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Chen J, Chen Y, He W, Liang H, Hong T, Li T, Du H. Transcriptome analysis reveals the molecular mechanism of differences in growth between photoautotrophy and heterotrophy in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2024; 15:1407915. [PMID: 38962244 PMCID: PMC11219824 DOI: 10.3389/fpls.2024.1407915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/20/2024] [Indexed: 07/05/2024]
Abstract
Background The green alga Chlamydomonas reinhardtii can grow photoautotrophically utilizing light and CO2, and heterotrophically utilizing acetate. The physiological and biochemical responses of autotrophy and heterotrophy are different in C. reinhardtii. However, there is no complete understanding of the molecular physiology between autotrophy and heterotrophy. Therefore, we performed biochemical, molecular and transcriptome analysis of C. reinhardtii between autotrophy and heterotrophy. Results The cell growth characterization demonstrated that heterotrophic cell had enhanced growth rates, and autotrophic cell accumulated more chlorophyll. The transcriptome data showed that a total of 2,970 differentially expressed genes (DEGs) were identified from photoautotrophy 12h (P12h) to heterotrophy 12h (H12h). The DEGs were involved in photosynthesis, the tricarboxylic acid cycle (TCA), pyruvate and oxidative phosphorylation metabolisms. Moreover, the results of qRT-PCR revealed that the relative expression levels of malate dehydrogenase (MDH), succinate dehydrogenase (SDH), ATP synthase (ATPase), and starch synthase (SSS) were increased significantly from P12h and H12h. The protein activity of NAD-malate dehydrogenase (NAD-MDH) and succinate dehydrogenase (SDH) were significantly higher in the H12h group. Conclusion The above results indicated that the high growth rate observed in heterotrophic cell may be the effects of environmental or genetic regulation of photosynthesis. Therefore, the identification of novel candidate genes in heterotrophy will contribute to the development of microalga strains with higher growth capacity and better performance for biomass production.
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Affiliation(s)
- Jing Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Yuanhao Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Weiling He
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Honghao Liang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Ting Hong
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Tangcheng Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, Guangdong, China
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2
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Mokhtari M, Khoshbakht S, Ziyaei K, Akbari ME, Moravveji SS. New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics. Brief Bioinform 2024; 25:bbae074. [PMID: 38446742 PMCID: PMC10939336 DOI: 10.1093/bib/bbae074] [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: 07/21/2023] [Revised: 11/14/2023] [Accepted: 02/07/2021] [Indexed: 03/08/2024] Open
Abstract
Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data. Quantum mechanics has recently emerged as a promising tool for the analysis of biological systems, leading to the development of quantum bioinformatics. This new field employs the principles of quantum mechanics, quantum algorithms, and quantum computing to solve complex problems in molecular biology, drug design, and protein folding. However, the intersection of bioinformatics, biology, and quantum mechanics presents unique challenges. One significant challenge is the possibility of confusion among scientists between quantum bioinformatics and quantum biology, which have similar goals and concepts. Additionally, the diverse calculations in each field make it difficult to establish boundaries and identify purely quantum effects from other factors that may affect biological processes. This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics. We examine the challenges and unique features of this field and propose a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress. By unlocking the full potential of quantum bioinformatics, this review aims to contribute to our understanding of quantum mechanics in biological systems.
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Affiliation(s)
- Majid Mokhtari
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Samane Khoshbakht
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
- Duke Molecular Physiology Institute, Duke University School of Medicine-Cardiology, Durham, NC, 27701, USA
| | - Kobra Ziyaei
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | | | - Sayyed Sajjad Moravveji
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
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3
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Watson M, Saitis T, Shareef R, Harb C, Lakhani M, Ahmad Z. Shikonin and Alkannin inhibit ATP synthase and impede the cell growth in Escherichia coli. Int J Biol Macromol 2023; 253:127049. [PMID: 37758110 DOI: 10.1016/j.ijbiomac.2023.127049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/11/2023] [Accepted: 09/22/2023] [Indexed: 10/02/2023]
Abstract
Naturally occurring naphthoquinones, shikonin and alkannin, are important ingredients of traditional Chinese medicine Zicao. These constituents are reported to have many therapeutic uses, such as wound healing; scar treatment; and anti-inflammation, anti-acne, anti-ulcer, anti-HIV, anticancer, and antibacterial properties. The primary objective of this investigation was to explore the effect of shikonin and alkannin on Escherichia coli ATP synthase and its cell growth. Shikonin caused complete (100 %) inhibition, and alkannin caused partial (79 %) inhibition of wild-type E. coli ATP synthase. Both caused partial (4 %-27 %) inhibition of ATP synthase with genetically modified phytochemical binding site. The growth inhibition of strains expressing normal, deficient, and mutant ATP synthase by shikonin and alkannin, corroborated the inhibition observed in isolated normal wild-type and mutant ATP synthase. Trivial inhibition of mutant enzymes indicated αR283D, αE284R, βV265Q, and γT273A are essential for formation of the phytochemical binding site where shikonin and alkannin bind. Further, shikonin was a potent inhibitor of ATP synthase than alkannin. The antimicrobial properties of shikonin and alkannin were tied to the binding at phytochemical site of microbial ATP synthase. Selective targeting of bacterial ATP synthase by shikonin and alkannin may be an advantageous alternative to address the antibiotic resistance issue.
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Affiliation(s)
- Megan Watson
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Timoteea Saitis
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Rahim Shareef
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Christine Harb
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Muhaib Lakhani
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA.
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4
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Huang Q, Chen C, Wu X, Qin Y, Tan X, Zhang D, Liu Y, Li W, Chen Y. Overexpression of ATP Synthase Subunit Beta (Atp2) Confers Enhanced Blast Disease Resistance in Transgenic Rice. J Fungi (Basel) 2023; 10:5. [PMID: 38276021 PMCID: PMC10820023 DOI: 10.3390/jof10010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Previous research has shown that the pathogenicity and appressorium development of Magnaporthe oryzae can be inhibited by the ATP synthase subunit beta (Atp2) present in the photosynthetic bacterium Rhodopseudomonas palustris. In the present study, transgenic plants overexpressing the ATP2 gene were generated via genetic transformation in the Zhonghua11 (ZH11) genetic background. We compared the blast resistance and immune response of ATP2-overexpressing lines and wild-type plants. The expression of the Atp2 protein and the physiology, biochemistry, and growth traits of the mutant plants were also examined. The results showed that, compared with the wild-type plant ZH11, transgenic rice plants heterologously expressing ATP2 had no significant defects in agronomic traits, but the disease lesions caused by the rice blast fungus were significantly reduced. When infected by the rice blast fungus, the transgenic rice plants exhibited stronger antioxidant enzyme activity and a greater ratio of chlorophyll a to chlorophyll b. Furthermore, the immune response was triggered stronger in transgenic rice, especially the increase in reactive oxygen species (ROS), was more strongly triggered in plants. In summary, the expression of ATP2 as an antifungal protein in rice could improve the ability of rice to resist rice blast.
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Affiliation(s)
- Qiang Huang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Chunyan Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xiyang Wu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yingfei Qin
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Yong Liu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
| | - Wei Li
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
| | - Yue Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (Q.H.)
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China (D.Z.); (Y.L.)
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5
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Hao H, Adams EM, Funke S, Schwaab G, Havenith M, Head-Gordon T. Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles. J Am Chem Soc 2023; 145:1826-1834. [PMID: 36633459 PMCID: PMC9881006 DOI: 10.1021/jacs.2c11331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 01/13/2023]
Abstract
Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.
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Affiliation(s)
- Hongxia Hao
- Kenneth
S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
| | - Ellen M. Adams
- Cluster
of Excellence Physics of Life, Technische
Universität Dresden, 01307Dresden, Germany
- Helmholtz-Zentrum
Dresden-Rossendorf, Institute of Resource
Ecology, 01328Dresden, Germany
| | - Sarah Funke
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Martina Havenith
- Lehrstuhl
für Physkalische Chemie II, Ruhr
Universität Bochum, 44801Bochum, Germany
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California94720, United States
- Department
of Bioengineering, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California94720, United States
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
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6
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The Production of Pyruvate in Biological Technology: A Critical Review. Microorganisms 2022; 10:microorganisms10122454. [PMID: 36557706 PMCID: PMC9783380 DOI: 10.3390/microorganisms10122454] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Pyruvic acid has numerous applications in the food, chemical, and pharmaceutical industries. The high costs of chemical synthesis have prevented the extensive use of pyruvate for many applications. Metabolic engineering and traditional strategies for mutation and selection have been applied to microorganisms to enhance their ability to produce pyruvate. In the past decades, different microbial strains were generated to enhance their pyruvate production capability. In addition to the development of genetic engineering and metabolic engineering in recent years, the metabolic transformation of wild-type yeast, E. coli, and so on to produce high-yielding pyruvate strains has become a hot spot. The strategy and the understanding of the central metabolism directly related to pyruvate production could provide valuable information for improvements in fermentation products. One of the goals of this review was to collect information regarding metabolically engineered strains and the microbial fermentation processes used to produce pyruvate in high yield and productivity.
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7
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Shi R, Dong Z, Ma C, Wu R, Lv R, Liu S, Ren Y, Liu Z, van der Mei HC, Busscher HJ, Liu J. High-Yield, Magnetic Harvesting of Extracellular Outer-Membrane Vesicles from Escherichia coli. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204350. [PMID: 36269872 DOI: 10.1002/smll.202204350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Extracellular outer-membrane vesicles (OMVs) are attractive for use as drug nanocarriers, because of their high biocompatibility and ability to enter cells. However, widespread use is hampered by low yields. Here, a high-yield method for magnetic harvesting of OMVs from Escherichia coli is described. To this end, E. coli are grown in the presence of magnetic iron-oxide nanoparticles (MNPs). Uptake of MNPs by E. coli is low and does not increase secretion of OMVs. Uptake of MNPs can be enhanced through PEGylation of MNPs. E. coli growth in the presence of PEGylated MNPs increases bacterial MNP-uptake and OMV-secretion, accompanied by upregulation of genes involved in OMV-secretion. OMVs containing MNPs can be magnetically harvested at 60-fold higher yields than achieved by ultracentrifugation. Functionally, magnetically-harvested OMVs and OMVs harvested by ultracentrifugation are both taken-up in similar numbers by bacteria. Uniquely, in an applied magnetic field, magnetically-harvested OMVs with MNPs accumulate over the entire depth of an infectious biofilm. OMVs harvested by ultracentrifugation without MNPs only accumulate near the biofilm surface. In conclusion, PEGylation of MNPs is essential for their uptake in E. coli and yields magnetic OMVs allowing high-yield magnetic-harvesting. Moreover, magnetic OMVs can be magnetically targeted to a cargo delivery site in the human body.
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Affiliation(s)
- Rui Shi
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Ziliang Dong
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
| | - Chongqing Ma
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
| | - Renfei Wu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Rui Lv
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
| | - Sidi Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Yijin Ren
- Department of Orthodontics, University of Groningen and University Medical Center of Groningen, Hanzeplein 1, Groningen, 9700 RB, The Netherlands
| | - Zhuang Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
| | - Henny C van der Mei
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Henk J Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Jian Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, 199 Ren'ai Rd, Suzhou, Jiangsu, 215123, P. R. China
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8
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Lakhani M, Azim S, Akhtar S, Ahmad Z. Inhibition of Escherichia coli ATP synthase and cell growth by dietary pomegranate phenolics. Int J Biol Macromol 2022; 213:195-209. [PMID: 35597381 DOI: 10.1016/j.ijbiomac.2022.05.111] [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: 04/07/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/05/2022]
Abstract
Historically, people have been using pomegranate to alleviate many disease conditions. Pomegranate is known for its antiinflammatory, antioxidant, neuroprotective, anticancer, and antibacterial properties. In the current study, we examined effects of 8 dietary phenolics present in pomegranate (DPPs)-cyanidin-3-glucoside, cyanin chloride, delphinidin-3-glucoside, delphinidin-3,5-diglucoside, pelargonidin-3-glucoside, pelargonin chloride, punicalagin, and punicalin-on Escherichia coli ATP synthase and cell growth. DPPs caused complete or near complete (89%-100%) inhibition of wild-type E. coli ATP synthase and partial (5%-64%) inhibition of mutant enzymes αR283D, αE284R, βV265Q, and γT273A. Growth inhibition of wild-type, null, and mutant strains in the presence of DPPs were lower than that of isolated wild-type and mutant ATP synthase. On a molar scale, cyanin chloride was the most potent, and pelargonidin-3-glucoside was the least effective inhibitor of wild-type ATP synthase. Partial inhibition of mutant enzymes confirmed that αR283D, αE284R, βV265Q, and γT273A are essential in the formation of the phytochemical binding site. Our results establish that DPPs are potent inhibitors of wild-type E. coli ATP synthase and that the antimicrobial nature of DPPs can be associated with the binding and inhibition of microbial ATP synthase. Additionally, selective inhibition of microbial ATP synthase by DPPs is a useful method to combat antimicrobial resistance.
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Affiliation(s)
- Muhaib Lakhani
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Samiya Azim
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO 64108, USA
| | - Suhail Akhtar
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA.
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9
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Li C, Voth GA. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J Phys Chem B 2021; 125:10471-10480. [PMID: 34520198 PMCID: PMC8480781 DOI: 10.1021/acs.jpcb.1c05992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Chemical reactions
constitute the central feature of many liquid,
material, and biomolecular processes. Conventional molecular dynamics
(MD) is inadequate for simulating chemical reactions given the fixed
bonding topology of most force fields, while modeling chemical reactions
using ab initio molecular dynamics is limited to
shorter time and length scales given its high computational cost.
As such, the multiscale reactive molecular dynamics method provides
one promising alternative for simulating complex chemical systems
at atomistic detail on a reactive potential energy surface. However,
the parametrization of such models is a key barrier to their applicability
and success. In this work, we present reactive MD models derived from
constrained density functional theory that are both accurate and transferable.
We illustrate the features of these models for proton dissociation
reactions of amino acids in both aqueous and protein environments.
Specifically, we present models for ionizable glutamate and lysine
that predict accurate absolute pKa values
in water as well as their significantly shifted pKa in staphylococcal nuclease (SNase) without any modification
of the models. As one outcome of the new methodology, the simulations
show that the deprotonation of ionizable residues in SNase can be
closely coupled with side chain rotations, which is a concept likely
generalizable to many other proteins. Furthermore, the present approach
is not limited to only pKa prediction
but can enable the fully atomistic simulation of many other reactive
systems along with a determination of the key aspects of the reaction
mechanisms.
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Affiliation(s)
- Chenghan Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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10
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Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Syst 2021; 12:924-944.e2. [PMID: 34214468 PMCID: PMC8460600 DOI: 10.1016/j.cels.2021.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nathan M Belliveau
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Griffin Chure
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina L Hueschen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hernan G Garcia
- Department of Molecular Cell Biology and Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA.
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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11
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Nirody JA, Budin I, Rangamani P. ATP synthase: Evolution, energetics, and membrane interactions. J Gen Physiol 2021; 152:152111. [PMID: 32966553 PMCID: PMC7594442 DOI: 10.1085/jgp.201912475] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.
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Affiliation(s)
- Jasmine A Nirody
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY.,All Souls College, University of Oxford, Oxford, UK
| | - Itay Budin
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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12
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Li Y, Valdez NA, Mnatsakanyan N, Weber J. The nucleotide binding affinities of two critical conformations of Escherichia coli ATP synthase. Arch Biochem Biophys 2021; 707:108899. [PMID: 33991499 PMCID: PMC8278868 DOI: 10.1016/j.abb.2021.108899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
ATP synthase is essential in aerobic energy metabolism, and the rotary catalytic mechanism is one of the core concepts to understand the energetic functions of ATP synthase. Disulfide bonds formed by oxidizing a pair of cysteine mutations halted the rotation of the γ subunit in two critical conformations, the ATP-waiting dwell (αE284C/γQ274C) and the catalytic dwell (αE284C/γL276C). Tryptophan fluorescence was used to measure the nucleotide binding affinities for MgATP, MgADP and MgADP-AlF4 (a transition state analog) to wild-type and mutant F1 under reducing and oxidizing conditions. In the reduced state, αE284C/γL276C F1 showed a wild-type-like nucleotide binding pattern; after oxidation to lock the enzyme in the catalytic dwell state, the nucleotide binding parameters remained unchanged. In contrast, αE284C/γQ274C F1 showed significant differences in the affinities of the oxidized versus the reduced state. Locking the enzyme in the ATP-waiting dwell reduced nucleotide binding affinities of all three catalytic sites. Most importantly, the affinity of the low affinity site was reduced to such an extent that it could no longer be detected in the binding assay (Kd > 5 mM). The results of the present study allow to present a model for the catalytic mechanism of ATP synthase under consideration of the nucleotide affinity changes during a 360° cycle of the rotor.
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Affiliation(s)
- Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Woman's University, Denton, TX, 76204, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Neydy A Valdez
- Department of Biology, Texas Woman's University, Denton, TX, 76204, USA
| | - Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA; School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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13
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Dai Z, Zhu Y, Dong H, Zhao C, Zhang Y, Li Y. Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum. Microb Cell Fact 2021; 20:149. [PMID: 34325704 PMCID: PMC8320212 DOI: 10.1186/s12934-021-01639-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Background The intracellular ATP level is an indicator of cellular energy state and plays a critical role in regulating cellular metabolism. Depletion of intracellular ATP in (facultative) aerobes can enhance glycolysis, thereby promoting end product formation. In the present study, we examined this s trategy in anaerobic ABE (acetone-butanol-ethanol) fermentation using Clostridium acetobutylicum DSM 1731. Results Following overexpression of atpAGD encoding the subunits of water-soluble, ATP-hydrolyzing F1-ATPase, the intracellular ATP level of 1731(pITF1) was significantly reduced compared to control 1731(pIMP1) over the entire batch fermentation. The glucose uptake was markedly enhanced, achieving a 78.8% increase of volumetric glucose utilization rate during the first 18 h. In addition, an early onset of acid re-assimilation and solventogenesis in concomitant with the decreased intracellular ATP level was evident. Consequently, the total solvent production was significantly improved with remarkable increases in yield (14.5%), titer (9.9%) and productivity (5.3%). Further genome-scale metabolic modeling revealed that many metabolic fluxes in 1731(pITF1) were significantly elevated compared to 1731(pIMP1) in acidogenic phase, including those from glycolysis, tricarboxylic cycle, and pyruvate metabolism; this indicates significant metabolic changes in response to intracellular ATP depletion. Conclusions In C. acetobutylicum DSM 1731, depletion of intracellular ATP significantly increased glycolytic rate, enhanced solvent production, and resulted in a wide range of metabolic changes. Our findings provide a novel strategy for engineering solvent-producing C. acetobutylicum, and many other anaerobic microbial cell factories. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01639-7.
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Affiliation(s)
- Zongjie Dai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yan Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - Hongjun Dong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhua Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
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14
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Hughes T, Azim S, Ahmad Z. Inhibition of Escherichia coli ATP synthase by dietary ginger phenolics. Int J Biol Macromol 2021; 182:2130-2143. [PMID: 34087308 DOI: 10.1016/j.ijbiomac.2021.05.168] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 11/26/2022]
Abstract
For centuries, dietary ginger has been known for its antioxidant, anticancer, and antibacterial properties. In the current study, we examined the link between antibacterial properties of 7 dietary ginger phenolics (DGPs)-gingerenone A, 6-gingerol, 8-gingerol, 10-gingerol, paradol, 6-shogaol, and zingerone-and inhibition of bacterial ATP synthase. DGPs caused complete (100%) inhibition of wild-type Escherichia coli membrane-bound F1Fo ATP synthase, but partial and variable (0%-87%) inhibition of phytochemical binding site mutant enzymes αR283D, αE284R, βV265Q, and γT273A. The mutant enzyme ATPase activity was 16-fold to 100-fold lower than that of the wild-type enzyme. The growth of wild-type, null, and mutant strains in the presence of the 7 DGPs were abrogated to variable degrees on limiting glucose and succinate media. DGPs-caused variable inhibitory profiles of wild-type and mutant ATP synthase confirm that residues of α-, β-, and γ-subunits are involved in the formation of phytochemical binding site. The variable degree of growth in the presence of DGPs also indicates the possibility of molecular targets other than ATP synthase. Our results establish that antibacterial properties of DGPs can be linked to the binding and inhibition of bacterial ATP synthase. Therefore, bacterial ATP synthase is a valuable molecular target for DGPs.
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Affiliation(s)
- Taurin Hughes
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Samiya Azim
- University of Missouri-Kansas City, School of Medicine, Kansas City, MO 64108, USA
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA.
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15
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Da Luz CM, Da Broi MG, Plaça JR, Silva WA, Meola J, Navarro PA. Altered transcriptome in cumulus cells of infertile women with advanced endometriosis with and without endometrioma. Reprod Biomed Online 2021; 42:952-962. [PMID: 33736992 DOI: 10.1016/j.rbmo.2021.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 11/28/2022]
Abstract
RESEARCH QUESTION Is the transcriptome of cumulus cells of infertile women with advanced endometriosis (EIII/IV), with and without endometrioma, altered? DESIGN In this prospective case-control study, next-generation RNA sequencing was used to compare the transcript profile of cumulus cells among infertile patients undergoing ovarian stimulation for intracytoplasmic sperm injection with EIII/IV, with (n = 9) and without endometrioma (n = 9), and controls (n = 9). An in-silico enrichment analysis was conducted to establish the possibly altered pathways in cumulus cells of patients with endometriosis. RESULTS Most of the differentially expressed genes (DEG) were found when cumulus cells from women with EIII/IV with endometrioma were compared with controls (DEG, n = 461). In women with EIII/IV without endometrioma, only 66 DEG were verified compared with controls. The enrichment analysis showed that some DEG in cumulus cells of endometriosis are involved in important pathways for the oocyte competence acquisition, such as oxidative phosphorylation, metabolism, mitochondrial function, acetylation and steroid biosynthesis. No DEG were found when cumulus cells from women with EIII/IV with and without endometrioma were compared. CONCLUSION RNA sequencing results suggest that cumulus cells of infertile women with EIII/IV have an altered transcriptome, regardless of endometrioma. The present findings offer a better understanding of the genes and molecular mechanisms that may be involved in endometriosis-related infertility, mostly in the oocyte competence acquisition process.
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Affiliation(s)
- Caroline M Da Luz
- Division of Human Reproduction, Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto São Paulo 14049-900, Brazil.
| | - Michele G Da Broi
- Division of Human Reproduction, Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto São Paulo 14049-900, Brazil
| | - Jessica R Plaça
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto São Paulo 14049-900, Brazil
| | - Wilson A Silva
- Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto São Paulo 14049-900, Brazil; Center for Medical Genomics, HCFMRP/USP, Ribeirão Preto São Paulo 14049-900, Brazil; Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto São Paulo 14049-900, Brazil
| | - Juliana Meola
- Division of Human Reproduction, Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto São Paulo 14049-900, Brazil
| | - Paula A Navarro
- Division of Human Reproduction, Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto São Paulo 14049-900, Brazil; National Institute of Hormones and Women's Health, CNPq, Porto Alegre Rio Grande do Sul 90035-003, Brazil
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16
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The Rnf complex is a Na + coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima. Commun Biol 2020; 3:431. [PMID: 32770029 PMCID: PMC7414866 DOI: 10.1038/s42003-020-01158-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/15/2020] [Indexed: 11/21/2022] Open
Abstract
rnf genes are widespread in bacteria and biochemical and genetic data are in line with the hypothesis that they encode a membrane-bound enzyme that oxidizes reduced ferredoxin and reduces NAD and vice versa, coupled to ion transport across the cytoplasmic membrane. The Rnf complex is of critical importance in many bacteria for energy conservation but also for reverse electron transport to drive ferredoxin reduction. However, the enzyme has never been purified and thus, ion transport could not be demonstrated yet. Here, we have purified the Rnf complex from the anaerobic, fermenting thermophilic bacterium Thermotoga maritima and show that is a primary Na+ pump. These studies provide the proof that the Rnf complex is indeed an ion (Na+) translocating, respiratory enzyme. Together with a Na+-F1FO ATP synthase it builds a simple, two-limb respiratory chain in T. maritima. The physiological role of electron transport phosphorylation in a fermenting bacterium is discussed. From a fermenting bacterium, Thermotoga maritima, Kuhns, Trifunovi ć et al. purify a complex that includes a respiratory enzyme, Rnf. They find that the Rnf complex requires Na+ for activity and that it catalyzes Na+ transport in liposomes. This study shows that the Rnf complex is indeed an ion translocating, respiratory enzyme.
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17
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Mikoyan G, Karapetyan L, Vassilian A, Trchounian A, Trchounian K. External succinate and potassium ions influence Dcu dependent FOF1-ATPase activity and H+ flux of Escherichia coli at different pHs. J Bioenerg Biomembr 2020; 52:377-382. [DOI: 10.1007/s10863-020-09847-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/19/2020] [Indexed: 01/12/2023]
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18
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Li X, Zhang H, Yu H, Xia J, Zhu YB, Wu HA, Hou J, Lu J, Ou R, Easton CD, Selomulya C, Hill MR, Jiang L, Wang H. Unidirectional and Selective Proton Transport in Artificial Heterostructured Nanochannels with Nano-to-Subnano Confined Water Clusters. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001777. [PMID: 32390263 DOI: 10.1002/adma.202001777] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/07/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
The construction of biological proton channel analogues has attracted substantial interest owing to their wide potential in separation of ions, sensing, and energy conversion. Here, metal-organic framework (MOF)/polymer heterogeneous nanochannels are presented, in which water molecules are confined to disordered clusters in the nanometer-sized polymer regions and to ordered chains with unique molecular configurations in the 1D sub-1-nm porous MOF regions, to realize unidirectional, fast, and selective proton transport properties, analogous to natural proton channels. Given the nano-to-subnano confined water junctions, experimental proton conductivities in the polymer-to-MOF direction of the channels are much higher than those in the opposite direction, showing a high rectification up to 500 and one to two orders of magnitude enhancement compared to the conductivity of proton transport in bulk water. The channels also show a good proton selectivity over other cations. Theoretical simulations further reveal that the preferential and fast proton conduction in the nano-to-subnano channel direction is attributed to extremely low energy barriers for proton transport from disordered to ordered water clusters. This study opens a novel approach to regulate ion permeability and selectivity of artificial ion channels.
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Affiliation(s)
- Xingya Li
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Huacheng Zhang
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Hao Yu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jun Xia
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Yin-Bo Zhu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Heng-An Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jue Hou
- Manufacturing, CSIRO, Clayton, Victoria, 3168, Australia
| | - Jun Lu
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Ranwen Ou
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | | | | | - Matthew R Hill
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
- Manufacturing, CSIRO, Clayton, Victoria, 3168, Australia
| | - Lei Jiang
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
- Key Laboratory of Bioinspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huanting Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
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García-Molina G, Natale P, Valenzuela L, Alvarez-Malmagro J, Gutiérrez-Sánchez C, Iglesias-Juez A, López-Montero I, Vélez M, Pita M, De Lacey AL. Potentiometric detection of ATP based on the transmembrane proton gradient generated by ATPase reconstituted on a gold electrode. Bioelectrochemistry 2020; 133:107490. [PMID: 32126488 DOI: 10.1016/j.bioelechem.2020.107490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022]
Abstract
Adenosine triphosphate (ATP) is a key molecule as energy vector for living organisms, therefore its detection reveals the presence of microbial colonies. Environments where the existence of microbial pathogens suppose a health hazard can benefit from real time monitoring of such molecule. We report a potentiometric biosensor based on ATP-synthase from Escherichia coli reconstituted in a floating phospholipid bilayer over gold electrodes modified with a 4-aminothiophenol self-assembled monolayer. The use of a pH-dependent redox probe on the electrode surface allows a simple, specific and reliable on site determination of ATP concentration from 1 μM to 1 mM. The broad range ATP biosensor can offer an alternative way of measuring in a few minutes the presence of microbial contamination.
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Affiliation(s)
- Gabriel García-Molina
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Paolo Natale
- Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital Doce de Octubre (imas12), Avda. de Córdoba s/n, 28041 Madrid, Spain
| | - Laura Valenzuela
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain; Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | | | | | - Ana Iglesias-Juez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Iván López-Montero
- Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital Doce de Octubre (imas12), Avda. de Córdoba s/n, 28041 Madrid, Spain
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain
| | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain.
| | - Antonio L De Lacey
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie 2, 28049 Madrid, Spain.
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Kamel KS, Oh MS, Halperin ML. L-lactic acidosis: pathophysiology, classification, and causes; emphasis on biochemical and metabolic basis. Kidney Int 2020; 97:75-88. [DOI: 10.1016/j.kint.2019.08.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/01/2019] [Accepted: 08/20/2019] [Indexed: 11/30/2022]
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21
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Li Y, Ma X, Weber J. Interaction between γC87 and γR242 residues participates in energy coupling between catalysis and proton translocation in Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:679-687. [PMID: 31251901 DOI: 10.1016/j.bbabio.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/19/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022]
Abstract
Functioning as a nanomotor, ATP synthase plays a vital role in the cellular energy metabolism. Interactions at the rotor and stator interface are critical to the energy transmission in ATP synthase. From mutational studies, we found that the γC87K mutation impairs energy coupling between proton translocation and nucleotide synthesis/hydrolysis. An additional glutamine mutation at γR242 (γR242Q) can restore efficient energy coupling to the γC87K mutant. Arrhenius plots and molecular dynamics simulations suggest that an extra hydrogen bond could form between the side chains of γC87K and βTPE381 in the γC87K mutant, thus impeding the free rotation of the rotor complex. In the enzyme with γC87K/γR242Q double mutations, the polar moiety of γR242Q side chain can form a hydrogen bond with γC87K, so that the amine group in the side chain of γC87K will not hydrogen-bond with βE381. As a conclusion, the intra-subunit interaction between positions γC87 and γR242 modulates the energy transmission in ATP synthase. This study should provide more information of residue interactions at the rotor and stator interface in order to further elucidate the energetic mechanism of ATP synthase.
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Affiliation(s)
- Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | - Xinyou Ma
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; The Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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22
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Dutta Gupta S, Bommaka MK, Banerjee A. Inhibiting protein-protein interactions of Hsp90 as a novel approach for targeting cancer. Eur J Med Chem 2019; 178:48-63. [PMID: 31176095 DOI: 10.1016/j.ejmech.2019.05.073] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 12/26/2022]
Abstract
The ninety kilo Dalton molecular weight heat shock protein (Hsp90) is an attractive target for the discovery of novel anticancer agents. Several strategies have been employed for the development of inhibitors against this polypeptide. The most successful strategy is targeting the N-terminal ATP binding region of the chaperone. However, till date not a single molecule reached Phase-IV of clinical trials from this class of Hsp90 inhibitors. The other approach is to target the Cterminal region of the protein. The success with this approach has been limited due to lack of well-defined ligand binding pocket in this terminal. The other promising strategy is to prevent the interaction of client proteins/co-chaperones with Hsp90 protein, i.e., protein-protein interaction inhibitors of Hsp90. The review focuses on advantage of this approach along with the recent advances in the discovery of inhibitors by following this strategy. Additionally, the biology of the client protein/co-chaperone binding site of Hsp90 is also discussed.
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Affiliation(s)
- Sayan Dutta Gupta
- Department of Pharmaceutical Chemistry, Gokaraju Rangaraju College of Pharmacy, Osmania University, Hyderabad, India.
| | - Manish Kumar Bommaka
- Department of Pharmaceutical Chemistry, Gokaraju Rangaraju College of Pharmacy, Osmania University, Hyderabad, India; School of Chemistry, University of Hyderabad, Hyderabad, India
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Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications. Int J Mol Sci 2019; 20:ijms20061437. [PMID: 30901910 PMCID: PMC6472214 DOI: 10.3390/ijms20061437] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022] Open
Abstract
In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.
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Li XL, Huang WL, Yang HH, Jiang RC, Sun F, Wang HC, Zhao J, Xu CH, Tan BC. EMP18 functions in mitochondrial atp6 and cox2 transcript editing and is essential to seed development in maize. THE NEW PHYTOLOGIST 2019; 221:896-907. [PMID: 30168136 DOI: 10.1111/nph.15425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/02/2018] [Indexed: 05/02/2023]
Abstract
RNA editing plays an important role in organellar gene expression in plants, and pentatricopeptide repeat (PPR) proteins are involved in this function. Because of its large family size, many PPR proteins are not known for their function and roles in plant growth and development. Through genetic and molecular analyses of the empty pericarp18 (emp18) mutant in maize (Zea mays), we cloned the Emp18 gene, revealed its molecular function, and defined its role in the mitochondrial complex assembly and seed development. Emp18 encodes a mitochondrial-localized DYW-PPR protein. Null mutation of Emp18 arrests embryo and endosperm development at an early stage in maize, resulting in embryo lethality. Mutants are deficient in the cytidine (C)-to-uridine (U) editing at atp6-635 and cox2-449, which converts a Leu to Pro in ATP6 and a Met to Thr in Cox2. The atp6 gene encodes the subunit a of F1 Fo -ATPase. The Leu to Pro alteration disrupts an α-helix of subunit a, resulting in a dramatic reduction in assembly and activity of F1 Fo -ATPase holoenzyme and an accumulation of free F1 -subcomplex. These results demonstrate that EMP18 functions in the C-to-U editing of atp6 and cox2, and is essential to mitochondrial biogenesis and seed development in maize.
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Affiliation(s)
- Xiu-Lan Li
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Wen-Long Huang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Huan-Huan Yang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Rui-Cheng Jiang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Feng Sun
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Hong-Chun Wang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Jiao Zhao
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Chun-Hui Xu
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100, China
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Mnatsakanyan N, Li Y, Weber J. Identification of two segments of the γ subunit of ATP synthase responsible for the different affinities of the catalytic nucleotide-binding sites. J Biol Chem 2018; 294:1152-1160. [PMID: 30510135 DOI: 10.1074/jbc.ra118.002504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 11/26/2018] [Indexed: 11/06/2022] Open
Abstract
ATP synthase uses a rotary mechanism to couple transmembrane proton translocation to ATP synthesis and hydrolysis, which occur at the catalytic sites in the β subunits. In the presence of Mg2+, the three catalytic sites of ATP synthase have vastly different affinities for nucleotides, and the position of the central γ subunit determines which site has high, medium, or low affinity. Affinity differences and their changes as rotation progresses underpin the ATP synthase catalytic mechanism. Here, we used a series of variants with up to 45- and 60-residue-long truncations of the N- and C-terminal helices of the γ subunit, respectively, to identify the segment(s) responsible for the affinity differences of the catalytic sites. We found that each helix carries an affinity-determining segment of ∼10 residues. Our findings suggest that the affinity regulation by these segments is transmitted to the catalytic sites by the DELSEED loop in the C-terminal domain of the β subunits. For the N-terminal truncation variants, presence of the affinity-determining segment and therefore emergence of a high-affinity binding site resulted in WT-like catalytic activity. At the C terminus, additional residues outside of the affinity-determining segment were required for optimal enzymatic activity. Alanine substitutions revealed that the affinity changes of the catalytic sites required no specific interactions between amino acid side chains in the γ and α3β3 subunits but were caused by the presence of the helices themselves. Our findings help unravel the molecular basis for the affinity changes of the catalytic sites during ATP synthase rotation.
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Affiliation(s)
- Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409 and the Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430.
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Jia W, Wu P. Fast Proton Conduction in Denatured Bovine Serum Albumin-Coated Nafion Membranes. ACS APPLIED MATERIALS & INTERFACES 2018; 10:39768-39776. [PMID: 30387596 DOI: 10.1021/acsami.8b14587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bovine serum albumin (BSA) is a globular soluble protein, which has been extensively used in biochemical engineering. BSA materials possess abundant hydrophilic charged amino acids, H-bonded networks, and various secondary structures, which has great potential in facilitating proton transfer. Herein, BSA-N117 (BSA-Nafion 117) membranes are conveniently and eco-friendly prepared by utilizing the adsorption and denaturation of BSA on the Nafion 117 surface. The morphology and secondary structures of the BSA layer are studied with field-emission scanning electron microscopy, atomic force microscopy, and Fourier transform infrared spectroscopy. BSA-N117 membranes show highly increased proton conductivity under various conditions, which could be attributed to the improved wettability, water uptake, and the denaturation of BSA. The in-plane proton conductivity of BSA-N117-5 reaches 0.3 and 0.06 S cm-1 under 80 °C-95% RH and 100 °C-40% RH, respectively. The denaturation of BSA leads to the unfolding of α-helix structures and the formation of β-sheet structures. β-Sheet structures are more beneficial to proton conduction since β-sheet structures have stronger interactions with water molecules and protons could transport more directly in the parallel H-bonded network. Moreover, the denatured BSA modification layer could effectively help BSA-N117 membranes to possess higher selectivity and overcome the "trade-off" effect between proton conductivity and methanol resistance. The methanol permeability of BSA-N117 membranes is 1 order of magnitude lower than that of Nafion 117.
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Affiliation(s)
- Wei Jia
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
| | - Peiyi Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
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Ren X, Liu Y, Jeong HK, Jeong BR. Supplementary Light Source Affects the Growth and Development of Codonopsis lanceolata Seedlings. Int J Mol Sci 2018; 19:ijms19103074. [PMID: 30297684 PMCID: PMC6212986 DOI: 10.3390/ijms19103074] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/03/2018] [Accepted: 10/06/2018] [Indexed: 11/19/2022] Open
Abstract
Codonopsis lanceolata is widely used in traditional medicine and diets. However, there is no optimal protocol for the commercial production of C. lanceolata seedlings. This study was carried out to find the optimum supplementary light source for the production of C. lanceolata seedlings. Seedlings were grown for four weeks in a glasshouse with an average daily light intensity of 490 μmol·m−2·s−1 photosynthetic photon flux density (PPFD) coming from the sun and a 16-h daily supplementary lighting at 120 μmol·m−2·s−1 PPFD from either high-pressure sodium (HPS), metal halide (MH), far-red (FR), white LED (LED-w), or mixed (white: red: blue = 1:2:1) LEDs (LED-mix). The results showed that the greatest total biomass, stem diameter, ratio of shoot weight to shoot length, root biomass, and ratio of root weight to shoot weight were found in seedlings grown under supplementary LED-mix. Meanwhile, the stomatal properties and soluble sugar contents were improved for seedlings in LED-mix. The contents of starch, total phenols, and flavonoids were the greatest for seedlings in LED-w and LED-mix. The expression of photosynthetic proteins and genes in seedlings was also enhanced by LED-mix. Overall, these results suggest that LED-mix is advantageous to the photosynthetic potential and the accumulation of biomass, carbohydrates and secondary metabolites in C. lanceolata.
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Affiliation(s)
- Xiuxia Ren
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Ya Liu
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Hai Kyoung Jeong
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
| | - Byoung Ryong Jeong
- Division of Applied Life Science (BK21 Plus Program), Graduate School, Gyeongsang National University, Jinju 52828, Korea.
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea.
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Ing NL, El-Naggar MY, Hochbaum AI. Going the Distance: Long-Range Conductivity in Protein and Peptide Bioelectronic Materials. J Phys Chem B 2018; 122:10403-10423. [DOI: 10.1021/acs.jpcb.8b07431] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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30
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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Mariño-Crespo Ó, Fernández-Briera A, Gil-Martín E. Identification of proteins with the CDw75 epitope in human colorectal cancer. Oncol Lett 2018; 15:580-587. [PMID: 29391890 DOI: 10.3892/ol.2017.7336] [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: 11/07/2016] [Accepted: 07/28/2017] [Indexed: 11/05/2022] Open
Abstract
The CDw75 epitope is an α(2,6) sialylated antigen overexpressed in colorectal cancer (CRC), where its expression correlates with the progression of the disease. The CDw75 epitope is located mainly in N-glycoproteins, whose identity remains unknown. The aim of the present study was to identify proteins with the CDw75 epitope as a strategy to deepen the understanding of molecular pathogenesis of CRC and to identify novel biomarkers for this disease. For this purpose, a two-dimensional electrophoresis approach was employed. Protein spots in the gels were matched to the corresponding CDw75 positive spots in the immunoblotted polyvinylidene difluoride membranes, and further identification of the protein species was performed by mass spectrometry. Additionally, one-dimensional western blotting experiments were performed to verify the expression of these candidate proteins in the colorectal tissue and their coincidence in molecular mass with the CDw75-positive bands. The findings of the present study indicate that haptoglobin and the keratins 8 (K8) and 18 (K18) are proteins with the CDw75 epitope in the colorectal tissue from CRC patients and also suggest novel functions and cellular locations for these proteins in the colorectal tissue and in relation to CRC.
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Affiliation(s)
- Óscar Mariño-Crespo
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO, 'Centro Singular de Investigación de Galicia'), University of Vigo, 36310 Vigo, Spain
| | - Almudena Fernández-Briera
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO, 'Centro Singular de Investigación de Galicia'), University of Vigo, 36310 Vigo, Spain
| | - Emilio Gil-Martín
- Department of Biochemistry, Genetics and Immunology, Biomedical Research Center (CINBIO, 'Centro Singular de Investigación de Galicia'), University of Vigo, 36310 Vigo, Spain
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Naumenko N, Morgenstern M, Rucktäschel R, Warscheid B, Rehling P. INA complex liaises the F 1F o-ATP synthase membrane motor modules. Nat Commun 2017; 8:1237. [PMID: 29093463 PMCID: PMC5665977 DOI: 10.1038/s41467-017-01437-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 09/18/2017] [Indexed: 01/11/2023] Open
Abstract
The F1F0-ATP synthase translates a proton flux across the inner mitochondrial membrane into a mechanical rotation, driving anhydride bond formation in the catalytic portion. The complex’s membrane-embedded motor forms a proteinaceous channel at the interface between Atp9 ring and Atp6. To prevent unrestricted proton flow dissipating the H+-gradient, channel formation is a critical and tightly controlled step during ATP synthase assembly. Here we show that the INA complex (INAC) acts at this decisive step promoting Atp9-ring association with Atp6. INAC binds to newly synthesized mitochondrial-encoded Atp6 and Atp8 in complex with maturation factors. INAC association is retained until the F1-portion is built on Atp6/8 and loss of INAC causes accumulation of the free F1. An independent complex is formed between INAC and the Atp9 ring. We conclude that INAC maintains assembly intermediates of the F1 F0-ATP synthase in a primed state for the terminal assembly step–motor module formation. The inner membrane assembly complex (INAC) interacts with components of the F1F0-ATP synthase but its function remains unclear. Here the authors show that INAC associates with two distinct complexes during F1F0-ATP synthase formation, which points towards a safeguarding role during proton-conducting channel assembly.
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Affiliation(s)
- Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, GZMB, D-37073, Göttingen, Germany
| | - Marcel Morgenstern
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, D-79104, Freiburg, Germany
| | - Robert Rucktäschel
- Department of Cellular Biochemistry, University Medical Center Göttingen, GZMB, D-37073, Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology, University Freiburg, D-79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, GZMB, D-37073, Göttingen, Germany. .,Max Planck Institute for Biophysical Chemistry, D-37077, Göttingen, Germany.
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Amini A, Liu M, Ahmad Z. Understanding the link between antimicrobial properties of dietary olive phenolics and bacterial ATP synthase. Int J Biol Macromol 2017; 101:153-164. [PMID: 28322962 PMCID: PMC5884633 DOI: 10.1016/j.ijbiomac.2017.03.087] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/16/2017] [Accepted: 03/16/2017] [Indexed: 11/24/2022]
Abstract
The naturally occurring olive phenolics tyrosol, hydroxytyrosol, dihydroxyphenylglycol (DHPG), and oleuropein are known to have antioxidant, antitumor, and antibacterial properties. In the current study, we examined whether the antimicrobial properties of tyrosol, hydroxytyrosol, DHPG, and oleuropein were linked to the inhibition of bacterial ATP synthase. Tyrosol, hydroxytyrosol, DHPG, and oleuropein inhibited Escherichia coli wild-type and mutant membrane-bound F1Fo ATP synthase to variable degrees. The growth properties of wild-type, null, and mutant strains in presence of above olive phenolics were also abrogated to variable degrees on limiting glucose and succinate. Tyrosol and oleuropein synergistically inhibited the wild-type enzyme. Comparative wild-type and mutant F1Fo ATP synthase inhibitory profiles suggested that αArg-283 is an important residue and olive phenolics bind at the polyphenol binding pocket of ATP synthase. Growth patterns of wild-type, null, and mutant strains in the presence of tyrosol, hydroxytyrosol, DHPG, and oleuropein also hint at the possibility of additional molecular targets. Our results demonstrated that ATP synthase can be used as a molecular target and the antimicrobial properties of olive phenolics in general and tyrosol in particular can be linked to the binding and inhibition of bacterial ATP synthase.
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Affiliation(s)
- Amon Amini
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Mason Liu
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, USA.
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34
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Bâ A. Alcohol and thiamine deficiency trigger differential mitochondrial transition pore opening mediating cellular death. Apoptosis 2017; 22:741-752. [DOI: 10.1007/s10495-017-1372-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Liu M, Amini A, Ahmad Z. Safranal and its analogs inhibit Escherichia coli ATP synthase and cell growth. Int J Biol Macromol 2017; 95:145-152. [PMID: 27865956 PMCID: PMC5884629 DOI: 10.1016/j.ijbiomac.2016.11.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/09/2016] [Accepted: 11/09/2016] [Indexed: 10/20/2022]
Abstract
Safranal, a dominant component of saffron, is known to have antitumor, cytotoxic, and antibacterial properties. In this study, we examined safranal and its structural analogs-thymol, carvacrol, damascenone, cuminol, 2,6,6-trimethyl-2-cyclohexene-1,4-dione (TMCHD), 4-isopropylbenzyl bromide (IPBB), and 4-tert-butylphenol (TBP) induced inhibition of Escherichia coli membrane bound F1Fo ATP synthase. Safranal and its analogs inhibited wild-type enzyme to variable degrees. While safranal caused 100% inhibition of wild-type F1Fo ATP synthase, only about 50% inhibition occurred for αR283D mutant ATP synthase. Moreover, safranal, thymol, carvacrol, damascenone, cuminol, TMCHD, IPBB, and TBP all fully abrogated the growth of wild-type E. coli cells and had partial or no effect on the growth of null and mutant E. coli strains. Therefore, the antimicrobial properties of safranal, thymol, carvacrol, damascenone, cuminol, TMCHD, IPBB, and TBP can be linked to their binding and inhibition of ATP synthase. Total loss of growth in wild-type and partial or no growth loss in null or mutant E. coli strains demonstrates that ATP synthase is a molecular target for safranal and its structural analogs. Partial inhibition of the αArg-283 mutant enzyme establishes that αArg-283 residue is required in the polyphenol binding pocket of ATP synthase for the binding of safranal. Furthermore, partial growth loss for the null and mutant strains in the presence of inhibitors also suggests the role of other targets and residues in the process of inhibition.
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Affiliation(s)
- Mason Liu
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, United States
| | - Amon Amini
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, United States
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO 63501, United States.
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Huang HJ, Liu CW, Zhou X, Zhang CX, Bao YY. A mitochondrial membrane protein is a target for rice ragged stunt virus in its insect vector. Virus Res 2016; 229:48-56. [PMID: 28034779 DOI: 10.1016/j.virusres.2016.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Rice ragged stunt virus (RRSV; Reoviridae) is exclusively transmitted by the brown planthopper Nilaparvata lugens in a persistent-propagative manner. It is understood that RNA viral proliferation is associated with the intracellular membranes of the insect host cells. However, the molecular mechanisms of the interaction between the RRSV proliferation and the intracellular membranes remain essentially unknown. It will be of great interest to determine whether RRSV protein(s) directly interact with intracellular membrane components of its host cells. In this study, we identified a RRSV nonstructural protein Pns10 interacting with a host oligomycin-sensitivity conferral protein (OSCP) using yeast two-hybrid system. The interaction between RRSV Pns10 and N. lugens OSCP was verified by a glutathione S-transferase pull-down assay. Confocal miscopy revealed colocalization of these two proteins in the cytoplasm of the salivary gland cells during the viral infection. The virions were further detected in the mitochondria under confocal miscopy and transmission electron microscopy combined with western blotting assay. This is the first observation that RRSV protein has a direct link with mitochondria. Suppressing OSCP gene expression by RNA interference notably decreased the viral loads in RRSV-infected insects. These findings revealed novel aspects of a viral protein in targeting the host mitochondrial membrane and provide insights concerning the mitochondrial membrane protein-based virus proliferation mode in the insect vector.
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Affiliation(s)
- Hai-Jian Huang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Cheng-Wen Liu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Xiang Zhou
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Yan-Yuan Bao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China.
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Amdursky N, Wang X, Meredith P, Bradley DDC, Stevens MM. Long-Range Proton Conduction across Free-Standing Serum Albumin Mats. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2692-8. [PMID: 26840865 PMCID: PMC4862025 DOI: 10.1002/adma.201505337] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/28/2015] [Indexed: 05/26/2023]
Abstract
Free-standing serum-albumin mats can transport protons over millimetre length-scales. The results of photoinduced proton transfer and voltage-driven proton-conductivity measurements, together with temperature-dependent and isotope-effect studies, suggest that oxo-amino-acids of the protein serum albumin play a major role in the translocation of protons via an "over-the-barrier" hopping mechanism. The use of proton-conducting protein mats opens new possibilities for bioelectronic interfaces.
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Affiliation(s)
- Nadav Amdursky
- Departments of Materials, Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Xuhua Wang
- Department of Physics and Centre for Plastic Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Paul Meredith
- Centre for Organic Photonics and Electronics, School of Mathematics and Physics, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Donal D C Bradley
- Department of Physics and Centre for Plastic Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Molly M Stevens
- Departments of Materials, Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
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Chou YC, Hsiao YF, Hwang GJ, To K. Torque generation through the random movement of an asymmetric rotor: A potential rotational mechanism of the γ subunit of F(1)-ATPase. Phys Rev E 2016; 93:022408. [PMID: 26986363 DOI: 10.1103/physreve.93.022408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
The rotation of the γ subunit of F(1)-ATPase is stochastic, processive, unidirectional, reversible through an external torque, and stepwise with a slow rotation. We propose a mechanism that can explain these properties of the rotary molecular motor, and that can determine the direction of rotation. The asymmetric structures of the γ subunit, both at the tip of the shaft (C and N termini) and at the part (ε subunit) protruding from the α(3)β(3) subunits, are critical. The torque required for stochastic rotation is generated from the impulsive reactive force due to the random collisions between the γ subunit and the quasihexagonal α(3)β(3) subunits. The rotation is the result of the random motion of the confined asymmetric γ subunit. The steps originate from the chemical reactions of the γ subunit and physical interaction between the γ subunit and the flexible protrusions of the α(3)β(3) subunits. An external torque as well as a configurational modification in the γ subunit (the central rotor) can reverse the rotational direction. We demonstrate the applicability of the mechanism to a macroscopic simulation system, which has the essential ingredients of the F(1)-ATPase structure, by reproducing the dynamic properties of the rotation.
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Affiliation(s)
- Y C Chou
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Yi-Feng Hsiao
- Department of Physics, National Tsing-Hua University, Hsinchu, Taiwan, Republic of China
| | - Gwo-Jen Hwang
- Department of Electronic Engineering, St. John's University, Tamsui District, New Taipei City, Taiwan, Republic of China
| | - Kiwing To
- Institute of Physics, Academia Sinca, Taipei, Taiwan, Republic of China
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Dibrova DV, Galperin MY, Koonin EV, Mulkidjanian AY. Ancient Systems of Sodium/Potassium Homeostasis as Predecessors of Membrane Bioenergetics. BIOCHEMISTRY (MOSCOW) 2016; 80:495-516. [PMID: 26071768 DOI: 10.1134/s0006297915050016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cell cytoplasm of archaea, bacteria, and eukaryotes contains substantially more potassium than sodium, and potassium cations are specifically required for many key cellular processes, including protein synthesis. This distinct ionic composition and requirements have been attributed to the emergence of the first cells in potassium-rich habitats. Different, albeit complementary, scenarios have been proposed for the primordial potassium-rich environments based on experimental data and theoretical considerations. Specifically, building on the observation that potassium prevails over sodium in the vapor of inland geothermal systems, we have argued that the first cells could emerge in the pools and puddles at the periphery of primordial anoxic geothermal fields, where the elementary composition of the condensed vapor would resemble the internal milieu of modern cells. Marine and freshwater environments generally contain more sodium than potassium. Therefore, to invade such environments, while maintaining excess of potassium over sodium in the cytoplasm, primordial cells needed means to extrude sodium ions. The foray into new, sodium-rich habitats was the likely driving force behind the evolution of diverse redox-, light-, chemically-, or osmotically-dependent sodium export pumps and the increase of membrane tightness. Here we present a scenario that details how the interplay between several, initially independent sodium pumps might have triggered the evolution of sodium-dependent membrane bioenergetics, followed by the separate emergence of the proton-dependent bioenergetics in archaea and bacteria. We also discuss the development of systems that utilize the sodium/potassium gradient across the cell membranes.
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Affiliation(s)
- D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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40
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Azim S, McDowell D, Cartagena A, Rodriguez R, Laughlin TF, Ahmad Z. Venom peptides cathelicidin and lycotoxin cause strong inhibition of Escherichia coli ATP synthase. Int J Biol Macromol 2016; 87:246-51. [PMID: 26930579 DOI: 10.1016/j.ijbiomac.2016.02.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 12/29/2022]
Abstract
Venom peptides are known to have strong antimicrobial activity and anticancer properties. King cobra cathelicidin or OH-CATH (KF-34), banded krait cathelicidin (BF-30), wolf spider lycotoxin I (IL-25), and wolf spider lycotoxin II (KE-27) venom peptides were found to strongly inhibit Escherichia coli membrane bound F1Fo ATP synthase. The potent inhibition of wild-type E. coli in comparison to the partial inhibition of null E. coli by KF-34, BF-30, Il-25, or KE-27 clearly links the bactericidal properties of these venom peptides to the binding and inhibition of ATP synthase along with the possibility of other inhibitory targets. The four venom peptides KF-34, BF-30, IL-25, and KE-27, caused ≥85% inhibition of wild-type membrane bound E.coli ATP synthase. Venom peptide induced inhibition of ATP synthase and the strong abrogation of wild-type E. coli cell growth in the presence of venom peptides demonstrates that ATP synthase is a potent membrane bound molecular target for venom peptides. Furthermore, the process of inhibition was found to be fully reversible.
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Affiliation(s)
- Sofiya Azim
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, United States; Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37614, United States
| | - Derek McDowell
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, United States
| | - Alec Cartagena
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, United States
| | - Ricky Rodriguez
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, United States
| | - Thomas F Laughlin
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN 37614, United States
| | - Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A.T. Still University, Kirksville, MO, United States.
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Zhu X, Shi D, Li X, Gong W, Wu F, Guo X, Xiao H, Liu L, Zhou H. TLR signalling affects sperm mitochondrial function and motility via phosphatidylinositol 3-kinase and glycogen synthase kinase-3α. Cell Signal 2015; 28:148-156. [PMID: 26658093 DOI: 10.1016/j.cellsig.2015.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 12/03/2015] [Accepted: 12/03/2015] [Indexed: 02/08/2023]
Abstract
Infection in male and female genital tracts can lead to infertility. The underlying mechanisms of this process remain unclear. Toll-like receptors (TLRs) recognize conserved structures and respond to pathogens by initiating signals that activate inflammatory gene transcription. Here, we demonstrate that TLR activation in sperm reduces sperm motility via signalling through myeloid differentiation factor 88 (MyD88), phosphatidylinositol 3-kinase (PI3K), and glycogen synthase kinase (GSK)-3α. Upon TLR activation, phosphorylated forms of PI3K and GSK3α were detected in the mitochondria, and the mitochondrial membrane potential was impaired in sperm. In addition, mitochondrial ATP levels were decreased after TLR agonist stimulation. Furthermore, blocking PI3K or GSK3α activation abrogated these effects and reversed the TLR-induced reduction in sperm motility. These results identify a previously unrecognized TLR signalling pathway that leads to dysfunctional sperm mitochondria, which reduce sperm motility. Our study reveals a novel mechanism by which pathogenic infection affects sperm motility and possibly leads to infertility.
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Affiliation(s)
- Xingxing Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Dongyan Shi
- Department of Immunology, Nanjing Medical University, Nanjing 210029, China
| | - Xiaoqian Li
- Department of Immunology, Nanjing Medical University, Nanjing 210029, China
| | - Weijuan Gong
- Department of Microbiology & Immunology, Yangzhou University, Yangzhou 225009, China
| | - Fengjiao Wu
- Department of Immunology, Nanjing Medical University, Nanjing 210029, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Hui Xiao
- Institute of Pasteur Shanghai, Chinese Academy of Sciences, Shanghai 200025, China
| | - Lixin Liu
- Department of Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Hong Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China.
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Chen Z, Peng Y, Liu F, Le Z, Zhu J, Shen G, Zhang D, Wen M, Xiao S, Liu CP, Lu Y, Li H. Hierarchical Nanostructured WO3 with Biomimetic Proton Channels and Mixed Ionic-Electronic Conductivity for Electrochemical Energy Storage. NANO LETTERS 2015; 15:6802-8. [PMID: 26406938 DOI: 10.1021/acs.nanolett.5b02642] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein channels in biologic systems can effectively transport ions such as proton (H(+)), sodium (Na(+)), and calcium (Ca(+)) ions. However, none of such channels is able to conduct electrons. Inspired by the biologic proton channels, we report a novel hierarchical nanostructured hydrous hexagonal WO3 (h-WO3) which can conduct both protons and electrons. This mixed protonic-electronic conductor (MPEC) can be synthesized by a facile single-step hydrothermal reaction at low temperature, which results in a three-dimensional nanostructure self-assembled from h-WO3 nanorods. Such a unique h-WO3 contains biomimetic proton channels where single-file water chains embedded within the electron-conducting matrix, which is critical for fast electrokinetics. The mixed conductivities, high redox capacitance, and structural robustness afford the h-WO3 with unprecedented electrochemical performance, including high capacitance, fast charge/discharge capability, and very long cycling life (>50,000 cycles without capacitance decay), thus providing a new platform for a broad range of applications.
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Affiliation(s)
- Zheng Chen
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Yiting Peng
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
- Shanghai University of Electric Power , Shanghai 200090, China
| | - Fang Liu
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Zaiyuan Le
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Jian Zhu
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Normal University , Shanghai 200234, China
| | - Gurong Shen
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Dieqing Zhang
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Normal University , Shanghai 200234, China
| | - Meicheng Wen
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Normal University , Shanghai 200234, China
| | - Shuning Xiao
- The Education Ministry Key Lab of Resource Chemistry, Shanghai Normal University , Shanghai 200234, China
| | - Chi-Ping Liu
- Department of Materials Science and Engineering, University of California , Los Angeles, California 90095, United States
| | - Yunfeng Lu
- Department of Chemical and Biomolecular Engineering, University of California , Los Angeles, California 90095, United States
| | - Hexing Li
- Shanghai University of Electric Power , Shanghai 200090, China
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Lu H, Yuan W, Zhou J, Chong PLG. Glucose Synthesis in a Protein-Based Artificial Photosynthesis System. Appl Biochem Biotechnol 2015; 177:105-17. [PMID: 26170084 DOI: 10.1007/s12010-015-1731-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/22/2015] [Indexed: 11/28/2022]
Abstract
The objective of this study was to understand glucose synthesis of a protein-based artificial photosynthesis system affected by operating conditions, including the concentrations of reactants, reaction temperature, and illumination. Results from non-vesicle-based glyceraldehyde-3-phosphate (GAP) and glucose synthesis showed that the initial concentrations of ribulose-1,5-bisphosphate (RuBP) and adenosine triphosphate (ATP), lighting source, and temperature significantly affected glucose synthesis. Higher initial concentrations of RuBP and ATP significantly enhanced GAP synthesis, which was linearly correlated to glucose synthesis, confirming the proper functions of all catalyzing enzymes in the system. White fluorescent light inhibited artificial photosynthesis and reduced glucose synthesis by 79.2 % compared to in the dark. The reaction temperature of 40 °C was optimum, whereas lower or higher temperature reduced glucose synthesis. Glucose synthesis in the vesicle-based artificial photosynthesis system reconstituted with bacteriorhodopsin, F 0 F 1 ATP synthase, and polydimethylsiloxane-methyloxazoline-polydimethylsiloxane triblock copolymer was successfully demonstrated. This system efficiently utilized light-induced ATP to drive glucose synthesis, and 5.2 μg ml(-1) glucose was synthesized in 0.78-ml reaction buffer in 7 h. Light-dependent reactions were found to be the bottleneck of the studied artificial photosynthesis system.
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Affiliation(s)
- Hao Lu
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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Thymoquinone Inhibits Escherichia coli ATP Synthase and Cell Growth. PLoS One 2015; 10:e0127802. [PMID: 25996607 PMCID: PMC4440651 DOI: 10.1371/journal.pone.0127802] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/19/2015] [Indexed: 11/19/2022] Open
Abstract
We examined the thymoquinone induced inhibition of purified F1 or membrane bound F1FO E. coli ATP synthase. Both purified F1 and membrane bound F1FO were completely inhibited by thymoquinone with no residual ATPase activity. The process of inhibition was fully reversible and identical in both membrane bound F1Fo and purified F1 preparations. Moreover, thymoquinone induced inhibition of ATP synthase expressing wild-type E. coli cell growth and non-inhibition of ATPase gene deleted null control cells demonstrates that ATP synthase is a molecular target for thymoquinone. This also links the beneficial dietary based antimicrobial and anticancer effects of thymoquinone to its inhibitory action on ATP synthase.
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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Ahmad Z, Tayou J, Laughlin TF. Asp residues of βDELSEED-motif are required for peptide binding in the Escherichia coli ATP synthase. Int J Biol Macromol 2015; 75:37-43. [PMID: 25603139 DOI: 10.1016/j.ijbiomac.2014.12.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/27/2014] [Accepted: 12/30/2014] [Indexed: 01/01/2023]
Abstract
This study demonstrates the requirement of Asp-380 and Asp-386 in the βDELSEED-motif of Escherichia coli ATP synthase for peptide binding and inhibition. We studied the inhibition profiles of wild-type and mutant E. coli ATP synthase in presence of c-terminal amide bound melittin and melittin related peptide. Melittin and melittin related peptide inhibited wild-type ATPase almost completely while only partial inhibition was observed in single mutations with replacement of Asp to Ala, Gln, or Arg. Additionally, very little or no inhibition occurred among double mutants βD380A/βD386A, βD380Q/βD386Q, or βD380R/βD386R signifying that removal of one Asp residue allows limited peptide binding. Partial or substantial loss of oxidative phosphorylation among double mutants demonstrates the functional requirement of βD380 and βD386 Asp residues. Moreover, abrogation of wild-type E. coli cell growth and normal growth of mutant cells in presence of peptides provides strong evidence for the requirement of βDELSEED-motif Asp residues for peptide binding. It is concluded that while presence of one Asp residue may allow partial peptide binding, both Asp residues, βD380 and βD386, are essential for proper peptide binding and inhibition of ATP synthase.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, MO 63501, United States.
| | - Junior Tayou
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, MO 63501, United States
| | - Thomas F Laughlin
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, MO 63501, United States
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Zhang Y, Li CS, Wu CJ, Yang J, Hang CC. Neuroprotective effect of Shenfu Injection () following cardiac arrest in pig correlates with improved mitochondrial function and cerebral glucose uptake. Chin J Integr Med 2014; 20:835-43. [PMID: 25411019 DOI: 10.1007/s11655-014-1890-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 01/03/2023]
Abstract
OBJECTIVE To test whether Shenfu Injection (, SFI) might attenuate the impact of cerebral energy dysfunction after resuscitation in a pig model of cardiac arrest (CA). METHODS Thirty-four Wuzhishan miniature inbred pigs were randomly divided into three groups: the SFI group (n=12), the saline group (SA group, n=12), and the sham-operated group (sham group, n=10). Following successful return of spontaneous circulation (ROSC) from 8-min untreated ventricular fibrillation, animals received a continuous infusion of either SFI (0.2 mL/min) or saline for 6 h. Cerebral performance category score was evaluated at 24 and 48 h after ROSC, followed by positron emission tomography and computed tomography scans of cerebral glucose uptake. Surviving pigs were euthanized 48 h after ROSC, and the brains were removed for detecting mitochondrial function. RESULTS Compared with the SA group, SFI treatment produced a better neurologic outcome 48 h after ROSC (P<0.05). However, there was no significant difference of survival rate between the SA and SFI groups (83.3% vs. 81.8%, P>0.05). After ROSC, the SA group showed a decrease in the maximum standardized uptake value of different regions in the brain tissue, where SFI treatment can ameliorate these decreases (P<0.01 or P<0.05). Improved mitochondrial respiratory properties and higher mitochondrial membrane potential were also found following SFI treatment compared with the SA group at 48 h after ROSC (P<0.05 or P<0.01). CONCLUSION SFI treatment after resuscitation has significant neuroprotective effects against disruption of cerebral energy metabolism from CA by improving glucose uptake and by normalizing mitochondrial function.
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Affiliation(s)
- Yi Zhang
- Department of Hyperbaric Oxygen, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
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Ahmad Z, Winjobi M, Kabir MA. Significance of αThr-349 in the catalytic sites of Escherichia coli ATP synthase. Biochemistry 2014; 53:7376-85. [PMID: 25375895 PMCID: PMC4255642 DOI: 10.1021/bi5013063] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
This
paper describes the role of α-subunit VISIT-DG sequence
residue αThr-349 in the catalytic sites of Escherichia
coli F1Fo ATP synthase. X-ray structures
show the highly conserved αThr-349 in the proximity (2.68 Å)
of the conserved phosphate binding residue βR182 in the phosphate
binding subdomain. αT349A, -D, -Q, and -R mutations caused 90–100-fold
losses of oxidative phosphorylation and reduced ATPase activity of
F1Fo in membranes. Double mutation αT349R/βR182A
was able to partially compensate for the absence of known phosphate
binding residue βR182. Azide, fluoroaluminate, and fluoroscandium
caused insignificant inhibition of αT349A, -D, and -Q mutants,
slight inhibition of the αT349R mutant, partial inhibition of
the αT349R/βR182A double mutant, and complete inhibition
of the wild type. Whereas NBD-Cl (7-chloro-4-nitrobenzo-2-oxa-1,3-diazole)
inhibited wild-type ATPase and its αT349A, -D, -R, and -Q mutants
essentially completely, βR182A ATPase and double mutant αT349A/βR182A
were inhibited partially. Inhibition characteristics supported the
conclusion that NBD-Cl reacts in βE (empty) catalytic sites,
as shown previously by X-ray structure analysis. Phosphate protected
against NBD-Cl inhibition in the wild type, αT349R, and double
mutant αT349R/βR182A but not in αT349A, αT349D,
or αT349Q. The results demonstrate that αThr-349 is a
supplementary residue involved in phosphate binding and transition
state stabilization in ATP synthase catalytic sites through its interaction
with βR182.
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Affiliation(s)
- Zulfiqar Ahmad
- Department of Biochemistry, Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences , Kirksville, Missouri 63501, United States
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49
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Malyan AN. Noncatalytic nucleotide binding sites: properties and mechanism of involvement in ATP synthase activity regulation. BIOCHEMISTRY (MOSCOW) 2014; 78:1512-23. [PMID: 24490737 DOI: 10.1134/s0006297913130099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
ATP synthases (FoF1-ATPases) of chloroplasts, mitochondria, and bacteria catalyze ATP synthesis or hydrolysis coupled with the transmembrane transfer of protons or sodium ions. Their activity is regulated through their reversible inactivation resulting from a decreased transmembrane potential difference. The inactivation is believed to conserve ATP previously synthesized under conditions of sufficient energy supply against unproductive hydrolysis. This review is focused on the mechanism of nucleotide-dependent regulation of the ATP synthase activity where the so-called noncatalytic nucleotide binding sites are involved. Properties of these sites varying upon free enzyme transition to its membrane-bound form, their dependence on membrane energization, and putative mechanisms of noncatalytic site-mediated regulation of the ATP synthase activity are discussed.
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Affiliation(s)
- A N Malyan
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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50
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Lytovchenko O, Naumenko N, Oeljeklaus S, Schmidt B, von der Malsburg K, Deckers M, Warscheid B, van der Laan M, Rehling P. The INA complex facilitates assembly of the peripheral stalk of the mitochondrial F1Fo-ATP synthase. EMBO J 2014; 33:1624-38. [PMID: 24942160 DOI: 10.15252/embj.201488076] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial F1Fo-ATP synthase generates the bulk of cellular ATP. This molecular machine assembles from nuclear- and mitochondria-encoded subunits. Whereas chaperones for formation of the matrix-exposed hexameric F1-ATPase core domain have been identified, insight into how the nuclear-encoded F1-domain assembles with the membrane-embedded Fo-region is lacking. Here we identified the INA complex (INAC) in the inner membrane of mitochondria as an assembly factor involved in this process. Ina22 and Ina17 are INAC constituents that physically associate with the F1-module and peripheral stalk, but not with the assembled F1Fo-ATP synthase. Our analyses show that loss of Ina22 and Ina17 specifically impairs formation of the peripheral stalk that connects the catalytic F1-module to the membrane embedded Fo-domain. We conclude that INAC represents a matrix-exposed inner membrane protein complex that facilitates peripheral stalk assembly and thus promotes a key step in the biogenesis of mitochondrial F1Fo-ATP synthase.
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Affiliation(s)
- Oleksandr Lytovchenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Nataliia Naumenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Bernhard Schmidt
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Karina von der Malsburg
- Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty for Biology, University of Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Martin van der Laan
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany Institute for Biochemistry and Molecular Biology, ZBMZ, University of Freiburg, Freiburg, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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