1
|
Shi J, Tian F, Ren J, Li R, Yang M, Li W. Diesel exhaust particulate matter induces GC-1 spg cells oxidative stress by KEAP1-NRF2 pathway and inhibition of ATP5α1 S-sulfhydration. Food Chem Toxicol 2024; 189:114746. [PMID: 38768936 DOI: 10.1016/j.fct.2024.114746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/10/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
Diesel exhaust particle (DEP) exposure induces a variety of toxicological effects through oxidative stress and inflammation responses. This research investigated the mechanisms underlying DEP-induced GC-1spg cells oxidative stress by examining ROS accumulation, antioxidant defense systems activation, mitochondrial dysfunction, and the Nrf2/Keap1/HO-1 pathway response. Subsequently, we further evaluated the ATP levels, ATP5α synthase activity and ATP5α synthase S-sulfhydrated modification in DEP-exposed GC-1 spg cells. The results showed that DEP exposure significantly inhibited cell proliferation and viability, increased intracellular ROS production, decreased MMP, down-regulated antioxidant capacity, activated the Nrf2/Keap1/HO-1 pathway. However, DEP-induced oxidative stress was partially alleviated by GSH and exogenous H2S. In addition, DEP exposure induced ATP depletion and ATP5α synthase inactivity in GC-1 spg cells, accompanied by ATP5α synthase S-sulfhydrated modification. In conclusion, our research showed that DEP may incapacitate mitochondria through oxidative stress injury, leading to GC-1 spg cells oxidative stress. This process may be associated with the reduction of ATP5α1 S-sulfhydrated modification. It provides a new perspective for the research of the mechanism related to male reproductive toxicity due to air pollution.
Collapse
Affiliation(s)
- Jiayi Shi
- Department of Environmental Health, School of Public Health, Fudan University, Shanghai, 200032, China; NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Fang Tian
- NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jianke Ren
- NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Runsheng Li
- NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Mingjun Yang
- NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Weihua Li
- NHC Key Lab of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drugs and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| |
Collapse
|
2
|
Guerin MN, Ellis T, Ware MJ, Manning A, Coley A, Amini A, Chung G, Gunsalus KC, Bracht JR. Evolution of a biological thermocouple by adaptation of cytochrome c oxidase in a subterrestrial metazoan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570156. [PMID: 38106155 PMCID: PMC10723328 DOI: 10.1101/2023.12.05.570156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
In this study we report a naturally evolved temperature-sensing electrical regulator in the cytochrome c oxidase of the Devil Worm, Halicephalobus mephisto. This extremophile metazoan was isolated 1.3 km underground in a South African goldmine, where it adapted to heat and potentially to hypoxia, making its mitochondrial sequence a likely target of adaptational change. We obtained the full mitochondrial genome sequence of this organism, and show through dN/dS analysis statistically robust evidence of positive selection in H. mephisto cytochrome c oxidase subunits. Seventeen of these positively-selected amino acid substitutions were localized in proximity to the H- and K-pathway proton channels of the complex. Surprisingly, the H. mephisto cytochrome c oxidase proton pump completely shuts down at low temperatures (20°C) leading to approximately a 4.8-fold reduction in the transmembrane proton gradient voltage (ΔΨm) compared to optimal temperature (37°C). Direct measurement of oxygen consumption found a corresponding 4.7-fold drop at 20°C compared to 37°C. Correspondingly, the lifecycle of H. mephisto takes four-fold longer at the low temperature compared to higher. This elegant evolutionary adaptation creates a finely-tuned mitochondrial temperature sensor, allowing this ectothermic organism to maximize its reproductive success in varying environmental temperatures. Our study shows that evolutionary innovation may remodel core metabolism to make it more accurately map onto environmental variation.
Collapse
Affiliation(s)
- Megan N Guerin
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - TreVaughn Ellis
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Mark J Ware
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Alexandra Manning
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Ariana Coley
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - Ali Amini
- American University Mathematics and Statistics Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| | - George Chung
- New York University, Center for Genomics and Systems Biology, New York, NY 10003
| | - Kristin C Gunsalus
- New York University, Center for Genomics and Systems Biology, New York, NY 10003
| | - John R Bracht
- American University Biology Department, 4400 Massachusetts Avenue, NW, Washington, DC, United States, 20016
| |
Collapse
|
3
|
Amos A, Amos A, Wu L, Xia H. The Warburg effect modulates DHODH role in ferroptosis: a review. Cell Commun Signal 2023; 21:100. [PMID: 37147673 PMCID: PMC10161480 DOI: 10.1186/s12964-022-01025-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/22/2022] [Indexed: 05/07/2023] Open
Abstract
Ferroptosis is an iron-dependent regulated cell death that suppresses tumor growth. It is activated by extensive peroxidation of membrane phospholipids caused by oxidative stress. GPX4, an antioxidant enzyme, reduces these peroxidized membrane phospholipids thereby inhibiting ferroptosis. This enzyme has two distinct subcellular localization; the cytosol and mitochondria. Dihydroorotate dehydrogenase (DHODH) complements mitochondrial GPX4 in reducing peroxidized membrane phospholipids. It is the rate-limiting enzyme in de novo pyrimidine nucleotide biosynthesis. Its role in ferroptosis inhibition suggests that DHODH inhibitors could have two complementary mechanisms of action against tumors; inhibiting de novo pyrimidine nucleotide biosynthesis and enhancing ferroptosis. However, the link between mitochondrial function and ferroptosis, and the involvement of DHODH in the ETC suggests that its role in ferroptosis could be modulated by the Warburg effect. Therefore, we reviewed relevant literature to get an insight into the possible effect of this metabolic reprogramming on the role of DHODH in ferroptosis. Furthermore, an emerging link between DHODH and cellular GSH pool has also been highlighted. These insights could contribute to the rational design of ferroptosis-based anticancer drugs. Video Abstract.
Collapse
Affiliation(s)
- Alvan Amos
- Department of Radiation Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting Road, Nanjing, 210009, China
- Department of Biochemistry, Faculty of Science, Kaduna State University, PMB 2339 Tafawa Balewa Way, Kaduna, Nigeria
| | - Alex Amos
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Ahmadu Bello University Zaria, Zaria, Nigeria
| | - Lirong Wu
- Department of Radiation Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting Road, Nanjing, 210009, China
| | - He Xia
- Department of Radiation Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, 42 Baiziting Road, Nanjing, 210009, China.
| |
Collapse
|
4
|
Stuchebrukhov AA, Hayashi T. Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping. FEBS Lett 2023; 597:237-245. [PMID: 36251339 PMCID: PMC9877130 DOI: 10.1002/1873-3468.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023]
Abstract
Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.
Collapse
Affiliation(s)
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, Davis, CA 95616
| |
Collapse
|
5
|
Wang P, Leontyev I, Stuchebrukhov AA. Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I. J Phys Chem B 2022; 126:4080-4088. [PMID: 35612955 DOI: 10.1021/acs.jpcb.2c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.
Collapse
Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Igor Leontyev
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
6
|
Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site. Photochem Photobiol Sci 2021; 21:1-12. [PMID: 34813075 PMCID: PMC8799541 DOI: 10.1007/s43630-021-00113-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/04/2021] [Indexed: 02/02/2023]
Abstract
At the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction—due to a need for a rare opening of the bottleneck—of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction.
Collapse
|
7
|
Kaur D, Khaniya U, Zhang Y, Gunner MR. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient. Front Chem 2021; 9:660954. [PMID: 34211960 PMCID: PMC8239185 DOI: 10.3389/fchem.2021.660954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.
Collapse
Affiliation(s)
- Divya Kaur
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| | - M R Gunner
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Department of Physics, City College of New York, New York, NY, United States.,Department of Physics, The Graduate Center, City University of New York, New York, NY, United States
| |
Collapse
|
8
|
Lin TK, Lin KJ, Lin KL, Liou CW, Chen SD, Chuang YC, Wang PW, Chuang JH, Wang TJ. When Friendship Turns Sour: Effective Communication Between Mitochondria and Intracellular Organelles in Parkinson's Disease. Front Cell Dev Biol 2020; 8:607392. [PMID: 33330511 PMCID: PMC7733999 DOI: 10.3389/fcell.2020.607392] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease with pathological hallmarks including progressive neuronal loss from the substantia nigra pars compacta and α-synuclein intraneuronal inclusions, known as Lewy bodies. Although the etiology of PD remains elusive, mitochondrial damage has been established to take center stage in the pathogenesis of PD. Mitochondria are critical to cellular energy production, metabolism, homeostasis, and stress responses; the association with PD emphasizes the importance of maintenance of mitochondrial network integrity. To accomplish the pleiotropic functions, mitochondria are dynamic not only within their own network but also in orchestrated coordination with other organelles in the cellular community. Through physical contact sites, signal transduction, and vesicle transport, mitochondria and intracellular organelles achieve the goals of calcium homeostasis, redox homeostasis, protein homeostasis, autophagy, and apoptosis. Herein, we review the finely tuned interactions between mitochondria and surrounding intracellular organelles, with focus on the nucleus, endoplasmic reticulum, Golgi apparatus, peroxisomes, and lysosomes. Participants that may contribute to the pathogenic mechanisms of PD will be highlighted in this review.
Collapse
Affiliation(s)
- Tsu-Kung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Jung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Lieh Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shang-Der Chen
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yao-Chung Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Center of Parkinson's Disease, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Wen Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Metabolism, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jiin-Haur Chuang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tzu-Jou Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Pediatric, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| |
Collapse
|
9
|
Wang P, Dhananjayan N, Hagras MA, Stuchebrukhov AA. Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148326. [PMID: 33045211 DOI: 10.1016/j.bbabio.2020.148326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022]
Abstract
The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.
Collapse
Affiliation(s)
- Panyue Wang
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Nithin Dhananjayan
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Muhammad A Hagras
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America
| | - Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, CA 95616, United States of America.
| |
Collapse
|
10
|
Palese LL. Explaining leak states in the proton pump of heme-copper oxidases observed in single-molecule experiments. Biophys Chem 2019; 256:106276. [PMID: 31731070 DOI: 10.1016/j.bpc.2019.106276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 11/28/2022]
Abstract
Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Generally, these models associate, more or less directly, all translocation events with redox transitions. Although they can account for many phenomenological aspects of the pump, evidences from single-molecules experiments about leak states of the pump represent a formidable challenge. Disconnecting the redox-linked pKa shifts of the proton loading site from the external barriers, we obtain a simple stochastic mechanism which behaves similarly to the real enzyme, able to reverse the flow of the proton transfer.
Collapse
|
11
|
Abstract
Complexes I to IV, with the exception of Complex II, are redox-driven proton pumps that convert redox energy of oxygen reduction to proton gradient across the mitochondrial or bacterial membrane; in turn, the created electrochemical gradient drives the adenosine triphosphate synthesis in the cells by utilizing complex V of the chain. Here we address a general question of the efficiency of such enzymes, considering them as molecular machines that couple endergonic and exergonic reactions and converting one form of free energy into another. One well-known example of the efficiency is given by Carnot's theorem for heat engines. Here we extend the concept to respiratory enzymes and specifically focus on the proton pumping by Complex I of the respiratory chain, nicotinamide adenine dinucleotide dehydrogenase. To discuss the efficiency issues, we develop a model of enzyme kinetics, which generalizes the Michaelis-Menten model. Our model includes several substrates and products and, in general, can be considered as Generalized Michaelis-Menten Kinetic model. The model might be useful for describing complex enzyme kinetics, regardless of the efficiency issues that are addressed in this paper.
Collapse
Affiliation(s)
- Alexei A Stuchebrukhov
- Department of Chemistry , University of California at Davis , Davis , California 95616 , United States
| |
Collapse
|
12
|
Zhao M, Liu Y, Su B. Anomalous Proton Transport across Silica Nanochannel Membranes Investigated by Ion Conductance Measurements. Anal Chem 2019; 91:13433-13438. [DOI: 10.1021/acs.analchem.9b01914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meijiao Zhao
- Department of Chemistry, Institute of Analytical Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yanhuan Liu
- Department of Chemistry, Institute of Analytical Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Bin Su
- Department of Chemistry, Institute of Analytical Chemistry, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
13
|
Maróti P. Thermodynamic View of Proton Activated Electron Transfer in the Reaction Center of Photosynthetic Bacteria. J Phys Chem B 2019; 123:5463-5473. [PMID: 31181159 DOI: 10.1021/acs.jpcb.9b03506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The temperature dependence of the sequential coupling of proton transfer to the second interquinone electron transfer is studied in the reaction center proteins of photosynthetic bacteria modified by different mutations and treatment by divalent cations. The Eyring plots of kinetics were evaluated by the Marcus theory of electron and proton transfer. In mutants of electron transfer limitation (including the wild type), the observed thermodynamic parameters had to be corrected for those of the fast proton pre-equilibrium. The electron transfer is nonadiabatic with transmission coefficient 6 × 10-4, and the reorganization energy amounts to 1.2 eV. If the proton transfer is the rate limiting step, the reorganization energy and the works terms fall in the range of 200-500 meV, depending on the site of damage in the proton transfer chain. The product term is 100-150 meV larger than the reactant term. While the electron transfer mutants have a low free energy of activation (∼200 meV), the proton transfer variants show significantly elevated levels of the free energy barrier (∼500 meV). The second electron transfer in the bacterial reaction center can serve as a model system of coupled electron and proton transfer in other proteins or ion channels.
Collapse
Affiliation(s)
- Péter Maróti
- Institute of Medical Physics , University of Szeged , Rerrich Béla tér 1 , Szeged , H-6720 , Hungary
| |
Collapse
|
14
|
Hagras MA, Stuchebrukhov AA. Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I. J Phys Chem B 2019; 123:5265-5273. [DOI: 10.1021/acs.jpcb.9b04082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|