follow-up analysis is required to evaluate the affinity of these inhibitors for ADP/ATP translocase SLC25A4 in more detail. Additionally, the analysis of different binding sites within the EGF receptor and the voltage-dependent anion channel 2 revealed secondary binding sites of both probes and provided insights into the binding poses of inhibitors on these proteins. Insights from the PhosID-ABPP analysis of these two ABPs serve as a valuable resource for understanding drug on- and off-target engagement in a dose- and site-specific manner.
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Affiliation(s)
- Wouter van Bergen
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Kristina Žuna
- Physiology
and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Wien, Vienna 1210, Austria
| | - Jan Fiala
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Elena E. Pohl
- Physiology
and Biophysics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine, Wien, Vienna 1210, Austria
| | - Albert J.R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Marc P. Baggelaar
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
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2
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Pan T, Yang B, Yao S, Wang R, Zhu Y. Exploring the multifaceted role of adenosine nucleotide translocase 2 in cellular and disease processes: A comprehensive review. Life Sci 2024; 351:122802. [PMID: 38857656 DOI: 10.1016/j.lfs.2024.122802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/04/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Adenosine nucleotide translocases (ANTs) are a family of proteins abundant in the inner mitochondrial membrane, primarily responsible for shuttling ADP and ATP across the mitochondrial membrane. Additionally, ANTs are key players in balancing mitochondrial energy metabolism and regulating cell death. ANT2 isoform, highly expressed in undifferentiated and proliferating cells, is implicated in the development and drug resistance of various tumors. We conduct a detailed analysis of the potential mechanisms by which ANT2 may influence tumorigenesis and drug resistance. Notably, the significance of ANT2 extends beyond oncology, with roles in non-tumor cell processes including blood cell development, gastrointestinal motility, airway hydration, nonalcoholic fatty liver disease, obesity, chronic kidney disease, and myocardial development, making it a promising therapeutic target for multiple pathologies. To better understand the molecular mechanisms of ANT2, this review summarizes the structural properties, expression patterns, and basic functions of the ANT2 protein. In particular, we review and analyze the controversy surrounding ANT2, focusing on its role in transporting ADP/ATP across the inner mitochondrial membrane, its involvement in the composition of the mitochondrial permeability transition pore, and its participation in apoptosis.
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Affiliation(s)
- Tianhui Pan
- Laboratory of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, PR China
| | - Bin Yang
- Laboratory of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, PR China
| | - Sheng Yao
- Laboratory of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, PR China
| | - Rui Wang
- Laboratory of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, PR China
| | - Yongliang Zhu
- Laboratory of Gastroenterology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, PR China.
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Woyda-Ploszczyca AM. Direct and indirect targets of carboxyatractyloside, including overlooked toxicity toward nucleoside diphosphate kinase (NDPK) and mitochondrial H + leak. PHARMACEUTICAL BIOLOGY 2023; 61:372-390. [PMID: 36799406 PMCID: PMC9946330 DOI: 10.1080/13880209.2023.2168704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
CONTEXT The toxicity of atractyloside/carboxyatractyloside is generally well recognized and commonly ascribed to the inhibition of mitochondrial ADP/ATP carriers, which are pivotal for oxidative phosphorylation. However, these glycosides may 'paralyze' additional target proteins. OBJECTIVE This review presents many facts about atractyloside/carboxyatractyloside and their plant producers, such as Xanthium spp. (Asteraceae), named cockleburs. METHODS Published studies and other information were obtained from databases, such as 'CABI - Invasive Species Compendium', 'PubMed', and 'The World Checklist of Vascular Plants', from 1957 to December 2022. The following major keywords were used: 'carboxyatractyloside', 'cockleburs', 'hepatotoxicity', 'mitochondria', 'nephrotoxicity', and 'Xanthium'. RESULTS In the third decade of the twenty first century, public awareness of the severe toxicity of cockleburs is still limited. Such toxicity is often only perceived by specialists in Europe and other continents. Interestingly, cocklebur is among the most widely distributed invasive plants worldwide, and the recognition of new European stands of Xanthium spp. is provided here. The findings arising from field and laboratory research conducted by the author revealed that (i) some livestock populations may instinctively avoid eating cocklebur while grazing, (ii) carboxyatractyloside inhibits ADP/GDP metabolism, and (iii) the direct/indirect target proteins of carboxyatractyloside are ambiguous. CONCLUSIONS Many aspects of the Xanthium genus still require substantial investigation/revision in the future, such as the unification of the Latin nomenclature of currently distinguished species, bur morphology status, true fruit (achene) description and biogeography of cockleburs, and a detailed description of the physiological roles of atractyloside/carboxyatractyloside and the toxicity of these glycosides, mainly toward mammals. Therefore, a more careful interpretation of atractyloside/carboxyatractyloside data, including laboratory tests using Xanthium-derived extracts and purified toxins, is needed.
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Roh S, Kim J, Kim S, So B, Lee K. A case of carboxyatractyloside intoxication by ingestion of the cocklebur ( Xanthium strumarium) in a Korean native cow. VET MED-CZECH 2022; 67:538-543. [PMID: 38846426 PMCID: PMC11154875 DOI: 10.17221/183/2020-vetmed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/02/2022] [Indexed: 06/09/2024] Open
Abstract
A 19-month-old Korean native cow died the following day after consuming new silage. Grossly, the liver showed enlargement, redness, and haemorrhages in all the lobes. Additionally, many of the bur-shaped fruits of the cocklebur (Xanthium strumarium) were found in the gastric contents. The histological evaluation confirmed centrilobular hepatic necrosis. Additionally, carboxyatractyloside (CATR), a material fatal to animals found in the cocklebur, was detected in the gastric contents using high-performance liquid chromatography-quadrupole-time of flight mass spectrometry (HPLC-Q-TOF-MS). Based on the pathological findings and analytical confirmation, CATR intoxication was diagnosed. Therefore, careful feeding and elimination of the cocklebur is essential for minimising economic loss.
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Affiliation(s)
- SuGwon Roh
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency (APQA), Gimcheon, Republic of Korea
| | - Jongho Kim
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency (APQA), Gimcheon, Republic of Korea
| | - Sunchun Kim
- National Forensic Service, Wonju, Republic of Korea
| | - ByungJae So
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency (APQA), Gimcheon, Republic of Korea
| | - Kyunghyun Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency (APQA), Gimcheon, Republic of Korea
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Elbaradei A, Wang Z, Malmstadt N. Oxidation of Membrane Lipids Alters the Activity of the Human Serotonin 1A Receptor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6798-6807. [PMID: 35608952 DOI: 10.1021/acs.langmuir.1c03238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lipid oxidation has significant effects on lipid bilayer properties; these effects can be expected to extend to interactions between the lipid bilayer and integral membrane proteins. Given that G protein-coupled receptor (GPCR) activity is known to depend on the properties of the surrounding lipid bilayer, these proteins represent an intriguing class of molecules in which the impact of lipid oxidation on protein behavior is studied. Here, we study the effects of lipid oxidation on the human serotonin 1A receptor (5-HT1AR). Giant unilamellar vesicles (GUVs) containing integral 5-HT1AR were fabricated by the hydrogel swelling method; these GUVs contained polyunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (PLinPC) and its oxidation product 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC) at various ratios. 5-HT1AR-integrated GUVs were also fabricated from lipid mixtures that had been oxidized by extended exposure to the atmosphere. Both types of vesicles were used to evaluate 5-HT1AR activity using an assay to quantify GDP-GTP exchange by the coupled G protein α subunit. Results indicated that 5-HT1AR activity increases significantly in bilayers containing oxidized lipids. This work is an important step in understanding how hyperbaric oxidation can change plasma membrane properties and lead to physiological dysfunction.
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7
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Zhang P, Cheng X, Sun H, Li Y, Mei W, Zeng C. Atractyloside Protect Mice Against Liver Steatosis by Activation of Autophagy via ANT-AMPK-mTORC1 Signaling Pathway. Front Pharmacol 2021; 12:736655. [PMID: 34621170 PMCID: PMC8490973 DOI: 10.3389/fphar.2021.736655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/23/2021] [Indexed: 12/02/2022] Open
Abstract
Objective: Adenine nucleotide translocase (ANT) can transport ADP from cytoplasm to mitochondrial matrix and provide raw materials for ATP synthesis by oxidative phosphorylation. Dysfunction of ANT leads to limitation of ADP transport and decrease of ATP production. Atractyloside (ATR) is considered as a cytotoxic competitive inhibitor binding to ANT, making ANT vulnerable to transport ADP, and reduces ATP synthesis. Moreover, the blockage of ANT by ATR may increase ADP/ATP ratio, activate AMPK-mTORC1-autophagy signaling pathway, and promote lipid degradation in steatosis hepatocytes. The present study was conducted to investigate the mechanism of ATR, regulate ANT-AMPK-mTORC1 signaling pathway to activate autophagy, and promote the degradation of lipid droplets in high-fat diet (HFD) induced liver steatosis. Methods: ICR mice were fed with HFD for 8 weeks to induce liver steatosis, and ATR solution was given by intraperitoneal injection. Intracellular triglyceride level and oil red O staining-lipid droplets (LDs) were assessed, the expression of proteins related to ANT-AMPK-mTORC1 signaling pathway and autophagy were determined, and the colocalization of LC3B and Perilipin 2 was performed. Results: ATR treatment decreased the serum AST level, relative weight of liver and epididymal fat, and body weight of HFD mice. The LDs in HFD mice livers were reduced in the presence of ATR, and the TG level in serum and liver of HFD mice was significantly reduced by ATR. In addition, ATR inhibited ANT2 expression, promoted the activation of AMPK, then increased Raptor expression, and finally decreased the mTOR activity. Furthermore, ATR increased the protein level of LC3A/B and ATG7, and a strong colocalization of LC3B and PLIN2 was observed. Conclusion: ATR treatment blocks ANT2 expression, promotes the activation of AMPK, then decreases the mTOR activity, and finally promotes autophagosomes formation, thus accelerating the degradation of HFD-induced accumulated lipids in the liver. This will provide new therapeutic ideas and experimental data for clinical prevention and treatment of non-alcoholic fatty liver disease.
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Affiliation(s)
- Pengfei Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Xinyu Cheng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Huimin Sun
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Yajing Li
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Wuxuan Mei
- Clinical Medical College, Hubei University of Science and Technology, Xianning, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
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8
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The mitochondrial ADP/ATP carrier exists and functions as a monomer. Biochem Soc Trans 2021; 48:1419-1432. [PMID: 32725219 PMCID: PMC7458400 DOI: 10.1042/bst20190933] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
For more than 40 years, the oligomeric state of members of the mitochondrial carrier family (SLC25) has been the subject of debate. Initially, the consensus was that they were dimeric, based on the application of a large number of different techniques. However, the structures of the mitochondrial ADP/ATP carrier, a member of the family, clearly demonstrated that its structural fold is monomeric, lacking a conserved dimerisation interface. A re-evaluation of previously published data, with the advantage of hindsight, concluded that technical errors were at the basis of the earlier dimer claims. Here, we revisit this topic, as new claims for the existence of dimers of the bovine ADP/ATP carrier have emerged using native mass spectrometry of mitochondrial membrane vesicles. However, the measured mass does not agree with previously published values, and a large number of post-translational modifications are proposed to account for the difference. Contrarily, these modifications are not observed in electron density maps of the bovine carrier. If they were present, they would interfere with the structure and function of the carrier, including inhibitor and substrate binding. Furthermore, the reported mass does not account for three tightly bound cardiolipin molecules, which are consistently observed in other studies and are important stabilising factors for the transport mechanism. The monomeric carrier has all of the required properties for a functional transporter and undergoes large conformational changes that are incompatible with a stable dimerisation interface. Thus, our view that the native mitochondrial ADP/ATP carrier exists and functions as a monomer remains unaltered.
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Zhang P, Li L, Sun H, Zhang Y, Zhang G, Zhang T, Zeng C. Mitochondrial Energy-Regulating Effect of Atractyloside Inhibits Hepatocellular Steatosis Through the Activation of Autophagy. Front Pharmacol 2020; 11:575695. [PMID: 33101031 PMCID: PMC7556285 DOI: 10.3389/fphar.2020.575695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Background and Aim Atractyloside (ATR), a mitochondrial uncoupler, is known for its specific inhibition of mitochondrial oxidative phosphorylation. Previous studies have reported that moderate mitochondrial uncoupling effect is beneficial to increase the decomposition and clearance of hepatic lipid, prevent the occurrence of fatty liver diseases. Moreover, the beneficial effects of mitochondrial uncouplers on type 2 diabetes and metabolic syndromes have been consistently observed. The present study investigated the effect of ATR on steatosis level of HepG2 cells treated with free fatty acid (FFA). Methods Intracellular triglyceride level and Oil Red O staining were assessed, the mitochondrial adaptation and ADP/ATP ratio were analyzed, the protein level of AMPK, mTOR and LC3B, autophagic flux, and the co-localization of LC3B with lipid droplets was performed. Results ATR treatment inhibited the activity of mitochondrial respiratory chain complexes I and IV, decreased the mitochondrial membrane potential, and increased the ADP/ATP ratio in the FFA-treated cells. Furthermore, ATR increased the gene expression and protein level of LC3B and promoted the autophagic flux processing from early autophagosome to late autolysosome by increasing the protein level of AMPKα and decreasing the protein level of mTOR. An increased number of autophagosomes (LC3B) was also observed in the lipid droplets. ATR treatment accelerated lipid degradation in the FFA-treated cells, and the lowest lipid content was observed in the cell group with 7.5 μM ATR. Conclusion Low concentrations (2.5, 5, and 7.5 μM) of ATR treatment could activate autophagy to accelerate the degradation of TGs in steatosis HepG2 cells; the mechanism may be related to the activation of the AMPK/mTOR pathway induced by the increased ADP/ATP ratio. In addition, the ideal concentration of ATR for improving steatotic HepG2 cells was 7.5 μM.
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Affiliation(s)
- Pengfei Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lijun Li
- Department of Quality Control, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Huimin Sun
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Yipeng Zhang
- Clinical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Shenzhen, China
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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Pan H, Yang F, Xiang D, Shi F. Simultaneous quantification of atractyloside and carboxyatractyloside in rat plasma by LC-MS/MS: Application to a pharmacokinetic study after oral administration of Xanthii Fructus extract. J Sep Sci 2019; 43:590-597. [PMID: 31701660 DOI: 10.1002/jssc.201900888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/22/2019] [Accepted: 11/03/2019] [Indexed: 11/07/2022]
Abstract
Xanthii Fructus is extensively used as an herbal medicine. Ingestion of this herb is associated with severe hepatotoxicity and nephrotoxicity. Atractyloside and carboxyatractyloside are two dominative toxic constituents in Xanthii Fructus. However, their pharmacokinetic study is lacking. In this study, a novel high-performance liquid chromatography-tandem mass spectrometry method was developed to simultaneously quantify the rat plasma concentrations of atractyloside and carboxyatractyloside. After protein precipitation, the analytes were chromatographic separated on a ZORBAX Eclipse Plus column (2.1 × 150 mm id, 5 µm) under gradient elute. In the negative electrospray ionization mode, the transitions at m/z 725.3→645.4 for atractyloside, m/z 769.3→689.4 for carboxyatractyloside, and m/z 479.2→121.1 for paeoniflorin (the internal standard) were acquired by multiple reaction monitoring. This analytical method showed good linearity over 1-500 ng/mL for atractyloside and 2-500 ng/mL for carboxyatractyloside with acceptable precision and accuracy. No matrix effect, instability and carryover occurred in the analysis procedure. The extraction recoveries were greater than 85.0%. This method was applied to a preliminary pharmacokinetic study by orally administering Xanthii Fructus extract (9 g/kg) to rats, which was useful to evaluate the role of these two compounds in Xanthii Fructus-induced toxicity.
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Affiliation(s)
- Hong Pan
- Department of clinical pharmacy, School of pharmacy, Zunyi Medical University, Zunyi, P. R. China.,Key Laboratory of Basic Pharmacology of Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, P. R. China
| | - Feng Yang
- Key Laboratory of Basic Pharmacology of Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, P. R. China
| | - Daiyuan Xiang
- Department of clinical pharmacy, School of pharmacy, Zunyi Medical University, Zunyi, P. R. China
| | - Fuguo Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, P. R. China
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12
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Jiang H, Yang L, Xing X, Yan M, Guo X, Man W, Hou A, Yang B, Wang QH, Kuang HX. A simple liquid chromatography coupled with tandem mass spectrometry approach for the simultaneous quantification of thirteen compounds in rats following oral administration of raw and processed Fructus Xanthii: Application in a comparative pharmacokinetic study. J Sep Sci 2019; 42:3403-3412. [PMID: 31513345 DOI: 10.1002/jssc.201900506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/30/2019] [Accepted: 09/08/2019] [Indexed: 12/12/2022]
Abstract
A simple and sensitive analysis using ultra high performance liquid chromatography with a tandem mass spectrometric system operated in selected reaction monitoring mode was developed for the determination of 11 phenolic acids, atractyloside, and carboxyatractyloside in rat plasma. The two classes of analytes were then separated on a Waters ACQUITY™ UPLC HSS T3 column (50 mm × 2.1 mm, 1.8 µm) using gradient elution with a mobile phase of 0.2% formic acid in water containing 10 mM ammonium acetate and methanol. Detection was accomplished by selected reaction monitoring scanning via an electrospray source operating in negative ionization mode. The calibration curve was linear (R2 = 0.990) over a concentration range of 1.20-3500 ng/mL, while the validated lower limit of quantification was 1.20 ng/mL. The precision varied from 0.84 to 4.62%, and the accuracy varied within ±5%. The method proved robust with sample freezing and thawing and with short- and long-term sample storage. The established method was used for simultaneous quantification and was successfully used for the first time for the pharmacokinetic evaluation of 13 compounds after the intragastric administration of raw and processed Fructus Xanthii in rats. The results indicated that processing affects the absorption and metabolism of Fructus Xanthii extract. Importantly, the results also indicated the importance of processing for the clinical application of traditional Chinese medicine.
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Affiliation(s)
- Hai Jiang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Liu Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Xudong Xing
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Meiling Yan
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Xinyue Guo
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Wenjing Man
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Ajiao Hou
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
| | - Qiu-Hong Wang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China.,Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Hai-Xue Kuang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, P. R. China
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13
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Jiang H, Yang L, Xing X, Yan M, Guo X, Hou A, Man W, Yang B, Wang Q, Kuang H. A UPLC-MS/MS application for comparisons of the hepatotoxicity of raw and processed Xanthii Fructus by energy metabolites. RSC Adv 2019; 9:2756-2762. [PMID: 35520491 PMCID: PMC9059864 DOI: 10.1039/c8ra08272c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/05/2019] [Indexed: 11/21/2022] Open
Abstract
The ripe fruit of Xanthium strumarium L. (Xanthii Fructus) cannot be widely used as a Chinese herbal medicine (CHM) owing to its hepatotoxicity. However, Xanthii Fructus (XF) can be used effectively and safely after correct processing based on traditional experience, although a high hepatotoxicity risk remains owing to improper usage. Therefore, the processing methods used must be clarified to ensure safety. The adenosine-5'-triphosphate (ATP) level in tissues is an important indicator reflecting the functional status of liver cells. Therefore, this study aims to evaluate the hepatotoxicity of XF using UPLC-MS/MS. The hepatotoxicity of raw XF (RXF) and XF processed by intermediary energy metabolites (PXF) is compared. The method is evaluated for its analytical performance and successfully applied to the quantification of ATP, adenosine-5'-diphosphate (ADP), adenosine-5'-monophosphate (AMP), atractyloside, and carboxyatractyloside in mouse liver. The hepatotoxicity results also indicate that the toxicity of XF is decreased after processing, perhaps due to the decrease in atractyloside and carboxyatractyloside contents. Importantly, the experimental evidence provides a rationale for the reduction in toxicity. These data show that mouse livers are damaged between the days 20 and 30 of RXF oral administration, and that the ATP level is decreased. Importantly, no significant difference is observed between the PXF treatment group and control group, while the RXF treatment group is significantly different. Therefore, processing can reduce the toxicity of XF.
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Affiliation(s)
- Hai Jiang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Liu Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Xudong Xing
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Meiling Yan
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Xinyue Guo
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Ajiao Hou
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Wenjing Man
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Bingyou Yang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
| | - Qiuhong Wang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University Guangzhou 528458 PR China
| | - Haixue Kuang
- Key Laboratory of Chinese Materia Medica, Heilongjiang University of Chinese Medicine, Ministry of Education Harbin 150040 PR China
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14
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Yang M, Xu Y, Heisner JS, Sun J, Stowe DF, Kwok WM, Camara AKS. Peroxynitrite nitrates adenine nucleotide translocase and voltage-dependent anion channel 1 and alters their interactions and association with hexokinase II in mitochondria. Mitochondrion 2018; 46:380-392. [PMID: 30391711 DOI: 10.1016/j.mito.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/26/2018] [Accepted: 10/22/2018] [Indexed: 12/17/2022]
Abstract
Cardiac ischemia and reperfusion (IR) injury induces excessive emission of deleterious reactive O2 and N2 species (ROS/RNS), including the non-radical oxidant peroxynitrite (ONOO-) that can cause mitochondria dysfunction and cell death. In this study, we explored whether IR injury in isolated hearts induces tyrosine nitration of adenine nucleotide translocase (ANT) and alters its interaction with the voltage-dependent anion channel 1 (VDAC1). We found that IR injury induced tyrosine nitration of ANT and that exposure of isolated cardiac mitochondria to ONOO- induced ANT tyrosine, Y81, nitration. The exposure of isolated cardiac mitochondria to ONOO- also led ANT to form high molecular weight proteins and dissociation of ANT from VDAC1. We found that IR injury in isolated hearts, hypoxic injury in H9c2 cells, and ONOO- treatment of H9c2 cells and isolated mitochondria, each decreased mitochondrial bound-hexokinase II (HK II), which suggests that ONOO- caused HK II to dissociate from mitochondria. Moreover, we found that mitochondria exposed to ONOO- induced VDAC1 oligomerization which may decrease its binding with HK II. We have reported that ONOO- produced during cardiac IR injury induced tyrosine nitration of VDAC1, which resulted in conformational changes of the protein and increased channel conductance associated with compromised cardiac function on reperfusion. Thus, our results imply that ONOO- produced during IR injury and hypoxic stress impeded HK II association with VDAC1. ONOO- exposure nitrated mitochondrial proteins and also led to cytochrome c (cyt c) release from mitochondria. In addition, in isolated mitochondria exposed to ONOO- or obtained after IR, there was significant compromise in mitochondrial respiration and delayed repolarization of membrane potential during oxidative (ADP) phosphorylation. Taken together, ONOO- produced during cardiac IR injury can nitrate tyrosine residues of two key mitochondrial membrane proteins involved in bioenergetics and energy transfer to contribute to mitochondrial and cellular dysfunction.
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Affiliation(s)
- Meiying Yang
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yanji Xu
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Preventive Medicine, Medical College of Yanbian University, Yanji, Jilin, China
| | - James S Heisner
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Sun
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA; Institute of Clinical Medicine Research, Suzhou Hospital affiliated with Nanjing Medical University, Suzhou, Jiangsu, China; Department of Gastroenterology and Hepatology, Suzhou Hospital affiliated with Nanjing Medical University, Suzhou, Jiangsu, China
| | - David F Stowe
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA; Research Service, Zablocki VA Medical Center, Milwaukee, WI, USA
| | - Wai-Meng Kwok
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA; Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA; Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Amadou K S Camara
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA; Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
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15
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King MS, Crichton PG, Ruprecht JJ, Kunji ERS. Concerns with yeast mitochondrial ADP/ATP carrier's integrity in DPC. Nat Struct Mol Biol 2018; 25:747-749. [PMID: 30177757 DOI: 10.1038/s41594-018-0125-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul G Crichton
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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16
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Spoerri PM, Kato HE, Pfreundschuh M, Mari SA, Serdiuk T, Thoma J, Sapra KT, Zhang C, Kobilka BK, Müller DJ. Structural Properties of the Human Protease-Activated Receptor 1 Changing by a Strong Antagonist. Structure 2018; 26:829-838.e4. [DOI: 10.1016/j.str.2018.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 02/16/2018] [Accepted: 03/29/2018] [Indexed: 12/12/2022]
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17
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Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1035-1045. [PMID: 29366674 PMCID: PMC5988563 DOI: 10.1016/j.bbamem.2018.01.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 11/24/2022]
Abstract
Cardiolipin in eukaryotes is found in the mitochondrial inner membrane, where it interacts with membrane proteins and, although not essential, is necessary for the optimal activity of a number of proteins. One of them is the mitochondrial ADP/ATP carrier, which imports ADP into the mitochondrion and exports ATP. In the crystal structures, cardiolipin is bound to three equivalent sites of the ADP/ATP carrier, but its role is unresolved. Conservation of residues at these cardiolipin binding sites across other members of the mitochondrial carrier superfamily indicates cardiolipin binding is likely to be important for the function of all mitochondrial carriers. Multiscale simulations were performed in a cardiolipin-containing membrane to investigate the dynamics of cardiolipin around the yeast and bovine ADP/ATP carriers in a lipid bilayer and the properties of the cardiolipin-binding sites. In coarse-grain simulations, cardiolipin molecules bound to the carriers for longer periods of time than phosphatidylcholine and phosphatidylethanolamine lipids—with timescales in the tens of microseconds. Three long-lived cardiolipin binding sites overlapped with those in the crystal structures of the carriers. Other shorter-lived cardiolipin interaction sites were identified in both membrane leaflets. However, the timescales of the interactions were of the same order as phosphatidylcholine and phosphatidylethanolamine, suggesting that these sites are not specific for cardiolipin binding. The calculation of lipid binding times and the overlap of the cardiolipin binding sites between the structures and simulations demonstrate the potential of multiscale simulations to investigate the dynamics and behavior of lipids interacting with membrane proteins. Coarse-grained models of AAC in mixed lipid bilayers were simulated. Three long-lived cardiolipin sites correspond to those in the crystal structures. No other long-lived binding sites were observed for cardiolipin or other phospholipids. Trimethylation of Lys-51 of AAC had no effect on cardiolipin interactions.
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18
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The transport mechanism of the mitochondrial ADP/ATP carrier. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2379-93. [PMID: 27001633 DOI: 10.1016/j.bbamcr.2016.03.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 12/18/2022]
Abstract
The mitochondrial ADP/ATP carrier imports ADP from the cytosol and exports ATP from the mitochondrial matrix, which are key transport steps for oxidative phosphorylation in eukaryotic organisms. The transport protein belongs to the mitochondrial carrier family, a large transporter family in the inner membrane of mitochondria. It is one of the best studied members of the family and serves as a paradigm for the molecular mechanism of mitochondrial carriers. Structurally, the carrier consists of three homologous domains, each composed of two transmembrane α-helices linked with a loop and short α-helix on the matrix side. The transporter cycles between a cytoplasmic and matrix state in which a central substrate binding site is alternately accessible to these compartments for binding of ADP or ATP. On both the cytoplasmic and matrix side of the carrier are networks consisting of three salt bridges each. In the cytoplasmic state, the matrix salt bridge network is formed and the cytoplasmic network is disrupted, opening the central substrate binding site to the intermembrane space and cytosol, whereas the converse occurs in the matrix state. In the transport cycle, tighter substrate binding in the intermediate states allows the interconversion of conformations by lowering the energy barrier for disruption and formation of these networks, opening and closing the carrier to either side of the membrane in an alternating way. Conversion between cytoplasmic and matrix states might require the simultaneous rotation of three domains around a central translocation pathway, constituting a unique mechanism among transport proteins. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.
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19
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Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity. Sci Rep 2015; 5:14533. [PMID: 26416158 PMCID: PMC4586513 DOI: 10.1038/srep14533] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/27/2015] [Indexed: 01/01/2023] Open
Abstract
Cannabinoid receptor 1 (CB1R) antagonists appear to be promising drugs for the treatment of obesity, however, serious side effects have hampered their clinical application. Rimonabant, the first in class CB1R antagonist, was withdrawn from the market because of psychiatric side effects. This has led to the search for more peripherally restricted CB1R antagonists, one of which is ibipinabant. However, this 3,4-diarylpyrazoline derivative showed muscle toxicity in a pre-clinical dog study with mitochondrial dysfunction. Here, we studied the molecular mechanism by which ibipinabant induces mitochondrial toxicity. We observed a strong cytotoxic potency of ibipinabant in C2C12 myoblasts. Functional characterization of mitochondria revealed increased cellular reactive oxygen species generation and a decreased ATP production capacity, without effects on the catalytic activities of mitochondrial enzyme complexes I-V or the complex specific-driven oxygen consumption. Using in silico off-target prediction modelling, combined with in vitro validation in isolated mitochondria and mitoplasts, we identified adenine nucleotide translocase (ANT)-dependent mitochondrial ADP/ATP exchange as a novel molecular mechanism underlying ibipinabant-induced toxicity. Minor structural modification of ibipinabant could abolish ANT inhibition leading to a decreased cytotoxic potency, as observed with the ibipinabant derivative CB23. Our results will be instrumental in the development of new types of safer CB1R antagonists.
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20
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Abstract
The lactose permease (LacY) of Escherichia coli, a paradigm for the major facilitator superfamily, catalyzes the coupled stoichiometric translocation of a galactopyranoside and an H(+) across the cytoplasmic membrane. To catalyze transport, LacY undergoes large conformational changes that allow alternating access of sugar- and H(+)-binding sites to either side of the membrane. Despite strong evidence for an alternating access mechanism, it remains unclear how H(+)- and sugar-binding trigger the cascade of interactions leading to alternating conformational states. Here we used dynamic single-molecule force spectroscopy to investigate how substrate binding induces this phenomenon. Galactoside binding strongly modifies kinetic, energetic, and mechanical properties of the N-terminal 6-helix bundle of LacY, whereas the C-terminal 6-helix bundle remains largely unaffected. Within the N-terminal 6-helix bundle, the properties of helix V, which contains residues critical for sugar binding, change most radically. Particularly, secondary structures forming the N-terminal domain exhibit mechanically brittle properties in the unbound state, but highly flexible conformations in the substrate-bound state with significantly increased lifetimes and energetic stability. Thus, sugar binding tunes the properties of the N-terminal domain to initiate galactoside/H(+) symport. In contrast to wild-type LacY, the properties of the conformationally restricted mutant Cys154→Gly do not change upon sugar binding. It is also observed that the single mutation of Cys154→Gly alters intramolecular interactions so that individual transmembrane helices manifest different properties. The results support a working model of LacY in which substrate binding induces alternating conformational states and provides insight into their specific kinetic, energetic, and mechanical properties.
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21
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Peptide transporter DtpA has two alternate conformations, one of which is promoted by inhibitor binding. Proc Natl Acad Sci U S A 2013; 110:E3978-86. [PMID: 24082128 DOI: 10.1073/pnas.1312959110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Peptide transporters (PTRs) of the large PTR family facilitate the uptake of di- and tripeptides to provide cells with amino acids for protein synthesis and for metabolic intermediates. Although several PTRs have been structurally and functionally characterized, how drugs modulate peptide transport remains unclear. To obtain insight into this mechanism, we characterize inhibitor binding to the Escherichia coli PTR dipeptide and tripeptide permease A (DtpA), which shows substrate specificities similar to its human homolog hPEPT1. After demonstrating that Lys[Z-NO2]-Val, the strongest inhibitor of hPEPT1, also acts as a high-affinity inhibitor for DtpA, we used single-molecule force spectroscopy to localize the structural segments stabilizing the peptide transporter and investigated which of these structural segments change stability upon inhibitor binding. This characterization was done with DtpA embedded in the lipid membrane and exposed to physiologically relevant conditions. In the unbound state, DtpA adopts two main alternate conformations in which transmembrane α-helix (TMH) 2 is either stabilized (in ∼43% of DtpA molecules) or not (in ∼57% of DtpA molecules). The two conformations are understood to represent the inward- and outward-facing conformational states of the transporter. With increasing inhibitor concentration, the conformation characterized by a stabilized TMH 2 becomes increasingly prevalent, reaching ∼92% at saturation. Our measurements further suggest that Lys[Z-NO2]-Val interacts with discrete residues in TMH 2 that are important for ligand binding and substrate affinity. These interactions in turn stabilize TMH 2, thereby promoting the inhibited conformation of DtpA.
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22
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Whited AM, Park PSH. Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:56-68. [PMID: 23603221 DOI: 10.1016/j.bbamem.2013.04.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/22/2013] [Accepted: 04/09/2013] [Indexed: 01/31/2023]
Abstract
Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding.
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Affiliation(s)
- Allison M Whited
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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23
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Kawamura S, Gerstung M, Colozo AT, Helenius J, Maeda A, Beerenwinkel N, Park PSH, Müller DJ. Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin. Structure 2013; 21:426-37. [PMID: 23434406 DOI: 10.1016/j.str.2013.01.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 01/05/2013] [Accepted: 01/15/2013] [Indexed: 11/20/2022]
Abstract
Rhodopsin, the photoreceptor pigment of the retina, initiates vision upon photon capture by its covalently linked chromophore 11-cis-retinal. In the absence of light, the chromophore serves as an inverse agonist locking the receptor in the inactive dark state. In the absence of chromophore, the apoprotein opsin shows low-level constitutive activity. Toward revealing insight into receptor properties controlled by the chromophore, we applied dynamic single-molecule force spectroscopy to quantify the kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin in native membranes from the retina of mice. Both rhodopsin and opsin are stabilized by ten structural segments. Compared to dark-state rhodopsin, the structural segments stabilizing opsin showed higher interaction strengths and mechanical rigidities and lower conformational variabilities, lifetimes, and free energies. These changes outline a common mechanism toward activating G-protein-coupled receptors. Additionally, we detected that opsin was more pliable and frequently stabilized alternate structural intermediates.
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Affiliation(s)
- Shiho Kawamura
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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24
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The degradation mechanism of toxic atractyloside in herbal medicines by decoction. Molecules 2013; 18:2018-28. [PMID: 23385339 PMCID: PMC6270218 DOI: 10.3390/molecules18022018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 11/17/2022] Open
Abstract
Atractyloside (ATR) is found in many Asteraceae plants that are commonly used as medicinal herbs in China and other eastern Asian countries. ATR binds specifically to the adenine nucleotide translocator in the inner mitochondrial membrane and competitively inhibits ADP and ATP transport. The toxicity of ATR in medical herbs can be reduced by hydrothermal processing, but the mechanisms of ATR degradation are not well understood. In this study, GC-MS coupled with SPE and TMS derivatisation was used to detect ATR levels in traditional Chinese medicinal herbs. Our results suggest that ATR molecules were disrupted by decomposition, hydrolysis and saponification after heating with water (decoction) for a long period of time. Hydrothermal processing could decompose the endogenous toxic compounds and also facilitate the detoxification of raw materials used in the Chinese medicine industry.
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25
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Sapra KT. Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers. Methods Mol Biol 2013; 974:73-110. [PMID: 23404273 DOI: 10.1007/978-1-62703-275-9_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.
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Affiliation(s)
- K Tanuj Sapra
- Department of Chemistry, University of Oxford, Oxford, UK.
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26
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Cholesterol increases kinetic, energetic, and mechanical stability of the human β2-adrenergic receptor. Proc Natl Acad Sci U S A 2012; 109:E3463-72. [PMID: 23151510 DOI: 10.1073/pnas.1210373109] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The steroid cholesterol is an essential component of eukaryotic membranes, and it functionally modulates membrane proteins, including G protein-coupled receptors. To reveal insight into how cholesterol modulates G protein-coupled receptors, we have used dynamic single-molecule force spectroscopy to quantify the mechanical strength and flexibility, conformational variability, and kinetic and energetic stability of structural segments stabilizing the human β(2)-adrenergic receptor (β(2)AR) in the absence and presence of the cholesterol analog cholesteryl hemisuccinate (CHS). CHS considerably increased the kinetic, energetic, and mechanical stability of almost every structural segment at sufficient magnitude to alter the structure and functional relationship of β(2)AR. One exception was the structural core segment of β(2)AR, which establishes multiple ligand binding sites, and its properties were not significantly influenced by CHS.
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27
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Zocher M, Fung JJ, Kobilka BK, Müller DJ. Ligand-specific interactions modulate kinetic, energetic, and mechanical properties of the human β2 adrenergic receptor. Structure 2012; 20:1391-402. [PMID: 22748765 DOI: 10.1016/j.str.2012.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/22/2012] [Accepted: 05/22/2012] [Indexed: 11/28/2022]
Abstract
G protein-coupled receptors (GPCRs) are a class of versatile proteins that transduce signals across membranes. Extracellular stimuli induce inter- and intramolecular interactions that change the functional state of GPCRs and activate intracellular messenger molecules. How these interactions are established and how they modulate the functional state of GPCRs remain to be understood. We used dynamic single-molecule force spectroscopy to investigate how ligand binding modulates the energy landscape of the human β2 adrenergic receptor (β2 AR). Five different ligands representing either agonists, inverse agonists or neutral antagonists established a complex network of interactions that tuned the kinetic, energetic, and mechanical properties of functionally important structural regions of β2 AR. These interactions were specific to the efficacy profile of the ligands investigated and suggest that the functional modulation of GPCRs follows structurally well-defined interaction patterns.
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Affiliation(s)
- Michael Zocher
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstr. 26, 4058 Basel, Switzerland
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28
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Brucoli F, Borrello MT, Stapleton P, Parkinson GN, Gibbons S. Structural characterization and antimicrobial evaluation of atractyloside, atractyligenin, and 15-didehydroatractyligenin methyl ester. JOURNAL OF NATURAL PRODUCTS 2012; 75:1070-1075. [PMID: 22594797 DOI: 10.1021/np300080w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report the first complete structure elucidation of the ent-kaurane diterpenoid glycoside atractyloside (1) by means of NMR and X-ray diffractometry techniques. Extensive one- and two-dimensional NMR experiments were employed to assign the proton and carbon signals of 1, and crystallography experiments established the configurations of all stereogenic centers. Furthermore, we present a novel semisynthetic route for the preparation of the highly cytotoxic aglycone derivative of 1, 15-didehydroatractyligenin methyl ester (3). All compounds were tested for their antibiotic activity against Enterococcus faecalis, Escherichia coli, and several strains of Staphylococcus aureus, including fluoroquinolone-resistant (SA1199B) and two epidemic MRSA (EMRSA-15 and -16) strains. Compound 3 exhibited moderate activity against all of the Staph. aureus strains with an MIC value of 128 mg/L.
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29
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Unambiguous structure of atractyloside and carboxyatractyloside. Bioorg Med Chem Lett 2012; 22:2973-5. [DOI: 10.1016/j.bmcl.2012.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/11/2012] [Accepted: 02/14/2012] [Indexed: 11/22/2022]
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Zocher M, Roos C, Wegmann S, Bosshart PD, Dötsch V, Bernhard F, Müller DJ. Single-molecule force spectroscopy from nanodiscs: an assay to quantify folding, stability, and interactions of native membrane proteins. ACS NANO 2012; 6:961-71. [PMID: 22196235 DOI: 10.1021/nn204624p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Single-molecule force spectroscopy (SMFS) can quantify and localize inter- and intramolecular interactions that determine the folding, stability, and functional state of membrane proteins. To conduct SMFS the membranes embedding the membrane proteins must be imaged and localized in a rather time-consuming manner. Toward simplifying the investigation of membrane proteins by SMFS, we reconstituted the light-driven proton pump bacteriorhodopsin into lipid nanodiscs. The advantage of using nanodiscs is that membrane proteins can be handled like water-soluble proteins and characterized with similar ease. SMFS characterization of bacteriorhodopsin in native purple membranes and in nanodiscs reveals no significant alterations of structure, function, unfolding intermediates, and strengths of inter- and intramolecular interactions. This demonstrates that lipid nanodiscs provide a unique approach for in vitro studies of native membrane proteins using SMFS and open an avenue to characterize membrane proteins by a wide variety of SMFS approaches that have been established on water-soluble proteins.
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Affiliation(s)
- Michael Zocher
- Biosystems Science and Engineering (BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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Locating an extracellular K+-dependent interaction site that modulates betaine-binding of the Na+-coupled betaine symporter BetP. Proc Natl Acad Sci U S A 2011; 108:E890-8. [PMID: 21987793 DOI: 10.1073/pnas.1109597108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BetP, a trimeric Na(+)-coupled betaine symporter, senses hyperosmotic stress via its cytoplasmic C-terminal domain and regulates transport activity in dependence of the cytoplasmic K(+)-concentration. This transport regulation of BetP depends on a sophisticated interaction network. Using single-molecule force spectroscopy we structurally localize and quantify these interactions changing on K(+)-dependent transport activation and substrate-binding. K(+) significantly strengthened all interactions, modulated lifetimes of functionally important structural regions, and increased the mechanical rigidity of the symporter. Substrate-binding could modulate, but not establish most of these K(+)-dependent interactions. A pronounced effect triggered by K(+) was observed at the periplasmic helical loop EH2. Tryptophan quenching experiments revealed that elevated K(+)-concentrations akin to those BetP encounters during hyperosmotic stress trigger the formation of a periplasmic second betaine-binding (S2) site, which was found to be at a similar position reported previously for the BetP homologue CaiT. In BetP, the presence of the S2 site strengthened the interaction between EH2, transmembrane α-helix 12 and the K(+)-sensing C-terminal domain resulting in a K(+)-dependent cooperative betaine-binding.
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Stewart MP, Toyoda Y, Hyman AA, Muller DJ. Force probing cell shape changes to molecular resolution. Trends Biochem Sci 2011; 36:444-50. [DOI: 10.1016/j.tibs.2011.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/26/2011] [Accepted: 05/02/2011] [Indexed: 11/25/2022]
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Song R, Bian H, Huang X, Zhao KS. Atractyloside induces low contractile reaction of arteriolar smooth muscle through mitochondrial damage. J Appl Toxicol 2011; 32:402-8. [PMID: 21598287 DOI: 10.1002/jat.1688] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 11/08/2022]
Abstract
Atractyloside is the principal naturally occurring active ingredient in ethnomedicines and animal grazing forage. Evidence that atractyloside can induce opening of the mitochondrial permeability transition pore (mPTP) indicates that mitochondrial mechanisms may play an important role in pathophysiological lesions of the heart, liver and kidney after atractyloside poisoning. Therefore, in this study we investigated the association of atractyloside-induced mitochondrial damage in arteriolar smooth muscle cells (ASMCs) with contractile reaction. Atractyloside led to depolarized and swollen or damaged ASMC mitochondria, which might be related to the concentration-dependent induction of mPTP opening. Relative ATP content in ASMCs was significantly reduced by 48%, 63% and 66% of control when cells were treated with 7.5, 10, and 15 µm atractyloside for 10 min, respectively, and ASMCs were hyperpolarized. In addition, the contractile responsiveness of ASMCs was eventually weakened. These results suggest that atractyloside has a toxic effect on vasoreactivity, which is possibly related to mitochondrial damage.
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Affiliation(s)
- Rui Song
- Guangdong Key Laboratory of Shock and Microcirculation Research, Department of Pathophysiology, Southern Medical University, Guangzhou, People's Republic of China
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Kawamura S, Colozo AT, Müller DJ, Park PSH. Conservation of molecular interactions stabilizing bovine and mouse rhodopsin. Biochemistry 2010; 49:10412-20. [PMID: 21038881 DOI: 10.1021/bi101345x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhodopsin is the light receptor that initiates phototransduction in rod photoreceptor cells. The structure and function of rhodopsin are tightly linked to molecular interactions that stabilize and determine the receptor's functional state. Single-molecule force spectroscopy (SMFS) was used to localize and quantify molecular interactions that structurally stabilize bovine and mouse rhodopsin from native disk membranes of rod photoreceptor cells. The mechanical unfolding of bovine and mouse rhodopsin revealed nine major unfolding intermediates, each intermediate defining a structurally stable segment in the receptor. These stable structural segments had similar localization and occurrence in both bovine and mouse samples. For each structural segment, parameters describing their unfolding energy barrier were determined by dynamic SMFS. No major differences were observed between bovine and mouse rhodopsin, thereby implying that the structures of both rhodopsins are largely stabilized by similar molecular interactions.
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Affiliation(s)
- Shiho Kawamura
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Kunji ERS, Crichton PG. Mitochondrial carriers function as monomers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:817-31. [PMID: 20362544 DOI: 10.1016/j.bbabio.2010.03.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 03/05/2010] [Accepted: 03/25/2010] [Indexed: 10/19/2022]
Abstract
Mitochondrial carriers link biochemical pathways in the mitochondrial matrix and cytosol by transporting metabolites, inorganic ions, nucleotides and cofactors across the mitochondrial inner membrane. Uncoupling proteins that dissipate the proton electrochemical gradient also belong to this protein family. For almost 35 years the general consensus has been that mitochondrial carriers are dimeric in structure and function. This view was based on data from inhibitor binding studies, small-angle neutron scattering, electron microscopy, differential tagging/affinity chromatography, size-exclusion chromatography, analytical ultracentrifugation, native gel electrophoresis, cross-linking experiments, tandem-fusions, negative dominance studies and mutagenesis. However, the structural folds of the ADP/ATP carriers were found to be monomeric, lacking obvious dimerisation interfaces. Subsequently, the yeast ADP/ATP carrier was demonstrated to function as a monomer. Here, we revisit the data that have been published in support of a dimeric state of mitochondrial carriers. Our analysis shows that when critical factors are taken into account, the monomer is the only plausible functional form of mitochondrial carriers. We propose a transport model based on the monomer, in which access to a single substrate binding site is controlled by two flanking salt bridge networks, explaining uniport and strict exchange of substrates.
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Affiliation(s)
- Edmund R S Kunji
- The Medical Research Council, Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, UK.
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