1
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Taha A, Patón M, Penas DR, Banga JR, Rodríguez J. Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants. PLoS Comput Biol 2023; 19:e1011264. [PMID: 37410779 DOI: 10.1371/journal.pcbi.1011264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces as a function of the concentration of metabolic intermediates. The tool, based on thermodynamic principles and multi-objective optimisation, accounts for pathway variants in terms of different electron carriers, as well as energy conservation (proton translocating) reactions within the pathway. The method also accommodates other constraints, some of them non-linear, such as the balance of conserved moieties. The approach involves the transformation of the maximum energy yield problem into a multi-objective mixed-integer linear optimisation problem which is then subsequently solved using the epsilon-constraint method, highlighting the trade-off between yield and rate in metabolic reactions. The methodology is applied to analyse several pathway alternatives occurring during propionate oxidation in anaerobic fermentation processes, as well as to the reverse TCA cycle pathway occurring during autotrophic microbial CO2 fixation. The results obtained using the developed methodology match previously reported literature and bring about insights into the studied pathways.
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Affiliation(s)
- Ahmed Taha
- Department of Chemical Engineering, Research and Innovation Center on CO2 and H2 (RICH) Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mauricio Patón
- Department of Chemical Engineering, Research and Innovation Center on CO2 and H2 (RICH) Khalifa University, Abu Dhabi, United Arab Emirates
| | - David R Penas
- Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Galicia, Spain
| | - Julio R Banga
- Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Galicia, Spain
| | - Jorge Rodríguez
- Department of Chemical Engineering, Research and Innovation Center on CO2 and H2 (RICH) Khalifa University, Abu Dhabi, United Arab Emirates
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2
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Two specific domains of the γ subunit of chloroplast F oF 1 provide redox regulation of the ATP synthesis through conformational changes. Proc Natl Acad Sci U S A 2023; 120:e2218187120. [PMID: 36716358 PMCID: PMC9964038 DOI: 10.1073/pnas.2218187120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chloroplast FoF1-ATP synthase (CFoCF1) converts proton motive force into chemical energy during photosynthesis. Although many studies have been done to elucidate the catalytic reaction and its regulatory mechanisms, biochemical analyses using the CFoCF1 complex have been limited because of various technical barriers, such as the difficulty in generating mutants and a low purification efficiency from spinach chloroplasts. By taking advantage of the powerful genetics available in the unicellular green alga Chlamydomonas reinhardtii, we analyzed the ATP synthesis reaction and its regulation in CFoCF1. The domains in the γ subunit involved in the redox regulation of CFoCF1 were mutated based on the reported structure. An in vivo analysis of strains harboring these mutations revealed the structural determinants of the redox response during the light/dark transitions. In addition, we established a half day purification method for the entire CFoCF1 complex from C. reinhardtii and subsequently examined ATP synthesis activity by the acid-base transition method. We found that truncation of the β-hairpin domain resulted in a loss of redox regulation of ATP synthesis (i.e., constitutively active state) despite retaining redox-sensitive Cys residues. In contrast, truncation of the redox loop domain containing the Cys residues resulted in a marked decrease in the activity. Based on this mutation analysis, we propose a model of redox regulation of the ATP synthesis reaction by the cooperative function of the β-hairpin and the redox loop domains specific to CFoCF1.
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3
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Jin X, Zhang P, Zhang Y, Zhou M, Liu B, Quan D, Jia M, Zhang Z, Guo W, Kong XY, Jiang L. Light-driven proton transmembrane transport enabled by bio-semiconductor 2D membrane: A general peptide-induced WS 2 band shifting strategy. Biosens Bioelectron 2022; 218:114741. [PMID: 36209531 DOI: 10.1016/j.bios.2022.114741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/02/2022]
Abstract
Light-driven proton directional transport is important in living beings as it could subtly realize the light energy conversion for living uses. In the past years, 2D materials-based nanochannels have shown great potential in active ion transport due to controllable properties, including surface charge distribution, wettability, functionalization, electric structure, and external stimuli responsibility, etc. However, to fuse the inorganic materials into bio-membranes still faces several challenges. Here, we proposed peptide-modified WS2 nanosheets via cysteine linkers to realize tunable band structure and, hence, enable light-driven proton transmembrane transport. The modification was achieved through the thiol chemistry of the -SH groups in the cysteine linker and the S vacancy on the WS2 nanosheets. By tuning the amino residues sequences (lysine-rich peptides, denoted as KFC; and aspartate-rich peptides, denoted as DFC), the ζ-potential, surface charge, and band energy of WS2 nanosheets could be rationally regulated. Janus membranes formed by assembling the peptide-modified WS2 nanosheets could realize the proton transmembrane transport under visible light irradiation, driven by a built-in potential due to a type II band alignment between the KFC-WS2 and DFC-WS2. As a result, the proton would be driven across the formed nanochannels. These results demonstrate a general strategy to build bio-semiconductor materials and provide a new way for embedding inorganic materials into biological systems toward the development of bioelectronic devices.
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Affiliation(s)
- Xiaoyan Jin
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Peikun Zhang
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, Institute for Frontier Science of Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Yuhui Zhang
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Min Zhou
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biying Liu
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Di Quan
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meijuan Jia
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhuhua Zhang
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, Institute for Frontier Science of Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China.
| | - Wei Guo
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lei Jiang
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Tivony R, Fletcher M, Keyser UF. Quantifying proton-induced membrane polarization in single biomimetic giant vesicles. Biophys J 2022; 121:2223-2232. [DOI: 10.1016/j.bpj.2022.05.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
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5
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Li Z, Xu X, Yu F, Fei J, Li Q, Dong M, Li J. Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a F o F 1 -ATPase-Based Assembly System. Angew Chem Int Ed Engl 2022; 61:e202116220. [PMID: 35129265 DOI: 10.1002/anie.202116220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Indexed: 12/23/2022]
Abstract
Energy conversion plays an important role in the metabolism of photosynthetic organisms. Improving energy transformation by promoting a proton gradient has been a great challenge for a long time. In the present study, we realize a directional proton migration through the construction of oriented bacteriorhodopsin (BR) microcapsules coated by Fo F1 -ATPase molecular motors through layer-by-layer (LBL) assembly. The changes in the conformation of BR under illumination lead to proton transfer in a radial direction, which generates a higher proton gradient to drive the synthesis of adenosine triphosphate (ATP) by Fo F1 -ATPase. Furthermore, to promote the photosynthetic activity, optically matched quantum dots were introduced into the artificial coassembly system of BR and Fo F1 -ATPase. Such a design creates a new path for the use of light energy.
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Affiliation(s)
- Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fanchen Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
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6
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Vlasov AV, Osipov SD, Bondarev NA, Uversky VN, Borshchevskiy VI, Yanyushin MF, Manukhov IV, Rogachev AV, Vlasova AD, Ilyinsky NS, Kuklin AI, Dencher NA, Gordeliy VI. ATP synthase F OF 1 structure, function, and structure-based drug design. Cell Mol Life Sci 2022; 79:179. [PMID: 35253091 PMCID: PMC11072866 DOI: 10.1007/s00018-022-04153-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022]
Abstract
ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.
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Affiliation(s)
- Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Stepan D Osipov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay A Bondarev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mikhail F Yanyushin
- Institute of Basic Biological Problems, Russian Academy of Sciences, 142290, Pushchino, Moscow region, Russia
| | - Ilya V Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Andrey V Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Alexandr I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, 141980, Dubna, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
- Physical Biochemistry, Department Chemistry, Technische Universität Darmstadt, Alarich-Weiss-Straße 4, 64287, Darmstadt, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany.
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027, Grenoble, France.
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7
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Li Z, Xu X, Yu F, Fei J, Li Q, Dong M, Li J. Oriented Nanoarchitectonics of Bacteriorhodopsin for Enhancing ATP Generation in a F
o
F
1
‐ATPase‐Based Assembly System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education School of Chemistry and Chemical Engineering Shandong University Jinan 250100 China
| | - Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Fanchen Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education School of Chemistry and Chemical Engineering Shandong University Jinan 250100 China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C 8000 Denmark
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100049 Beijing China
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8
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Lyu Y, Thai PN, Ren L, Timofeyev V, Jian Z, Park S, Ginsburg KS, Overton J, Bossuyt J, Bers DM, Yamoah EN, Chen-Izu Y, Chiamvimonvat N, Zhang XD. Beat-to-beat dynamic regulation of intracellular pH in cardiomyocytes. iScience 2022; 25:103624. [PMID: 35005560 PMCID: PMC8718820 DOI: 10.1016/j.isci.2021.103624] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/10/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
The mammalian heart beats incessantly with rhythmic mechanical activities generating acids that need to be buffered to maintain a stable intracellular pH (pHi) for normal cardiac function. Even though spatial pHi non-uniformity in cardiomyocytes has been documented, it remains unknown how pHi is regulated to match the dynamic cardiac contractions. Here, we demonstrated beat-to-beat intracellular acidification, termed pHi transients, in synchrony with cardiomyocyte contractions. The pHi transients are regulated by pacing rate, Cl-/HCO3 - transporters, pHi buffering capacity, and β-adrenergic signaling. Mitochondrial electron-transport chain inhibition attenuates the pHi transients, implicating mitochondrial activity in sculpting the pHi regulation. The pHi transients provide dynamic alterations of H+ transport required for ATP synthesis, and a decrease in pHi may serve as a negative feedback to cardiac contractions. Current findings dovetail with the prevailing three known dynamic systems, namely electrical, Ca2+, and mechanical systems, and may reveal broader features of pHi handling in excitable cells.
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Affiliation(s)
- Yankun Lyu
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Phung N. Thai
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Lu Ren
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Valeriy Timofeyev
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Zhong Jian
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Seojin Park
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Kenneth S. Ginsburg
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - James Overton
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Julie Bossuyt
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Donald M. Bers
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
| | - Ebenezer N. Yamoah
- Department of Physiology and Cell Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Ye Chen-Izu
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Nipavan Chiamvimonvat
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
- Department of Pharmacology, University of California, Davis, Davis, CA 95616, USA
- Department of Veterans Affairs, Northern California Health Care System, Mather, CA 95655, USA
| | - Xiao-Dong Zhang
- Department of Internal Medicine, University of California, Davis, Davis, CA 95616, USA
- Department of Veterans Affairs, Northern California Health Care System, Mather, CA 95655, USA
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9
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Selivanov VA, Zagubnaya OA, Foguet C, Nartsissov YR, Cascante M. MITODYN: An Open Source Software for Quantitative Modeling of Mitochondrial and Cellular Energy Metabolic Flux Dynamics in Health and Disease. Methods Mol Biol 2022; 2399:123-149. [PMID: 35604555 DOI: 10.1007/978-1-0716-1831-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mitochondrial respiratory chain (RC) transforms the reductive power of NADH or FADH2 oxidation into a proton gradient between the matrix and cytosolic sides of the inner mitochondrial membrane, that ATP synthase uses to generate ATP. This process constitutes a bridge between carbohydrates' central metabolism and ATP-consuming cellular functions. Moreover, the RC is responsible for a large part of reactive oxygen species (ROS) generation that play signaling and oxidizing roles in cells. Mathematical methods and computational analysis are required to understand and predict the possible behavior of this metabolic system. Here we propose a software tool that helps to analyze individual steps of respiratory electron transport in their dynamics, thus deepening understanding of the mechanism of energy transformation and ROS generation in the RC. This software's core is a kinetic model of the RC represented by a system of ordinary differential equations (ODEs). This model enables the analysis of complex dynamic behavior of the RC, including multistationarity and oscillations. The proposed RC modeling method can be applied to study respiration and ROS generation in various organisms and naturally extended to explore carbohydrates' metabolism and linked metabolic processes.
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Affiliation(s)
- Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
- CIBER of Hepatic and Digestive Diseases (CIBEREHD) and Metabolomics Node at Spanish National Bioinformatics Institute (INB-ISCIII-ES-ELIXIR), Institute of Health Carlos III (ISCIII), Madrid, Spain.
| | - Olga A Zagubnaya
- Department of Mathematical Modeling and Statistical Analysis, Institute of Cytochemistry and Molecular Pharmacology, Moscow, Russia
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD) and Metabolomics Node at Spanish National Bioinformatics Institute (INB-ISCIII-ES-ELIXIR), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Yaroslav R Nartsissov
- Department of Mathematical Modeling and Statistical Analysis, Institute of Cytochemistry and Molecular Pharmacology, Moscow, Russia
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
- CIBER of Hepatic and Digestive Diseases (CIBEREHD) and Metabolomics Node at Spanish National Bioinformatics Institute (INB-ISCIII-ES-ELIXIR), Institute of Health Carlos III (ISCIII), Madrid, Spain.
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10
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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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11
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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12
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Zhao G, Liu Y, Du J, Zhang H, Feng H, Lu X. Application of tetrahedral -deoxyribonucleic acid electrochemistry platform coupling aptazymes and hybridized hairpin reactions for the measurement of extracellular adenosine triphosphate in plants. Anal Chim Acta 2021; 1172:338681. [PMID: 34119022 DOI: 10.1016/j.aca.2021.338681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 11/29/2022]
Abstract
Extracellular ATP (eATP) is an important biological signal transduction molecule. Although a variety of detection methods have been extensively used in ATP sensing and analysis, accurate detection of eATP remains difficult due to its extremely low concentration and spatiotemporal distribution. Here, an eATP measurement strategy based on tetrahedral DNA (T-DNA)-modified electrode sensing platform and hybridization chain reaction (HCR) combined with G-quadruplex/Hemin (G4/Hemin) DNAzyme dual signal amplification is proposed. In this strategy, ATP aptamer and RNA-cleaving DNAzyme were combined to form a split aptazyme. In the presence of ATP, this aptazyme hydrolyzes the cleaving substrate strand with high selectivity, releasing cleaved ssDNA, which are captured by the T-DNA assembled on the electrode surface, triggering an HCR on the electrode surface to form numerous linker sequences of the HCR dsDNA product. When G-quadruplex@AuNPs (G4) spherical nucleic acid enzymes (SNAzymes) with other linkers are used as nanocatalyst tags, they are captured by HCR dsDNA through sticky linkers present on the electrode surface. An amplified electrochemical redox current signal is generated through SNAzyme-mediated catalysis of H2O2, enabling easy detection of picomole amounts of ATP. Using this strategy, eATP levels released by tobacco suspension cells were accurately measured and the distribution and concentration of eATP released on the surface of an Arabidopsis leaf was determined.
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Affiliation(s)
- Guoyan Zhao
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Yongmei Liu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Jie Du
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China; Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, Northwest Normal University, Lanzhou, 730070, Gansu, China.
| | - Huizi Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China
| | - Hanqing Feng
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, China.
| | - Xiaoquan Lu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, Northwest Normal University, Lanzhou, 730070, Gansu, China.
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13
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Xu X, Fei J, Xu Y, Li G, Dong W, Xue H, Li J. Boric Acid‐Fueled ATP Synthesis by F
o
F
1
ATP Synthase Reconstituted in a Supramolecular Architecture. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100190 Beijing China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100190 Beijing China
| | - Youqian Xu
- Third Military Medical University 400038 Chongqing China
| | - Guangle Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
| | - Weiguang Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
| | - Huimin Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100190 Beijing China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Lab of Colloid, Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences 100190 Beijing China
- University of Chinese Academy of Sciences 100190 Beijing China
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14
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Xu X, Fei J, Xu Y, Li G, Dong W, Xue H, Li J. Boric Acid-Fueled ATP Synthesis by F o F 1 ATP Synthase Reconstituted in a Supramolecular Architecture. Angew Chem Int Ed Engl 2021; 60:7617-7620. [PMID: 33369011 DOI: 10.1002/anie.202016253] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Significant strides toward producing biochemical fuels have been achieved by mimicking natural oxidative and photosynthetic phosphorylation. Here, different from these strategies, we explore boric acid as a fuel for tuneable synthesis of energy-storing molecules in a cell-like supramolecular architecture. Specifically, a proton locked in boric acid is released in a modulated fashion by the choice of polyols. As a consequence, controlled proton gradients across the lipid membrane are established to drive ATP synthase embedded in the biomimetic architecture, which facilitates tuneable ATP production. This strategy paves a unique route to achieve highly efficient bioenergy conversion, holding broad applications in synthesis and devices that require biochemical fuels.
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Affiliation(s)
- Xia Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Youqian Xu
- Third Military Medical University, 400038, Chongqing, China
| | - Guangle Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Weiguang Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China
| | - Huimin Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100190, Beijing, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, 100190, Beijing, China.,University of Chinese Academy of Sciences, 100190, Beijing, China
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15
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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16
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Hou R, Wang Z. Thermodynamic marking of F OF 1 ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148369. [PMID: 33454313 DOI: 10.1016/j.bbabio.2021.148369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/02/2020] [Accepted: 01/05/2021] [Indexed: 11/29/2022]
Abstract
FOF1 ATP synthase is a ~100% efficient molecular machine for energy conversion in biology, and holds great lessons for man-made energy technology and nanotechnology. In light of formidable biocomplexity of the FOF1 machinery, its modeling from pure physical principles remains difficult and rare. Here we construct a thermodynamic model of FOF1 from experimentally accessible quantities plus a single entropy production that generally has vanishingly small values (<1kB). Based on the physical inputs, this model captures FOF1 performance observed over an exhaustively wide range of proton-motive force and nucleotide concentrations. The model predicts a distinct 1/8kBT slope for ATP synthesis rate versus proton-motive force, which is verified by experimental data and represents a profound thermodynamic marking of this amazingly efficient machine operating near a universal limit of the 2nd law of thermodynamics. The model further predicts two symmetries of heat productions, which are testable by available experimental techniques and offer quantitative constraints on FOF1's possible mechanisms behind its ~100% efficiency.
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Affiliation(s)
- Ruizheng Hou
- Department of Applied Physics, School of Science, Xi'an University of Technology, Xi'an, Shaan Xi 710048, China.
| | - Zhisong Wang
- Department of Physics and NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117542, Singapore
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17
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Response to "Molecular-level understanding of biological energy coupling and transduction: Response to "Chemiosmotic misunderstandings"". Biophys Chem 2020; 269:106512. [PMID: 33307371 DOI: 10.1016/j.bpc.2020.106512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/15/2020] [Accepted: 11/24/2020] [Indexed: 01/31/2023]
Abstract
The most recent contribution by Sunil Nath in these pages is, mostly, a repetition of his previous claims regarding failures of the chemiosmotic hypotheses, supplemented with some fresh misunderstandings of the points I had sought to clarify in my previous critique. Considerable portions rehash 50-60 years-old controversies, with no apparent understanding that the current chemiosmotic hypothesis, while birthed by Mitchell, differs from Mitchell's details in many respects. As such, Nath has devoted much time dealing with a few errors (or wrong hypotheses) by Mitchell (in a few places I would almost venture to say "typographical mistakes in typesetting") and presents the ensuing conclusions as "refutations" of the chemiosmotic paradigm, completely neglecting that such details (such as the precise H+/ATP or H+:O ratios) are completely irrelevant to the reality (or not) of an electron-transport chain that uses the free energy liberated by electron-transfer to remove H+ from a compartment, to which it returns through and ATP synthase which uses the energy in that spontaneous return to drive ATP synthesis. The thermodynamical mistakes and misunderstandings of the relevant literature present in Nath's new contribution are so numerous, though, that I feel forced to call the attention of the readers of "Biophysical Chemistry" to them.
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18
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Yang JH, Williams D, Kandiah E, Fromme P, Chiu PL. Structural basis of redox modulation on chloroplast ATP synthase. Commun Biol 2020; 3:482. [PMID: 32879423 PMCID: PMC7468127 DOI: 10.1038/s42003-020-01221-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/06/2020] [Indexed: 12/26/2022] Open
Abstract
In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the redox modulation, we used single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in both reduced and oxidized states. The disulfide linkage of the oxidized γ subunit introduces a torsional constraint to stabilize the two β hairpin structures. Once reduced, free cysteines alleviate this constraint, resulting in a concerted motion of the enzyme complex and a smooth transition between rotary states to facilitate the ATP synthesis. We added an uncompetitive inhibitor, tentoxin, in the reduced sample to limit the flexibility of the enzyme and obtained high-resolution details. Our cryo-EM structures provide mechanistic insight into the redox modulation of the energy regulation activity of chloroplast ATP synthase. Jay-How Yang et al. use single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in reduced and oxidized states. They report a torsional constraint in the oxidized γ subunit that is alleviated by free cysteines in the reduced state. Their work provides mechanistic insights into the redox modulation of the ATP synthesis by the chloroplast ATP synthase.
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Affiliation(s)
- Jay-How Yang
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dewight Williams
- Eyring Materials Center, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Petra Fromme
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Po-Lin Chiu
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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19
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Morelli AM, Ravera S, Calzia D, Panfoli I. An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane. Open Biol 2020; 9:180221. [PMID: 30966998 PMCID: PMC6501646 DOI: 10.1098/rsob.180221] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.
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Affiliation(s)
- Alessandro Maria Morelli
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Silvia Ravera
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
| | - Daniela Calzia
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Isabella Panfoli
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
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20
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Onyeabor M, Martinez R, Kurgan G, Wang X. Engineering transport systems for microbial production. ADVANCES IN APPLIED MICROBIOLOGY 2020; 111:33-87. [PMID: 32446412 DOI: 10.1016/bs.aambs.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The rapid development in the field of metabolic engineering has enabled complex modifications of metabolic pathways to generate a diverse product portfolio. Manipulating substrate uptake and product export is an important research area in metabolic engineering. Optimization of transport systems has the potential to enhance microbial production of renewable fuels and chemicals. This chapter comprehensively reviews the transport systems critical for microbial production as well as current genetic engineering strategies to improve transport functions and thus production metrics. In addition, this chapter highlights recent advancements in engineering microbial efflux systems to enhance cellular tolerance to industrially relevant chemical stress. Lastly, future directions to address current technological gaps are discussed.
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Affiliation(s)
- Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.
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21
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Jia Y, Xuan M, Feng X, Duan L, Li J, Li J. Reconstitution of Motor Proteins through Molecular Assembly. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yi Jia
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Mingjun Xuan
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Xiyun Feng
- Yunnan Normal University Kunming Yunnan 650500 China
| | - Li Duan
- Northwest Institute of Nuclear Technology Xi'an Shaanxi 710024 China
| | - Jieling Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
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22
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23
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Davis GA, Kramer DM. Optimization of ATP Synthase c-Rings for Oxygenic Photosynthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:1778. [PMID: 32082344 PMCID: PMC7003800 DOI: 10.3389/fpls.2019.01778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
The conversion of sunlight into useable cellular energy occurs via the proton-coupled electron transfer reactions of photosynthesis. Light is absorbed by photosynthetic pigments and transferred to photochemical reaction centers to initiate electron and proton transfer reactions to store energy in a redox gradient and an electrochemical proton gradient (proton motive force, pmf), composed of a concentration gradient (ΔpH) and an electric field (Δψ), which drives the synthesis of ATP through the thylakoid FoF1-ATP synthase. Although ATP synthase structure and function are conserved across biological kingdoms, the number of membrane-embedded ion-binding c subunits varies between organisms, ranging from 8 to 17, theoretically altering the H+/ATP ratio for different ATP synthase complexes, with profound implications for the bioenergetic processes of cellular metabolism. Of the known c-ring stoichiometries, photosynthetic c-rings are among the largest identified stoichiometries, and it has been proposed that decreasing the c-stoichiometry could increase the energy conversion efficiency of photosynthesis. Indeed, there is strong evidence that the high H+/ATP of the chloroplast ATP synthase results in a low ATP/nicotinamide adenine dinucleotide phosphate (NADPH) ratio produced by photosynthetic linear electron flow, requiring secondary processes such as cyclic electron flow to support downstream metabolism. We hypothesize that the larger c subunit stoichiometry observed in photosynthetic ATP synthases was selected for because it allows the thylakoid to maintain pmf in a range where ATP synthesis is supported, but avoids excess Δψ and ΔpH, both of which can lead to production of reactive oxygen species and subsequent photodamage. Numerical kinetic simulations of the energetics of chloroplast photosynthetic reactions with altered c-ring size predicts the energy storage of pmf and its effects on the photochemical reaction centers strongly support this hypothesis, suggesting that, despite the low efficiency and suboptimal ATP/NADPH ratio, a high H+/ATP is favored to avoid photodamage. This has important implications for the evolution and regulation of photosynthesis as well as for synthetic biology efforts to alter photosynthetic efficiency by engineering the ATP synthase.
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Affiliation(s)
- Geoffry A. Davis
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - David M. Kramer
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
- *Correspondence: David M. Kramer,
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24
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Methanogens: pushing the boundaries of biology. Emerg Top Life Sci 2018; 2:629-646. [PMID: 33525834 PMCID: PMC7289024 DOI: 10.1042/etls20180031] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 01/15/2023]
Abstract
Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioenergetics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. This review discusses the theoretical basis for energy conservation by methanogens and identifies gaps in methanogen biology that may be filled by undiscovered or yet-to-be engineered organisms.
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25
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Martins CHG, Abrão F, Moraes TS, Oliveira PF, Tavares DC, Magalhães LG, Galvão FC, Veneziani RCS, Ambrósio SR. Kaurenoic acid and its sodium salt derivative: antibacterial activity against Porphyromonas gingivalis and their mechanism of action. Future Microbiol 2018; 13:1585-1601. [DOI: 10.2217/fmb-2018-0140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To evaluate the antibacterial activity of 12 kaurane-type diterpenes against a panel of bacteria that cause endodontic infection. Methods & materials: We conducted tests against bacteria in the planktonic or in the sessile mode, cytotoxic assays for the most promising compounds against human normal lung fibroblast cells, and Porphyromonas gingivalis (ATCC 33277) proteomic analysis. Results & conclusion: Kaurenoic acid and its salt exhibited satisfactory antibacterial action against the evaluated bacteria. Proteomic analysis suggested that these compounds might interfere in bacterial metabolism and virulence factor expression. Kaurane-type diterpenes are an important class of natural products and should be considered in the search for new irrigating solutions to treat endodontic infections.
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Affiliation(s)
- Carlos HG Martins
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Fariza Abrão
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Thaís S Moraes
- Research Laboratory of Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Pollyanna F Oliveira
- Laboratory of Mutagenesis, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Denise C Tavares
- Laboratory of Mutagenesis, University of Franca - UNIFRAN, Franca, 14404-600, São Paulo, Brazil
| | - Lizandra G Magalhães
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
| | - Fábio C Galvão
- Department of Biological Sciences, São Paulo State University - UNESP, Araraquara, 14800-901, São Paulo, Brazil
| | - Rodrigo CS Veneziani
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
| | - Sérgio R Ambrósio
- Nucleus of Research in Sciences & Technology, University of Franca - UNIFRAN, 14404-600, São Paulo, Brazil
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26
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Roosterman D, Meyerhof W, Cottrell GS. Proton Transport Chains in Glucose Metabolism: Mind the Proton. Front Neurosci 2018; 12:404. [PMID: 29962930 PMCID: PMC6014028 DOI: 10.3389/fnins.2018.00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/25/2018] [Indexed: 01/11/2023] Open
Abstract
The Embden-Meyerhof-Parnas (EMP) pathway comprises eleven cytosolic enzymes interacting to metabolize glucose to lactic acid [CH3CH(OH)COOH]. Glycolysis is largely considered as the conversion of glucose to pyruvate (CH3COCOO-). We consider glycolysis to be a cellular process and as such, transporters mediating glucose uptake and lactic acid release and enable the flow of metabolites through the cell, must be considered as part of the EMP pathway. In this review, we consider the flow of metabolites to be coupled to a flow of energy that is irreversible and sufficient to form ordered structures. This latter principle is highlighted by discussing that lactate dehydrogenase (LDH) complexes irreversibly reduce pyruvate/H+ to lactate [CH3CH(OH)COO-], or irreversibly catalyze the opposite reaction, oxidation of lactate to pyruvate/H+. However, both LDH complexes are considered to be driven by postulated proton transport chains. Metabolism of glucose to two lactic acids is introduced as a unidirectional, continuously flowing pathway. In an organism, cell membrane-located proton-linked monocarboxylate transporters catalyze the final step of glycolysis, the release of lactic acid. Consequently, both pyruvate and lactate are discussed as intermediate products of glycolysis and substrates of regulated crosscuts of the glycolytic flow.
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Affiliation(s)
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
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27
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Abstract
Transmembrane protein 16F (TMEM16F) is a Ca2+-dependent phospholipid scramblase that translocates phospholipids bidirectionally between the leaflets of the plasma membrane. Phospholipid scrambling of TMEM16F causes exposure of phosphatidylserine in activated platelets to induce blood clotting and in differentiated osteoblasts to promote bone mineralization. Despite the importance of TMEM16F-mediated phospholipid scrambling in various biological reactions, the fundamental features of the scrambling reaction remain elusive due to technical difficulties in the preparation of a platform for assaying scramblase activity in vitro. Here, we established a method to express and purify mouse TMEM16F as a dimeric molecule by constructing a stable cell line and developed a microarray containing membrane bilayers with asymmetrically distributed phospholipids as a platform for single-molecule scramblase assays. The purified TMEM16F was integrated into the microarray, and monitoring of phospholipid translocation showed that a single TMEM16F molecule transported phospholipids nonspecifically between the membrane bilayers in a Ca2+-dependent manner. Thermodynamic analysis of the reaction indicated that TMEM16F transported 4.5 × 104 lipids per second at 25 °C, with an activation free energy of 47 kJ/mol. These biophysical features were similar to those observed with channels, which transport substrates by facilitating diffusion, and supported the stepping-stone model for the TMEM16F phospholipid scramblase.
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28
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Li Y, Fei J, Li G, Xie H, Yang Y, Li J, Xu Y, Sun B, Xia J, Fu X, Li J. Supramolecular Assembly of Photosystem II and Adenosine Triphosphate Synthase in Artificially Designed Honeycomb Multilayers for Photophosphorylation. ACS NANO 2018; 12:1455-1461. [PMID: 29361225 DOI: 10.1021/acsnano.7b07841] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plant thylakoids have a typical stacking structure, which is the site of photosynthesis, including light-harvesting, water-splitting, and adenosine triphosphate (ATP) production. This stacking structure plays a key role in exchange of substances with extremely high efficiency and minimum energy consumption through photosynthesis. Herein we report an artificially designed honeycomb multilayer for photophosphorylation. To mimic the natural thylakoid stacking structure, the multilayered photosystem II (PSII)-ATP synthase-liposome system is fabricated via layer-by-layer (LbL) assembly, allowing the three-dimensional distributions of PSII and ATP synthase. Under light illumination, PSII splits water into protons and generates a proton gradient for ATP synthase to produce ATP. Moreover, it is found that the ATP production is extremely associated with the numbers of PSII layers. With such a multilayer structure assembled via LbL, one can better understand the mechanism of PSII and ATP synthase integrated in one system, mimicking the photosynthetic grana structure. On the other hand, such an assembled system can be considered to improve the photophosphorylation.
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Affiliation(s)
- Yue Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology , Beijing 100190, China
- College of Life Science, Jilin University , Changchun 130012, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Guangle Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academic of Sciences , Beijing 100049, China
| | - Haiming Xie
- National & Local United Engineering Laboratory for Power Battery, Department of Chemistry, Northeast Normal University , Changchun 130024, China
| | - Yang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology , Beijing 100190, China
| | - Jieling Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Youqian Xu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academic of Sciences , Beijing 100049, China
| | - Bingbing Sun
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academic of Sciences , Beijing 100049, China
| | - Jiarui Xia
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academic of Sciences , Beijing 100049, China
| | - Xueqi Fu
- College of Life Science, Jilin University , Changchun 130012, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academic of Sciences , Beijing 100049, China
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29
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Morales A, Yin X, Harbinson J, Driever SM, Molenaar J, Kramer DM, Struik PC. In Silico Analysis of the Regulation of the Photosynthetic Electron Transport Chain in C3 Plants. PLANT PHYSIOLOGY 2018; 176:1247-1261. [PMID: 28924017 PMCID: PMC5813522 DOI: 10.1104/pp.17.00779] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/13/2017] [Indexed: 05/18/2023]
Abstract
We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and noncyclic alternative electron transport), and regulation of Rubisco activity leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis (Arabidopsis thaliana). A dataset was constructed from multiple sources, including measurements of steady-state and dynamic gas exchange, chlorophyll fluorescence, and absorbance spectroscopy under different light intensities and CO2, to test predictions of the model under different experimental conditions. Simulations suggested that there are strong interactions between cyclic and noncyclic alternative electron transport and that an excess capacity for alternative electron transport is required to ensure adequate redox state and lumen pH. Furthermore, the model predicted that, under specific conditions, reduction of ferredoxin by plastoquinol is possible after a rapid increase in light intensity. Further analysis also revealed that the relationship between ATP synthesis and proton motive force was highly regulated by the concentrations of ATP, ADP, and inorganic phosphate, and this facilitated an increase in nonphotochemical quenching and proton motive force under conditions where metabolism was limiting, such as low CO2, high light intensity, or combined high CO2 and high light intensity. The model may be used as an in silico platform for future research on the regulation of photosynthetic electron transport.
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Affiliation(s)
- Alejandro Morales
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK, Wageningen, The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK, Wageningen, The Netherlands
| | - Jeremy Harbinson
- Horticulture and Product Physiology, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Steven M Driever
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK, Wageningen, The Netherlands
| | - Jaap Molenaar
- Biometris, Mathematical and Statistical Methods Group, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - David M Kramer
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48823
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK, Wageningen, The Netherlands
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30
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Xu Y, Fei J, Li G, Yuan T, Li J. Compartmentalized Assembly of Motor Protein Reconstituted on Protocell Membrane toward Highly Efficient Photophosphorylation. ACS NANO 2017; 11:10175-10183. [PMID: 28933821 DOI: 10.1021/acsnano.7b04747] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecule assembly and functionalization of protocells have achieved a great success. However, the yield efficiency of photophosphorylation in the present cell-like systems is limited. Herein, inspired by natural photobacteria, we construct a protocell membrane reconstituting motor protein for highly efficient light-mediated adenosine triphosphate (ATP) synthesis through a layer-by-layer technique. The assembled membrane, compartmentally integrating photoacid generator, proton conductor, and ATP synthase, possesses excellent transparency, fast proton production, and quick proton transportation. Remarkably, these favorable features permit the formation of a large proton gradient in a confined region to drive ATP synthase to produce ATP with high efficiency (873 ATP s-1). It is the highest among the existing artificial photophosphorylation systems. Such a biomimetic system provides a bioenergy-supplying scenario for early photosynthetic life and holds promise in remotely controlled ATP-consumed biosensors, biocatalysts, and biodevices.
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Affiliation(s)
- Youqian Xu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Guangle Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tingting Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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31
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Yanagisawa S, Frasch WD. Protonation-dependent stepped rotation of the F-type ATP synthase c-ring observed by single-molecule measurements. J Biol Chem 2017; 292:17093-17100. [PMID: 28842481 PMCID: PMC5641864 DOI: 10.1074/jbc.m117.799940] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/02/2017] [Indexed: 11/06/2022] Open
Abstract
The two opposed rotary molecular motors of the F0F1-ATP synthase work together to provide the majority of ATP in biological organisms. Rotation occurs in 120° power strokes separated by dwells when F1 synthesizes or hydrolyzes ATP. F0 and F1 complexes connect via a central rotor stalk and a peripheral stator stalk. A major unresolved question is the mechanism in which the interaction between subunit-a and rotating subunit-c-ring in the F0 motor uses the flux of H+ across the membrane to induce clockwise rotation against the force of counterclockwise rotation driven by the F1-ATPase. In single-molecule measurements of F0F1 embedded in lipid bilayer nanodiscs, we observed that the ability of the F0 motor to form transient dwells increases with decreasing pH. Transient dwells can halt counterclockwise rotation powered by the F1-ATPase in steps equivalent to the rotation of single c-subunits in the c-ring of F0, and can push the common axle shared by the two motors clockwise by as much as one c-subunit. Because the F0 proton half-channels that access the periplasm and the cytoplasm are exposed to the same pH, these data are consistent with the conclusion that the periplasmic half-channel is more easily protonated in a manner that halts ATPase-driven rotation by blocking ATPase-dependent proton pumping. The fit of transient dwell occurrence to the sum of three Gaussian curves suggests that the asymmetry of the three ATPase-dependent 120° power strokes imposed by the relative positions of the central and peripheral stalks affects c-subunit stepping efficiency.
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Affiliation(s)
- Seiga Yanagisawa
- From the School of Life Sciences, Arizona State University, Tempe, Arizona, 85287-4501
| | - Wayne D Frasch
- From the School of Life Sciences, Arizona State University, Tempe, Arizona, 85287-4501
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32
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Abstract
FoF1-ATP synthase (FoF1) couples H+ flow in Fo domain and ATP synthesis/hydrolysis in F1 domain through rotation of the central rotor shaft, and the H+/ATP ratio is crucial to understand the coupling mechanism and energy yield in cells. Although H+/ATP ratio of the perfectly coupling enzyme can be predicted from the copy number of catalytic β subunits and that of H+ binding c subunits as c/β, the actual H+/ATP ratio can vary depending on coupling efficiency. Here, we report actual H+/ATP ratio of thermophilic Bacillus FoF1, whose c/β is 10/3. Proteoliposomes reconstituted with the FoF1 were energized with ΔpH and Δψ by the acid-base transition and by valinomycin-mediated diffusion potential of K+ under various [ATP]/([ADP]⋅[Pi]) conditions, and the initial rate of ATP synthesis/hydrolysis was measured. Analyses of thermodynamically equilibrated states, where net ATP synthesis/hydrolysis is zero, show linear correlation between the chemical potential of ATP synthesis/hydrolysis and the proton motive force, giving the slope of the linear function, that is, H+/ATP ratio, 3.3 ± 0.1. This value agrees well with the c/β ratio. Thus, chemomechanical coupling between Fo and F1 is perfect.
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33
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Czub J, Wieczór M, Prokopowicz B, Grubmüller H. Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F 1-ATPase. J Am Chem Soc 2017; 139:4025-4034. [PMID: 28253614 DOI: 10.1021/jacs.6b11708] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
F1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned energy conversion mechanism are not fully understood. Here, we use extensive molecular dynamics simulations to reconcile recent single-molecule experiments with structural data and provide a consistent thermodynamic, kinetic and mechanistic description of the main rotary substep in the synthetic cycle of mammalian ATP synthase. The calculated free energy profiles capture a discrete pattern in the rotation of the central γ-shaft, with a metastable intermediate located-consistently with recent experimental findings-at 70° relative to the X-ray position. We identify this rotary step as the ATP-dependent substep, and find that the associated free energy input supports the mechanism involving concurrent nucleotide binding and release. During the main substep, our simulations show no significant opening of the ATP-bound β subunit; instead, we observe that mechanical energy is transmitted to its nucleotide binding site, thus lowering the affinity for ATP. Simultaneously, the empty subunit assumes a conformation that enables the enzyme to harness the free energy of ADP binding to drive ATP release. Finally, we show that ligand exchange is regulated by a checkpoint mechanism, an apparent prerequisite for high efficiency in protein nanomotors.
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Affiliation(s)
- Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Bartosz Prokopowicz
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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34
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Vershubskii AV, Trubitsin BV, Priklonskii VI, Tikhonov AN. Lateral heterogeneity of the proton potential along the thylakoid membranes of chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:388-401. [DOI: 10.1016/j.bbamem.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/20/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023]
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35
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Turina P, Petersen J, Gräber P. Thermodynamics of proton transport coupled ATP synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:653-64. [PMID: 26940516 DOI: 10.1016/j.bbabio.2016.02.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 01/16/2016] [Accepted: 02/28/2016] [Indexed: 10/22/2022]
Abstract
The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°(ref)=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pH(in) or pH(out)) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F(0) to the catalytic nucleotide binding sites on the β-subunits in F(1), is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase.
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Affiliation(s)
- Paola Turina
- Department of Biology, BiGeA, University of Bologna, Via Irnerio 42, I-40126 Bologna, Italy
| | - Jan Petersen
- Biomedicine Discovery Institute, Monash University, 1 Wellington Rd., Clayton, Vic 3800, Australia
| | - Peter Gräber
- Institut für Physikalische Chemie, University of Freiburg, Albertstr, 23a, D-79104 Freiburg, Germany.
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36
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Feng X, Jia Y, Cai P, Fei J, Li J. Coassembly of Photosystem II and ATPase as Artificial Chloroplast for Light-Driven ATP Synthesis. ACS NANO 2016; 10:556-61. [PMID: 26615669 DOI: 10.1021/acsnano.5b05579] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Adenosine triphosphate (ATP) is one of the most important energy sources in living cells, which can drive serial key biochemical processes. However, generation of a proton gradient for ATP production in an artificial way poses a great challenge. In nature, photophosphorylation occurring in chloroplasts is an ideal prototype of ATP production. In this paper we imitate the light-to-ATP conversion process occurring in the thylakoid membrane by construction of FoF1-ATPase proteoliposome-coated PSII-based microspheres with well-defined core@shell structures using molecular assembly. Under light illumination, PSII can split water into protons, oxygen, and electrons and can generate a proton gradient for ATPase to produce ATP. Thus, an artificially designed chloroplast for PSII-driven ATP synthesis is realized. This biomimetic system will help to understand the photophosphorylation process and may facilitate the development of ATP-driven devices by remote light control.
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Affiliation(s)
- Xiyun Feng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Peng Cai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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37
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ATP hydrolysis assists phosphate release and promotes reaction ordering in F1-ATPase. Nat Commun 2015; 6:10223. [PMID: 26678797 PMCID: PMC4703894 DOI: 10.1038/ncomms10223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 11/16/2015] [Indexed: 12/28/2022] Open
Abstract
F1-ATPase (F1) is a rotary motor protein that can efficiently convert chemical energy to mechanical work of rotation via fine coordination of its conformational motions and reaction sequences. Compared with reactant binding and product release, the ATP hydrolysis has relatively little contributions to the torque and chemical energy generation. To scrutinize possible roles of ATP hydrolysis, we investigate the detailed statistics of the catalytic dwells from high-speed single wild-type F1 observations. Here we report a small rotation during the catalytic dwell triggered by the ATP hydrolysis that is indiscernible in previous studies. Moreover, we find in freely rotating F1 that ATP hydrolysis is followed by the release of inorganic phosphate with low synthesis rates. Finally, we propose functional roles of the ATP hydrolysis as a key to kinetically unlock the subsequent phosphate release and promote the correct reaction ordering.
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38
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von Ballmoos C, Biner O, Nilsson T, Brzezinski P. Mimicking respiratory phosphorylation using purified enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:321-31. [PMID: 26707617 DOI: 10.1016/j.bbabio.2015.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/17/2015] [Accepted: 12/16/2015] [Indexed: 11/26/2022]
Abstract
The enzymes of oxidative phosphorylation is a striking example of the functional association of multiple enzyme complexes, working together to form ATP from cellular reducing equivalents. These complexes, such as cytochrome c oxidase or the ATP synthase, are typically investigated individually and therefore, their functional interplay is not well understood. Here, we present methodology that allows the co-reconstitution of purified terminal oxidases and ATP synthases in synthetic liposomes. The enzymes are functionally coupled via proton translocation where upon addition of reducing equivalents the oxidase creates and maintains a transmembrane electrochemical proton gradient that energizes the synthesis of ATP by the F1F0 ATP synthase. The method has been tested with the ATP synthases from Escherichia coli and spinach chloroplasts, and with the quinol and cytochrome c oxidases from E. coli and Rhodobacter sphaeroides, respectively. Unlike in experiments with the ATP synthase reconstituted alone, the setup allows in vitro ATP synthesis under steady state conditions, with rates up to 90 ATP×s(-1)×enzyme(-1). We have also used the novel system to study the phenomenon of "mild uncoupling" as observed in mitochondria upon addition of low concentrations of ionophores (e.g. FCCP, SF6847) and the recoupling effect of 6-ketocholestanol. While we could reproduce the described effects, our data with the in vitro system does not support the idea of a direct interaction between a mitochondrial protein and the uncoupling agents as proposed earlier.
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Affiliation(s)
- Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | - Olivier Biner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tobias Nilsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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39
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Yang JH, Sarrou I, Martin-Garcia JM, Zhang S, Redding KE, Fromme P. Purification and biochemical characterization of the ATP synthase from Heliobacterium modesticaldum. Protein Expr Purif 2015; 114:1-8. [PMID: 25979464 DOI: 10.1016/j.pep.2015.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 11/26/2022]
Abstract
Heliobacterium modesticaldum is an anaerobic photosynthetic bacterium that grows optimally at pH 6-7 and 52°C and is the only phototrophic member of the Firmicutes phylum family (gram-positive bacteria with low GC content). The ATP synthase of H. modesticaldum was isolated and characterized at the biochemical and biophysical levels. The isolated holoenzyme exhibited the subunit patterns of F-type ATP synthases containing a 5-subunit hydrophilic F1 subcomplex and a 3-subunit hydrophobic F0 subcomplex. ATP hydrolysis by the isolated HF1F0 ATP synthase was successfully detected after pretreatment with different detergents by an in-gel ATPase activity assay, which showed that the highest activity was detected in the presence of mild detergents such as LDAO; moreover, high catalytic activity in the gel was already detected after the initial incubation period of 0.5h. In contrast, HF1F0 showed extremely low ATPase activity in harsher detergents such as TODC. The isolated fully functional enzyme will form the basis for future structural studies.
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Affiliation(s)
- Jay-How Yang
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Iosifina Sarrou
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology-Hellas, Nikolaou Plastira 100, GR-70013 Heraklion, Crete, Greece
| | - Jose M Martin-Garcia
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Shangji Zhang
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Kevin E Redding
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Petra Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA.
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40
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Effects of thermodynamically coupled reaction diffusion in microalgae growth and lipid accumulation: Model development and stability analysis. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2015.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Martin J, Hudson J, Hornung T, Frasch WD. Fo-driven Rotation in the ATP Synthase Direction against the Force of F1 ATPase in the FoF1 ATP Synthase. J Biol Chem 2015; 290:10717-28. [PMID: 25713065 DOI: 10.1074/jbc.m115.646430] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 11/06/2022] Open
Abstract
Living organisms rely on the FoF1 ATP synthase to maintain the non-equilibrium chemical gradient of ATP to ADP and phosphate that provides the primary energy source for cellular processes. How the Fo motor uses a transmembrane electrochemical ion gradient to create clockwise torque that overcomes F1 ATPase-driven counterclockwise torque at high ATP is a major unresolved question. Using single FoF1 molecules embedded in lipid bilayer nanodiscs, we now report the observation of Fo-dependent rotation of the c10 ring in the ATP synthase (clockwise) direction against the counterclockwise force of ATPase-driven rotation that occurs upon formation of a leash with Fo stator subunit a. Mutational studies indicate that the leash is important for ATP synthase activity and support a mechanism in which residues aGlu-196 and cArg-50 participate in the cytoplasmic proton half-channel to promote leash formation.
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Affiliation(s)
- James Martin
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Jennifer Hudson
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Tassilo Hornung
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
| | - Wayne D Frasch
- From the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501
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Kasumov EA, Kasumov RE, Kasumova IV. A mechano-chemiosmotic model for the coupling of electron and proton transfer to ATP synthesis in energy-transforming membranes: a personal perspective. PHOTOSYNTHESIS RESEARCH 2015; 123:1-22. [PMID: 25266924 PMCID: PMC4272416 DOI: 10.1007/s11120-014-0043-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 09/18/2014] [Indexed: 05/03/2023]
Abstract
ATP is synthesized using ATP synthase by utilizing energy either from the oxidation of organic compounds, or from light, via redox reactions (oxidative- or photo phosphorylation), in energy-transforming membranes of mitochondria, chloroplasts, and bacteria. ATP synthase undergoes several changes during its functioning. The generally accepted model for ATP synthesis is the well-known rotatory model (see e.g., Junge et al., Nature 459:364-370, 2009; Junge and Müller, Science 333:704-705, 2011). Here, we present an alternative modified model for the coupling of electron and proton transfer to ATP synthesis, which was initially developed by Albert Lester Lehninger (1917-1986). Details of the molecular mechanism of ATP synthesis are described here that involves cyclic low-amplitude shrinkage and swelling of mitochondria. A comparison of the well-known current model and the mechano-chemiosmotic model is also presented. Based on structural, and other data, we suggest that ATP synthase is a Ca(2+)/H(+)-K(+) Cl(-)-pump-pore-enzyme complex, in which γ-subunit rotates 360° in steps of 30°, and 90° due to the binding of phosphate ions to positively charged amino acid residues in the N-terminal γ-subunit, while in the electric field. The coiled coil b 2-subunits are suggested to act as ropes that are shortened by binding of phosphate ions to positively charged lysines or arginines; this process is suggested to pull the α 3 β 3-hexamer to the membrane during the energization process. ATP is then synthesized during the reverse rotation of the γ-subunit by destabilizing the phosphated N-terminal γ-subunit and b 2-subunits under the influence of Ca(2+) ions, which are pumped over from storage-intermembrane space into the matrix, during swelling of intermembrane space. In the process of ATP synthesis, energy is first, predominantly, used in the delivery of phosphate ions and protons to the α 3 β 3-hexamer against the energy barrier with the help of C-terminal alpha-helix of γ-subunit that acts as a lift; then, in the formation of phosphoryl group; and lastly, in the release of ATP molecules from the active center of the enzyme and the loading of ADP. We are aware that our model is not an accepted model for ATP synthesis, but it is presented here for further examination and test.
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Affiliation(s)
- Eldar A Kasumov
- Research and Production Centre «KORVET», Moscow Region, Domodedovo, Russia,
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Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity. Nat Commun 2014; 5:4519. [PMID: 25058452 PMCID: PMC4124872 DOI: 10.1038/ncomms5519] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/25/2014] [Indexed: 11/09/2022] Open
Abstract
Nano- to micron-size reaction chamber arrays (femtolitre chamber arrays) have facilitated the development of sensitive and quantitative biological assays, such as single-molecule enzymatic assays, digital PCR and digital ELISA. However, the versatility of femtolitre chamber arrays is limited to reactions that occur in aqueous solutions. Here we report an arrayed lipid bilayer chamber system (ALBiC) that contains sub-million femtolitre chambers, each sealed with a stable 4-μm-diameter lipid bilayer membrane. When reconstituted with a limiting amount of the membrane transporter proteins α-hemolysin or F0F1-ATP synthase, the chambers within the ALBiC exhibit stochastic and quantized transporting activities. This demonstrates that the single-molecule analysis of passive and active membrane transport is achievable with the ALBiC system. This new platform broadens the versatility of femtolitre chamber arrays and paves the way for novel applications aimed at furthering our mechanistic understanding of membrane proteins' function.
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Arnold A, Nikoloski Z. Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PLANT PHYSIOLOGY 2014; 165:1380-1391. [PMID: 24808102 PMCID: PMC4081344 DOI: 10.1104/pp.114.235358] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/12/2014] [Indexed: 05/07/2023]
Abstract
Large-scale modeling of plant metabolism provides the possibility to compare and contrast different cellular and environmental scenarios with the ultimate aim of identifying the components underlying the respective plant behavior. The existing models of Arabidopsis (Arabidopsis thaliana) are top-down assembled, whereby the starting point is the annotated genome, in particular, the metabolic genes. Hence, dead-end metabolites and blocked reactions can arise that are subsequently addressed by using gap-filling algorithms in combination with species-unspecific genes. Here, we present a bottom-up-assembled, large-scale model that relies solely on Arabidopsis-specific annotations and results in the inclusion of only manually curated reactions. While the existing models are largely condition unspecific by employing a single biomass reaction, we provide three biomass compositions that pertain to realistic and frequently examined scenarios: carbon-limiting, nitrogen-limiting, and optimal growth conditions. The comparative analysis indicates that the proposed Arabidopsis core model exhibits comparable efficiency in carbon utilization and flexibility to the existing network alternatives. Moreover, the model is utilized to quantify the energy demand of amino acid and enzyme de novo synthesis in photoautotrophic growth conditions. Illustrated by the case of the most abundant protein in the world, Rubisco, we determine its synthesis cost in terms of ATP requirements. This, in turn, allows us to explore the tradeoff between protein synthesis and growth in Arabidopsis. Altogether, the model provides a solid basis for completely species-specific integration of high-throughput data, such as gene expression levels, and for condition-specific investigations of in silico metabolic engineering strategies.
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Affiliation(s)
- Anne Arnold
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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Photocurrent generation based on a light-driven proton pump in an artificial liquid membrane. Nat Chem 2014; 6:202-7. [DOI: 10.1038/nchem.1858] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 12/17/2013] [Indexed: 12/23/2022]
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Hypothesis of lipid-phase-continuity proton transfer for aerobic ATP synthesis. J Cereb Blood Flow Metab 2013; 33:1838-42. [PMID: 24084698 PMCID: PMC3851912 DOI: 10.1038/jcbfm.2013.175] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 09/09/2013] [Accepted: 09/12/2013] [Indexed: 12/12/2022]
Abstract
The basic processes harvesting chemical energy for life are driven by proton (H(+)) movements. These are accomplished by the mitochondrial redox complex V, integral membrane supramolecular aggregates, whose structure has recently been described by advanced studies. These did not identify classical aqueous pores. It was proposed that H(+) transfer for oxidative phosphorylation (OXPHOS) does not occur between aqueous sources and sinks, where an energy barrier would be insurmountable. This suggests a novel hypothesis for the proton transfer. A lipid-phase-continuity H(+) transfer is proposed in which H(+) are always bound to phospholipid heads and cardiolipin, according to Mitchell's hypothesis of asymmetric vectorial H(+) diffusion. A phase separation is proposed among the proton flow, following an intramembrane pathway, and the ATP synthesis, occurring in the aqueous phase. This view reminiscent of Grotthus mechanism would better account for the distance among the Fo and F1 moieties of FoF1-ATP synthase, for its mechanical coupling, as well as the necessity of a lipid membrane. A unique active role for lipids in the evolution of life can be envisaged. Interestingly, this view would also be consistent with the evidence of an OXPHOS outside mitochondria also found in non-vesicular membranes, housing the redox complexes.
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Lucker B, Kramer DM. Regulation of cyclic electron flow in Chlamydomonas reinhardtii under fluctuating carbon availability. PHOTOSYNTHESIS RESEARCH 2013; 117:449-59. [PMID: 24113925 DOI: 10.1007/s11120-013-9932-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/24/2013] [Indexed: 05/08/2023]
Abstract
The chloroplast must rapidly and precisely adjust photosynthetic ATP and NADPH output to meet changing metabolic demands imposed by fluctuating environmental conditions. Cyclic electron flow (CEF) around photosystem I is thought to contribute to this adjustment by providing ATP in excess of that supplied by linear electron low, balancing chloroplast energy budget when relative demand for ATP is high. We assessed the kinetics and energy production of CEF activation in Chlamydomonas reinhardtii under rapid changes of organic and inorganic carbon availability. Comparisons of transient electric field and chlorophyll fluorescence measurements indicated CEF was activated under conditions where ATP demand is expected to be high, consistent with a role in balancing the cellular ATP/NADPH budget under fluctuating environmental or metabolic conditions. CEF activation was not correlated with antenna state transitions, both in wild-type and the state transition mutant stt7-9, suggesting that CEF is rapidly regulated by allosteric or redox modulators. Comparing the CEF under ambient and high CO2 conditions suggests an increase in required energy output of approximately 1ATP/CO2 fixed, nearly sufficient to power proposed mechanistic models for the carbon-concentrating mechanism. Additionally, we see three-fold higher CEF rates in cells under steady-state conditions than cells under similar conditions with inhibited photosystem II, and up to five times higher in cells with severe depletion of inorganic carbon, implying that CEF has larger energetic capacity than predicted from some previous work.
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Affiliation(s)
- Ben Lucker
- DOE-Plant Research Laboratory, Michigan State University, S222 Plant Biology Building, East Lansing, MI, 48824-1312, USA
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Subramanian S, Barry AN, Pieris S, Sayre RT. Comparative energetics and kinetics of autotrophic lipid and starch metabolism in chlorophytic microalgae: implications for biomass and biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:150. [PMID: 24139286 PMCID: PMC4015678 DOI: 10.1186/1754-6834-6-150] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/12/2013] [Indexed: 05/03/2023]
Abstract
Due to the growing need to provide alternatives to fossil fuels as efficiently, economically, and sustainably as possible there has been growing interest in improved biofuel production systems. Biofuels produced from microalgae are a particularly attractive option since microalgae have production potentials that exceed the best terrestrial crops by 2 to 10-fold. In addition, autotrophically grown microalgae can capture CO2 from point sources reducing direct atmospheric greenhouse gas emissions. The enhanced biomass production potential of algae is attributed in part to the fact that every cell is photosynthetic. Regardless, overall biological energy capture, conversion, and storage in microalgae are inefficient with less than 8% conversion of solar into chemical energy achieved. In this review, we examine the thermodynamic and kinetic constraints associated with the autotrophic conversion of inorganic carbon into storage carbohydrate and oil, the dominant energy storage products in Chlorophytic microalgae. We discuss how thermodynamic restrictions including the loss of fixed carbon during acetyl CoA synthesis reduce the efficiency of carbon accumulation in lipids. In addition, kinetic limitations, such as the coupling of proton to electron transfer during plastoquinone reduction and oxidation and the slow rates of CO2 fixation by Rubisco reduce photosynthetic efficiency. In some cases, these kinetic limitations have been overcome by massive increases in the numbers of effective catalytic sites, e.g. the high Rubisco levels (mM) in chloroplasts. But in other cases, including the slow rate of plastoquinol oxidation, there has been no compensatory increase in the abundance of catalytically limiting protein complexes. Significantly, we show that the energetic requirements for producing oil and starch relative to the recoverable energy stored in these molecules are very similar on a per carbon basis. Presently, the overall rates of starch and lipid synthesis in microalgae are very poorly characterized. Increased understanding of the kinetic constraints of lipid and starch synthesis, accumulation and turnover would facilitate the design of improved biomass production systems.
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Affiliation(s)
| | - Amanda N Barry
- Bioscience Division, Los Alamos National Lab, M888, Los Alamos, NM 87545, USA
| | - Shayani Pieris
- Natural Sciences Division, Missouri Baptist University, One College Park Drive, St. Louis, MO 63141, USA
| | - Richard T Sayre
- New Mexico Consortium, 100 Entrada Rd., Los Alamos, NM 87544, USA
- Bioscience Division, Los Alamos National Lab, M888, Los Alamos, NM 87545, USA
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Watanabe R. Rotary catalysis of FoF1-ATP synthase. Biophysics (Nagoya-shi) 2013; 9:51-6. [PMID: 27493540 PMCID: PMC4629669 DOI: 10.2142/biophysics.9.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/22/2013] [Indexed: 12/01/2022] Open
Abstract
The synthesis of ATP, the key reaction of biological energy metabolism, is accomplished by the rotary motor protein; FoF1-ATP synthase (FoF1). In vivo, FoF1, located on the cell membrane, carries out ATP synthesis by using the proton motive force. This heterologous energy conversion is supposed to be mediated by the mechanical rotation of FoF1; however, it still remained unclear. Recently, we developed the novel experimental setup to reproduce the proton motive force in vitro and succeeded in directly observing the proton-driven rotation of FoF1. In this review, we describe the interesting working principles determined so far for FoF1 and then introduce results from our recent study.
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Affiliation(s)
- Rikiya Watanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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Börsch M. Microscopy of single F(o) F(1) -ATP synthases--the unraveling of motors, gears, and controls. IUBMB Life 2013; 65:227-37. [PMID: 23378185 DOI: 10.1002/iub.1149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/12/2013] [Indexed: 11/09/2022]
Abstract
Optical microscopy of single F(1) -ATPase and F(o) F(1) -ATP synthases started 15 years ago. Direct demonstration of ATP-driven subunit rotation by videomicroscopy became the new exciting tool to analyze the conformational changes of this enzyme during catalysis. Stimulated by these experiments, technical improvements for higher time resolution, better angular resolution, and reduced viscous drag were developed rapidly. Optics and single-molecule enzymology were entangled to benefit both biochemists and microscopists. Today, several single-molecule microscopy methods are established including controls for the precise nanomanipulation of individual enzymes in vitro. Förster resonance energy transfer, which has been used for simultaneous monitoring of conformational changes of different parts of this rotary motor, is one of them and may become the tool for the analysis of single F(o) F(1) -ATP synthases in membranes of living cells. Here, breakthrough experiments are critically reviewed and challenges are discussed for the future microscopy of single ATP synthesizing enzymes at work.
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Affiliation(s)
- Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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