1
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Kaur G, Ravikanth M. Synthesis of triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers and bis-Re(I) triphyrin dimer complex. Dalton Trans 2024. [PMID: 39022912 DOI: 10.1039/d4dt01448k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
First examples of covalently linked triphyrin(2.1.1)-triphyrin(2.1.1) homo dimers connected via flexible alkoxy linkers at β-pyrrole positions were synthesized in 28-30% yields by reacting 2-bromo triphyrin(2.1.1) with three different alkane diols such as 1,2-ethanediol, 1,4-butanediol and 1,6-hexanediol in toluene under Pd2(dba)3/DPEphos catalyzed conditions by refluxing for 12-20 h. One of the free base triphyrin-triphyrin homo dimers was metallated by treating the homo dimer with Re(CO)5Cl in toluene under reflux and afforded bis-Re(I) homo dimer complex in 53% yield. Three free base homo dimers and one bis-Re(I) homo dimer complex were thoroughly characterized and studied using HR-MS, 1D and 2D NMR, absorption spectroscopy, cyclic voltammetry and DFT calculations. Our attempts to obtain the X-ray structure of homo dimers were not successful. However, DFT studies revealed that homo dimers prefer to exist in anti-conformation rather than syn-conformation and both triphyrin macrocycles in homo dimers were similar in terms of the deviation of pyrrole rings from the mean plane defined by the four meso carbons of the respective triphyrin unit. Absorption spectra of homo dimers showed similar absorption features such as in triphyrin(2.1.1) with slight changes in their absorption peak maxima. Electrochemical studies revealed that the homo dimers were electron rich, whereas the bis-Re(I) complex was electron deficient in nature.
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Affiliation(s)
- Gurpreet Kaur
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Mangalampalli Ravikanth
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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2
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Han Z, Wang Z, Rittschof D, Huang Z, Chen L, Hao H, Yao S, Su P, Huang M, Zhang YY, Ke C, Feng D. New genes helped acorn barnacles adapt to a sessile lifestyle. Nat Genet 2024; 56:970-981. [PMID: 38654131 DOI: 10.1038/s41588-024-01733-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.
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Affiliation(s)
- Zhaofang Han
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixuan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Daniel Rittschof
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liying Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huanhuan Hao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Shanshan Yao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Pei Su
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Danqing Feng
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China.
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3
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Cellini A, Shankar MK, Nimmrich A, Hunt LA, Monrroy L, Mutisya J, Furrer A, Beale EV, Carrillo M, Malla TN, Maj P, Vrhovac L, Dworkowski F, Cirelli C, Johnson PJM, Ozerov D, Stojković EA, Hammarström L, Bacellar C, Standfuss J, Maj M, Schmidt M, Weinert T, Ihalainen JA, Wahlgren WY, Westenhoff S. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Nat Chem 2024; 16:624-632. [PMID: 38225270 PMCID: PMC10997514 DOI: 10.1038/s41557-023-01413-9] [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: 01/18/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024]
Abstract
Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Leigh Anna Hunt
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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4
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Wang Y, Paidi VK, Wang W, Wang Y, Jia G, Yan T, Cui X, Cai S, Zhao J, Lee KS, Lee LYS, Wong KY. Spatial engineering of single-atom Fe adjacent to Cu-assisted nanozymes for biomimetic O 2 activation. Nat Commun 2024; 15:2239. [PMID: 38472201 DOI: 10.1038/s41467-024-46528-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
The precise design of single-atom nanozymes (SAzymes) and understanding of their biocatalytic mechanisms hold great promise for developing ideal bio-enzyme substitutes. While considerable efforts have been directed towards mimicking partial bio-inspired structures, the integration of heterogeneous SAzymes configurations and homogeneous enzyme-like mechanism remains an enormous challenge. Here, we show a spatial engineering strategy to fabricate dual-sites SAzymes with atomic Fe active center and adjacent Cu sites. Compared to planar Fe-Cu dual-atomic sites, vertically stacked Fe-Cu geometry in FePc@2D-Cu-N-C possesses highly optimized scaffolds, favorable substrate affinity, and fast electron transfer. These characteristics of FePc@2D-Cu-N-C SAzyme induces biomimetic O2 activation through homogenous enzymatic pathway, resembling functional and mechanistic similarity to natural cytochrome c oxidase. Furthermore, it presents an appealing alternative of cytochrome P450 3A4 for drug metabolism and drug-drug interaction. These findings are expected to deepen the fundamental understanding of atomic-level design in next-generation bio-inspired nanozymes.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Vinod K Paidi
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble, 38043, Cedex 9, France
| | - Weizhen Wang
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Yong Wang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Guangri Jia
- State Key Laboratory of Automotive Simulation and Control, Department of Materials Science, Key Laboratory of Automobile Materials of MOE, Jilin University, Changchun, 130012, China
| | - Tingyu Yan
- Key Laboratory of Photonic and Electronic Bandgap Materials of MOE, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China
| | - Xiaoqiang Cui
- State Key Laboratory of Automotive Simulation and Control, Department of Materials Science, Key Laboratory of Automobile Materials of MOE, Jilin University, Changchun, 130012, China
| | - Songhua Cai
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Jingxiang Zhao
- Key Laboratory of Photonic and Electronic Bandgap Materials of MOE, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin, 150025, PR China.
| | - Kug-Seung Lee
- Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Lawrence Yoon Suk Lee
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
- Research Institute for Smart Energy, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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5
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Schauenburg D, Weil T. Chemical Reactions in Living Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303396. [PMID: 37679060 PMCID: PMC10885656 DOI: 10.1002/advs.202303396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The term "in vivo ("in the living") chemistry" refers to chemical reactions that take place in a complex living system such as cells, tissue, body liquids, or even in an entire organism. In contrast, reactions that occur generally outside living organisms in an artificial environment (e.g., in a test tube) are referred to as in vitro. Over the past decades, significant contributions have been made in this rapidly growing field of in vivo chemistry, but it is still not fully understood, which transformations proceed efficiently without the formation of by-products or how product formation in such complex environments can be characterized. Potential applications can be imagined that synthesize drug molecules directly within the cell or confer new cellular functions through controlled chemical transformations that will improve the understanding of living systems and develop new therapeutic strategies. The guiding principles of this contribution are twofold: 1) Which chemical reactions can be translated from the laboratory to the living system? 2) Which characterization methods are suitable for studying reactions and structure formation in complex living environments?
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Affiliation(s)
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert‐Einstein‐Allee 1189081UlmGermany
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6
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Huang W, Zhao Y, Zhang L, Shi Y, Wang Z, Mai Y, Shu L. Soil physical structure drives N-glycan mediated trophic interactions in soil amoebae: Mechanisms and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167509. [PMID: 37788775 DOI: 10.1016/j.scitotenv.2023.167509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Soil protozoa are an essential part of the terrestrial ecosystem, playing a vital role in the global element cycling and energy flow. However, one research gap is what are the key factors driving their diversity and environmental fates. In this study, we hypothesized that soil texture could affect soil protozoa's predation and their interactions with environmental pollutants, and we tested it by using a soil amoeba Dictyostelium discoideum as a model system. We found that soil texture affected amoeba's growth and development. In addition, environmental factors cannot explain the variation of amoeba's fitness in different soil textures. Soil sandy particles and water content rather than particle size contribute to amoeba's fitness. Furthermore, different soil textures induced distinct transcriptional responses to amoebae, especially N-glycan-related and multiple signaling pathways and the expression of key genes (e.g., Ras superfamily, cxgE, trap1). The expression of N-glycan-related pathways, which is positively correlated with amoeba predation, was inhibited in sand soil, decreasing amoeba's fitness. Finally, the results showed that soil texture also affects amoeba's interaction with environmental pollutants. In conclusion, this study shows that soil physical structures affect amoeba's interactions with bacteria and environmental pollutants. SYNOPSIS: Soil texture affects soil protozoa's growth and development and their interactions with environmental pollutants.
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Affiliation(s)
- Wei Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanchen Zhao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yikun Shi
- Department of Mechanical and Electronic Engineering, Qingdao University of Technology, Qingdao 266520, China
| | - Zihe Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingwen Mai
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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7
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Shin J, Lee Y, Hahm S, Lee K, Park J. Effects of Exogenous Ethanol Treatment in Nutrient Solution on Growth and Secondary Metabolite Contents of Three Herb Species in an Indoor Vertical Farming System. PLANTS (BASEL, SWITZERLAND) 2023; 12:3842. [PMID: 38005739 PMCID: PMC10675256 DOI: 10.3390/plants12223842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
This study aimed to explore the possibility of exogenous ethanol treatment as a technology to regulate the growth and the synthesis of secondary metabolites in herbaceous plants. After transplantation, sweet basil, Korean mint, and sweet wormwood were cultivated in a controlled vertical farming system and consistently exposed to exogenous ethanol at concentrations of 0, 0.5, 1, 2, 4, and 8 mM. Their growth parameters, antioxidant activity, and secondary metabolite contents were Everything is fine. measured to investigate the effects of the exogenous ethanol treatment on the three plants. The low-concentration ethanol treatments increased the shoot dry weight of the sweet basil and sweet wormwood compared to that of the control. As the ethanol concentration increased, the shoot fresh weight and leaf area in the sweet basil and Korean mint decreased compared to those of the control (0 mM). The DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging activity and total phenolic content of the three plants increased with the ethanol concentration, while the total flavonoid content did not demonstrate a significant trend. The chlorophyll and carotenoids of the basil showed no apparent concentration-dependent trends; however, the chlorophyll and carotenoids of the Korean mint and sweet wormwood decreased with high ethanol concentrations. Moreover, the antioxidant enzyme activity increased with high ethanol concentrations, indicating that high ethanol concentrations induce oxidative stress in plants.
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Affiliation(s)
- Juhyung Shin
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
| | - YongJae Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
| | - Seungyong Hahm
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Kwangya Lee
- Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jongseok Park
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea;
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8
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Siletsky SA. Investigation of the Mechanism of Membrane Potential Generation by Heme-Copper Respiratory Oxidases in a Real Time Mode. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1513-1527. [PMID: 38105021 DOI: 10.1134/s0006297923100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 12/19/2023]
Abstract
Heme-copper respiratory oxidases are highly efficient molecular machines. These membrane enzymes catalyze the final step of cellular respiration in eukaryotes and many prokaryotes: the transfer of electrons from cytochromes or quinols to molecular oxygen and oxygen reduction to water. The free energy released in this redox reaction is converted by heme-copper respiratory oxidases into the transmembrane gradient of the electrochemical potential of hydrogen ions H+). Heme-copper respiratory oxidases have a unique mechanism for generating H+, namely, a redox-coupled proton pump. A combination of direct electrometric method for measuring the kinetics of membrane potential generation with the methods of prestationary kinetics and site-directed mutagenesis in the studies of heme-copper oxidases allows to obtain a unique information on the translocation of protons inside the proteins in real time. The review summarizes the data of studies employing time-resolved electrometry to decipher the mechanisms of functioning of these important bioenergetic enzymes.
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Affiliation(s)
- Sergei A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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9
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Limbu DK, Shakib FA. Real-Time Dynamics and Detailed Balance in Ring Polymer Surface Hopping: The Impact of Frustrated Hops. J Phys Chem Lett 2023; 14:8658-8666. [PMID: 37732811 DOI: 10.1021/acs.jpclett.3c02085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Ring polymer surface hopping (RPSH) has been recently introduced as a well-tailored method for incorporating nuclear quantum effects, such as zero-point energy and tunneling, into nonadiabatic molecular dynamics simulations. The practical widespread usage of RPSH demands a comprehensive benchmarking of different reaction regimes and conditions with equal emphasis on demonstrating both the cons and the pros of the method. Here, we investigate the fundamental questions related to the conservation of energy and detailed balance in the context of RPSH. Using Tully's avoided crossing model as well as a 2-state quantum system coupled to a classical bath undergoing Langevin dynamics, we probe the critical problem of the proper treatment of the classically forbidden transitions stemming from the surface hopping algorithm. We show that proper treatment of these frustrated hops is key to the accurate description of real-time dynamics as well as reproducing the correct quantum Boltzmann populations.
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Affiliation(s)
- Dil K Limbu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Farnaz A Shakib
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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10
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Zhou B, Gabbaï FP. Four-Electron Reduction of O 2 Using Distibines in the Presence of ortho-Quinones. J Am Chem Soc 2023; 145:13758-13767. [PMID: 37306561 PMCID: PMC10863049 DOI: 10.1021/jacs.3c02223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/13/2023]
Abstract
This study, which aims to identify atypical platforms for the reduction of dioxygen, describes the reaction of O2 with two distibines, namely, 4,5-bis(diphenylstibino)-2,7-di-tert-butyl-9,9-dimethylxanthene and 4,5-bis(diphenylstibino)-2,7-di-tert-butyl-9,9-dimethyldihydroacridine, in the presence of an ortho-quinone such as phenanthraquinone. The reaction proceeds by oxidation of the two antimony atoms to the + V state in concert with reductive cleavage of the O2 molecule. As confirmed by 18O labeling experiments, the two resulting oxo units combine with the ortho-quinone to form an α,α,β,β-tetraolate ligand that bridges the two antimony(V) centers. This process, which has been studied both experimentally and computationally, involves the formation of asymmetric, mixed-valent derivatives featuring a stibine as well as a catecholatostiborane formed by oxidative addition of the quinone to only one of the antimony centers. Under aerobic conditions, the catecholatostiborane moiety reacts with O2 to form a semiquinone/peroxoantimony intermediate, as supported by NMR spectroscopy in the case of the dimethyldihydroacridine derivative. These intermediates swiftly evolve into the symmetrical bis(antimony(V)) α,α,β,β-tetraolate complexes via low barrier processes. Finally, the controlled protonolysis and reduction of the bis(antimony(V)) α,α,β,β-tetraolate complex based on the 9,9-dimethylxanthene platform have been investigated and shown to regenerate the starting distibine and the ortho-quinone. More importantly, these last reactions also produce two equivalents of water as the product of O2 reduction.
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Affiliation(s)
- Benyu Zhou
- Texas A&M University, Department of Chemistry, College
Station, Texas 77843, United States
| | - François P. Gabbaï
- Texas A&M University, Department of Chemistry, College
Station, Texas 77843, United States
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11
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Gorriz RF, Volkenandt S, Imhof P. Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase. Int J Mol Sci 2023; 24:10464. [PMID: 37445646 DOI: 10.3390/ijms241310464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The ("chemical") protons required for this reaction and those pumped are taken up via two distinct channels, named D-channel and K-channel, in a step-wise and highly regulated fashion. In the reductive phase of the catalytic cycle, both channels transport protons so that the pumped proton passes the D-channel before the "chemical" proton has crossed the K-channel. By performing molecular dynamics simulations of CcO in the O→E redox state (after the arrival of the first reducing electron) with various combinations of protonation states of the D- and K-channels, we analysed the effect of protonation on the two channels. In agreement with previous work, the amount of water observed in the D-channel was significantly higher when the terminal residue E286 was not (yet) protonated than when the proton arrived at this end of the D-channel and E286 was neutral. Since a sufficient number of water molecules in the channel is necessary for proton transport, this can be understood as E286 facilitating its own protonation. K-channel hydration shows an even higher dependence on the location of the excess proton in the K-channel. Also in agreement with previous work, the K-channel exhibits a very low hydration level that likely hinders proton transfer when the excess proton is located in the lower part of the K-channel, that is, on the N-side of S365. Once the proton has passed S365 (towards the reaction site, the bi-nuclear centre (BNC)), the amount of water in the K-channel provides hydrogen-bond connectivity that renders proton transfer up to Y288 at the BNC feasible. No significant direct effect of the protonation state of one channel on the hydration level, hydrogen-bond connectivity, or interactions between protein residues in the other channel could be observed, rendering proton conductivity in the two channels independent of each other. Regulation of the order of proton uptake and proton passage in the two channels such that the "chemical" proton leaves its channel last must, therefore, be achieved by other means of communication, such as the location of the reducing electron.
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Affiliation(s)
- Rene F Gorriz
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Senta Volkenandt
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
| | - Petra Imhof
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
- Computer Chemistry Center, Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany
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12
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Cao YC, Liao RZ. QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase. Inorg Chem 2023; 62:4066-4075. [PMID: 36857027 DOI: 10.1021/acs.inorgchem.2c03742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b595. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b595 to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b595 to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.
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Affiliation(s)
- Yu-Chen Cao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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13
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Liu Y, Resch SG, Chen H, Dechert S, Demeshko S, Bill E, Ye S, Meyer F. Fully Delocalized Mixed-Valent Cu 1.5 Cu 1.5 Complex: Strong Cu-Cu interaction and Fast Electron Self-Exchange Rate Despite Large Structural Changes. Angew Chem Int Ed Engl 2023; 62:e202215840. [PMID: 36504436 DOI: 10.1002/anie.202215840] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
A flexible macrocyclic ligand with two tridentate {CNC} compartments can host two Cu ions in reversibly interconvertible states, CuI CuI (1) and mixed-valent Cu1.5 Cu1.5 (2). They were characterized by XRD and multiple spectroscopic methods, including EPR, UV/Vis absorption and MCD, in combination with TD-DFT and CASSCF calculations. 2 features a short Cu⋅⋅⋅Cu distance (≈2.5 Å; compared to ≈4.0 Å in 1) and a very high delocalization energy of 13 000 cm-1 , comparable to the mixed-valent state of the biological CuA site. Electron self-exchange between 1 and 2 is rapid despite large structural reorganization, and is proposed to proceed via a sequential mechanism involving an active conformer of 1, viz. 1'; the latter has been characterized by XRD. Such electron transfer (ET) process is reminiscent of the conformationally gated ET proposed for biological systems. This redox couple is a unique pair of flexible dicopper complexes, achieving fast electron self-exchange closely related to the function of the CuA site.
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Affiliation(s)
- Yang Liu
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - Stefan G Resch
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - Haowei Chen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China.,Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Sebastian Dechert
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
| | - Eckhard Bill
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P. R. China
| | - Franc Meyer
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstrasse 4, 37077, Göttingen, Germany
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14
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Noll N, Groß T, Shoyama K, Beuerle F, Würthner F. Folding-Induced Promotion of Proton-Coupled Electron Transfers via Proximal Base for Light-Driven Water Oxidation. Angew Chem Int Ed Engl 2023; 62:e202217745. [PMID: 36511298 PMCID: PMC10107485 DOI: 10.1002/anie.202217745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/14/2022]
Abstract
Proton-coupled electron-transfer (PCET) processes play a key role in biocatalytic energy conversion and storage, for example, photosynthesis or nitrogen fixation. Here, we report a series of bipyridine-containing di- to tetranuclear Ru(bda) macrocycles 2 C-4 C (bda: 2,2'-bipyridine-6,6'-dicarboxylate) to promote O-O bond formation. In photocatalytic water oxidation under neutral conditions, all complexes 2 C-4 C prevail in a folded conformation that support the water nucleophilic attack (WNA) pathway with remarkable turnover frequencies of up to 15.5 s-1 per Ru unit respectively. Single-crystal X-ray analysis revealed an increased tendency for intramolecular π-π stacking and preorganization of the proximal bases close to the active centers for the larger macrocycles. H/D kinetic isotope effect studies and electrochemical data demonstrate the key role of the proximal bipyridines as proton acceptors in lowering the activation barrier for the crucial nucleophilic attack of H2 O in the WNA mechanism.
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Affiliation(s)
- Niklas Noll
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Tobias Groß
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Kazutaka Shoyama
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Florian Beuerle
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany.,Institut für Organische Chemie, Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany
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15
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Čapek J, Večerek B. Why is manganese so valuable to bacterial pathogens? Front Cell Infect Microbiol 2023; 13:943390. [PMID: 36816586 PMCID: PMC9936198 DOI: 10.3389/fcimb.2023.943390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Apart from oxygenic photosynthesis, the extent of manganese utilization in bacteria varies from species to species and also appears to depend on external conditions. This observation is in striking contrast to iron, which is similar to manganese but essential for the vast majority of bacteria. To adequately explain the role of manganese in pathogens, we first present in this review that the accumulation of molecular oxygen in the Earth's atmosphere was a key event that linked manganese utilization to iron utilization and put pressure on the use of manganese in general. We devote a large part of our contribution to explanation of how molecular oxygen interferes with iron so that it enhances oxidative stress in cells, and how bacteria have learned to control the concentration of free iron in the cytosol. The functioning of iron in the presence of molecular oxygen serves as a springboard for a fundamental understanding of why manganese is so valued by bacterial pathogens. The bulk of this review addresses how manganese can replace iron in enzymes. Redox-active enzymes must cope with the higher redox potential of manganese compared to iron. Therefore, specific manganese-dependent isoenzymes have evolved that either lower the redox potential of the bound metal or use a stronger oxidant. In contrast, redox-inactive enzymes can exchange the metal directly within the individual active site, so no isoenzymes are required. It appears that in the physiological context, only redox-inactive mononuclear or dinuclear enzymes are capable of replacing iron with manganese within the same active site. In both cases, cytosolic conditions play an important role in the selection of the metal used. In conclusion, we summarize both well-characterized and less-studied mechanisms of the tug-of-war for manganese between host and pathogen.
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Affiliation(s)
- Jan Čapek
- *Correspondence: Jan Čapek, ; Branislav Večerek,
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16
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Insertion of unnatural metal ligand in the heme pocket of nitrophorin through protein semi-synthesis: toward biomimicking binuclear active sites. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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17
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Brand SE, Scharlau M, Geren L, Hendrix M, Parson C, Elmendorf T, Neel E, Pianalto K, Silva-Nash J, Durham B, Millett F. Accelerated Evolution of Cytochrome c in Higher Primates, and Regulation of the Reaction between Cytochrome c and Cytochrome Oxidase by Phosphorylation. Cells 2022; 11:cells11244014. [PMID: 36552779 PMCID: PMC9777161 DOI: 10.3390/cells11244014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Cytochrome c (Cc) underwent accelerated evolution from the stem of the anthropoid primates to humans. Of the 11 amino acid changes that occurred from horse Cc to human Cc, five were at Cc residues near the binding site of the Cc:CcO complex. Single-point mutants of horse and human Cc were made at each of these positions. The Cc:CcO dissociation constant KD of the horse mutants decreased in the order: T89E > native horse Cc > V11I Cc > Q12M > D50A > A83V > native human. The largest effect was observed for the mutants at residue 50, where the horse Cc D50A mutant decreased KD from 28.4 to 11.8 μM, and the human Cc A50D increased KD from 4.7 to 15.7 μM. To investigate the role of Cc phosphorylation in regulating the reaction with CcO, phosphomimetic human Cc mutants were prepared. The Cc T28E, S47E, and Y48E mutants increased the dissociation rate constant kd, decreased the formation rate constant kf, and increased the equilibrium dissociation constant KD of the Cc:CcO complex. These studies indicate that phosphorylation of these residues plays an important role in regulating mitochondrial electron transport and membrane potential ΔΨ.
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Affiliation(s)
| | - Martha Scharlau
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lois Geren
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Marissa Hendrix
- Independent Researcher, P.O. Box 603, Dardanelle, AR 72834, USA
| | - Clayre Parson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Tyler Elmendorf
- School of Medicine, University of Kansas Medical Center, 2060 W 39th Ave, Kansas City, KS 66103, USA
| | - Earl Neel
- Tulsa Bone and Joint Associates, Tulsa, OK 74146, USA
| | - Kaila Pianalto
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | | | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
- Correspondence:
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18
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Comparative oxidative metabolism in mammalian sperm. Anim Reprod Sci 2022; 247:107095. [DOI: 10.1016/j.anireprosci.2022.107095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022]
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19
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Electric fields control water-gated proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A 2022; 119:e2207761119. [PMID: 36095184 PMCID: PMC9499568 DOI: 10.1073/pnas.2207761119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome c oxidase (CcO) functions as a terminal electron acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O2 reduction into proton pumping. Here we show that CcO creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme a, leads to dissociation of an arginine (Arg438)-heme a3 D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V Å-1 along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.
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20
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Beignon F, Gueguen N, Tricoire-Leignel H, Mattei C, Lenaers G. The multiple facets of mitochondrial regulations controlling cellular thermogenesis. Cell Mol Life Sci 2022; 79:525. [PMID: 36125552 DOI: 10.1007/s00018-022-04523-8] [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: 05/19/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
Understanding temperature production and regulation in endotherm organisms becomes a crucial challenge facing the increased frequency and intensity of heat strokes related to global warming. Mitochondria, located at the crossroad of metabolism, respiration, Ca2+ homeostasis, and apoptosis, were recently proposed to further act as cellular radiators, with an estimated inner temperature reaching 50 °C in common cell lines. This inner thermogenesis might be further exacerbated in organs devoted to produce consistent efforts as muscles, or heat as brown adipose tissue, in response to acute solicitations. Consequently, pathways promoting respiratory chain uncoupling and mitochondrial activity, such as Ca2+ fluxes, uncoupling proteins, futile cycling, and substrate supplies, provide the main processes controlling heat production and cell temperature. The mitochondrial thermogenesis might be further amplified by cytoplasmic mechanisms promoting the over-consumption of ATP pools. Considering these new thermic paradigms, we discuss here all conventional wisdoms linking mitochondrial functions to cellular thermogenesis in different physiological conditions.
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Affiliation(s)
- Florian Beignon
- Univ Angers, MitoLab, Unité MITOVASC, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France.
| | - Naig Gueguen
- Univ Angers, MitoLab, Unité MITOVASC, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France.,Service de Biochimie et Biologie Moléculaire, CHU d'Angers, Angers, France
| | | | - César Mattei
- Univ Angers, CarMe, Unité MITOVASC, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France
| | - Guy Lenaers
- Univ Angers, MitoLab, Unité MITOVASC, UMR CNRS 6015, INSERM U1083, SFR ICAT, Angers, France. .,Service de Neurologie, CHU d'Angers, Angers, France.
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21
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Abstract
Controlled reduction of oxygen is important for developing clean energy technologies, such as fuel cells, and is vital to the existence of aerobic organisms. The process starts with oxygen in a triplet ground state and ends with products that are all in singlet states. Hence, spin constraints in the oxygen reduction must be considered. Here, we show that the electron transfer efficiency from chiral electrodes to oxygen (oxygen reduction reaction) is enhanced over that from achiral electrodes. We demonstrate lower overpotentials and higher current densities for chiral catalysts versus achiral ones. This finding holds even for electrodes composed of heavy metals with large spin-orbit coupling. The effect results from the spin selectivity conferred on the electron current by the chiral assemblies, the chiral-induced spin selectivity effect.
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22
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan.,Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan.,Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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23
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Arima H, Nakazono T, Wada T. Proton Relay Effects on Oxygen Reduction Reaction Catalyzed by Dinuclear Cobalt Polypyridyl Complexes with OH Groups on Bipyridine Ligands. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroaki Arima
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Takashi Nakazono
- Research Center for Artificial Photosynthesis (ReCAP), Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Tohru Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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24
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FfCOX17 is Involved in Fumonisins Production, Growth, Asexual Reproduction, and Fungicide Sensitivity in Fusarium fujikuroi. Toxins (Basel) 2022; 14:toxins14070427. [PMID: 35878165 PMCID: PMC9319711 DOI: 10.3390/toxins14070427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Fusarium fujikuroi, a causal agent of Rice Bakanae Disease, produces secondary metabolites such as gibberellin, pigments bikaverin, and mycotoxins fumonisins. Fumonisins produced by F. fujikuroi pose a severe threat to human and animal health. The copper chaperone protein plays a critical role in different growth stages of plants, fungi, and yeasts, but their functions and regulation in fumonisin biosynthesis are still unclear. Here, a copper chaperone protein, FfCOX17, was identified in F. fujikuroi. The FfCOX17 deletion mutant (∆FfCOX17) exhibited decreased vegetative growth and asexual reproduction. The transcriptional level of the FfFUM2 gene was significantly induced in ∆FfCOX17, and the fumonisin production in ∆FfCOX17 mutants was significantly increased compared to wild-type F. fujikuroi, but the pathogenicity of ∆FfCOX17 mutants was unaffected, which may be caused by the no significantly changed gibberellin content. ∆FfCOX17 showed decreased sensitivity to oxidative stress, osmotic stress, and increased sensitivity to cell wall stress, heat shock stress, and high concentration glucose. In addition, ∆FfCOX17 also showed increased sensitivity to fungicide fluazinam and fludioxonil, and decreased sensitivity to phenamacril and prochloraz. Taken together, this study suggested that FfCOX17 is critical for fumonisin production, vegetative growth, asexual reproduction, and fungicide sensitivity, but is not required for the virulence function of F. fujikuroi on rice.
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25
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Assembly of redox active metallo-enzymes and metallo-peptides on electrodes: Abiological constructs to probe natural processes. Curr Opin Chem Biol 2022; 68:102142. [DOI: 10.1016/j.cbpa.2022.102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
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26
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Amanullah S, Saha P, Dey A. Recent developments in the synthesis of bio-inspired iron porphyrins for small molecule activation. Chem Commun (Camb) 2022; 58:5808-5828. [PMID: 35474535 DOI: 10.1039/d2cc00430e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nature utilizes a diverse set of tetrapyrrole-based macrocycles (referred to as porphyrinoids) for catalyzing various biological processes. Investigation of the differences in electronic structure and reactivity in these reactions have revealed striking differences that lead to diverse reactivity from, apparently, similar looking active sites. Therefore, the role of the different heme cofactors as well as the distal superstructure in the proteins is important to understand. This article summarizes the role of a few synthetic metallo-porphyrinoids towards catalyzing several small molecule activation reactions, such as the ORR, NiRR, CO2RR, etc. The major focus of the article is to enlighten the synthetic routes to the well-decorated active-site mimic in a tailor-made fashion pursuing a retrosynthetic approach, learning from the biosynthesis of the cofactors. Techniques and the role of the second-sphere residues on the reaction rate, selectivity, etc. are incorporated emulating the basic amino acid residues fencing the active sites. These bioinspired mimics play an important role towards understanding the role of the prosthetic groups as well as the basic residues towards any reaction occurring in Nature.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
| | - Paramita Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB 700032, India.
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27
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Bhunia S, Ghatak A, Dey A. Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems. Chem Rev 2022; 122:12370-12426. [PMID: 35404575 DOI: 10.1021/acs.chemrev.1c01021] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation and reduction of O2 and H2O2 by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.
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Affiliation(s)
- Sarmistha Bhunia
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
| | - Arnab Ghatak
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata 700032, India
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Nanostructured, Metal-Free Electrodes for the Oxygen Reduction Reaction Containing Nitrogen-Doped Carbon Quantum Dots and a Hydroxide Ion-Conducting Ionomer. Molecules 2022; 27:molecules27061832. [PMID: 35335194 PMCID: PMC8953787 DOI: 10.3390/molecules27061832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 12/20/2022] Open
Abstract
In this work, we studied the combination of nitrogen-doped carbon quantum dots (N-CQD), a hydroxide-ion conducting ionomer based on polysulfone (PSU) and polyaniline (PANI), to explore the complementary properties of these materials in high-performance nanostructured electrodes for the oxygen reduction reaction (ORR) in alkaline solution. N-CQD were made by hydrothermal synthesis from glucosamine hydrochloride (GAH) or glucosamine hydrochloride and N-Octylamine (GAH-Oct), and PSU were quaternized with trimethylamine (PSU-TMA). The nanocomposite electrodes were prepared on carbon paper by drop-casting. Furthermore, we succeeded in preparing PSU-TMA + PANI + GAH-Oct fibers by electrospinning. The capacitance of the electrodes was investigated by cyclic voltammetry and impedance spectroscopy, which gave similar trends. The ORR was investigated by linear sweep voltammetry at rotating disk electrode speeds between 250 and 2000 rpm in an oxygen-saturated 1 M KOH solution. Koutecky–Levich plots showed that four electrons were exchanged for nanocomposite electrodes containing CQD. The highest reduction currents were measured for the electrodes containing GAH-Oct. The Tafel plots gave the lowest slope and the most positive half-wave potential for PSU-TMA + PANI + GAH-Oct fibers. The best electrocatalytic activity of this electrode could be related to the high amount of graphitic nitrogen in GAH-Oct. Long-term cycling tests showed no significant modification of the onset potential, but a change of the current in the mass transport limited region, indicated the evolution of the microstructure of the nanocomposite ORR electrode modifying the mass transport conditions during the first 400 cycles before reaching stationary conditions. FTIR spectra were used to study possible electrode degradation after the ORR in 1 M KOH: the only change was due to the reaction of PANI emeraldine salt to emeraldine base, whereas the other constituents of the multiphase electrode did not show any degradation.
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Direct Interaction of Mitochondrial Cytochrome c Oxidase with Thyroid Hormones: Evidence for Two Binding Sites. Cells 2022; 11:cells11050908. [PMID: 35269529 PMCID: PMC8909594 DOI: 10.3390/cells11050908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 12/18/2022] Open
Abstract
Thyroid hormones regulate tissue metabolism to establish an energy balance in the cell, in particular, by affecting oxidative phosphorylation. Their long-term impact is mainly associated with changes in gene expression, while the short-term effects may differ in their mechanisms. Our work was devoted to studying the short-term effects of hormones T2, T3 and T4 on mitochondrial cytochrome c oxidase (CcO) mediated by direct contact with the enzyme. The data obtained indicate the existence of two separate sites of CcO interaction with thyroid hormones, differing in their location, affinity and specificity to hormone binding. First, we show that T3 and T4 but not T2 inhibit the oxidase activity of CcO in solution and on membrane preparations with Ki ≈ 100–200 μM. In solution, T3 and T4 compete in a 1:1 ratio with the detergent dodecyl-maltoside to bind to the enzyme. The peroxidase and catalase partial activities of CcO are not sensitive to hormones, but electron transfer from heme a to the oxidized binuclear center is affected. We believe that T3 and T4 could be ligands of the bile acid-binding site found in the 3D structure of CcO by Ferguson-Miller’s group, and hormone-induced inhibition is associated with dysfunction of the K-proton channel. A possible role of this interaction in the physiological regulation of the enzyme is discussed. Second, we find that T2, T3, and T4 inhibit superoxide generation by oxidized CcO in the presence of excess H2O2. Inhibition is characterized by Ki values of 0.3–5 μM and apparently affects the formation of O2●− at the protein surface. The second binding site for thyroid hormones presumably coincides with the point of tight T2 binding on the Va subunit described in the literature.
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30
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Du WGH, Götz AW, Noodleman L. Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase. Chemphyschem 2022; 23:e202100831. [PMID: 35142420 PMCID: PMC9054037 DOI: 10.1002/cphc.202100831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/03/2022] [Indexed: 11/24/2022]
Abstract
Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fea33+−H2O−CuB2+ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H2O molecule between the Fea33+ and CuB2+ sites in different DNCs, whether or not this central H2O molecule has H‐bonding interaction with another H2O molecule, the different spin states having similar energies for the Fea33+ sites, and whether the Fea33+ and CuB2+ sites are ferromagnetically or antiferromagnetically spin‐coupled.
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Affiliation(s)
- Wen-Ge Han Du
- The Scripps Research Institute, Integrative Structural and Computational Biology, UNITED STATES
| | | | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, Hz112, 10550 North Torrey Pines Road, 92037, La Jolla, UNITED STATES
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31
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Kaur G, Ravikanth M. Recent developments in the chemistry of triphyrin(2.1.1)s. ADVANCES IN HETEROCYCLIC CHEMISTRY 2022. [DOI: 10.1016/bs.aihch.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Reid AG, Moreno JJ, Hooe SL, Baugh KR, Thomas IH, Dickie DA, Machan CW. Inverse Potential Scaling in Co-Electrocatalytic Activity for CO 2 Reduction Through Redox Mediator Tuning and Catalyst Design. Chem Sci 2022; 13:9595-9606. [PMID: 36091894 PMCID: PMC9400620 DOI: 10.1039/d2sc03258a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrocatalytic CO2 reduction is an attractive strategy to mitigate the continuous rise in atmospheric CO2 concentrations and generate value-added chemical products. A possible strategy to increase the activity of molecular...
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Affiliation(s)
- Amelia G Reid
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Juan J Moreno
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Shelby L Hooe
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Kira R Baugh
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Isobel H Thomas
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Diane A Dickie
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
| | - Charles W Machan
- Department of Chemistry, University of Virginia PO Box 400319 Charlottesville VA 22904-4319 USA
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Flores-Cotera LB, Chávez-Cabrera C, Martínez-Cárdenas A, Sánchez S, García-Flores OU. Deciphering the mechanism by which the yeast Phaffia rhodozyma responds adaptively to environmental, nutritional, and genetic cues. J Ind Microbiol Biotechnol 2021; 48:kuab048. [PMID: 34302341 PMCID: PMC8788774 DOI: 10.1093/jimb/kuab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
Phaffia rhodozyma is a basidiomycetous yeast that synthesizes astaxanthin (ASX), which is a powerful and highly valuable antioxidant carotenoid pigment. P. rhodozyma cells accrue ASX and gain an intense red-pink coloration when faced with stressful conditions such as nutrient limitations (e.g., nitrogen or copper), the presence of toxic substances (e.g., antimycin A), or are affected by mutations in the genes that are involved in nitrogen metabolism or respiration. Since cellular accrual of ASX occurs under a wide variety of conditions, this yeast represents a valuable model for studying the growth conditions that entail oxidative stress for yeast cells. Recently, we proposed that ASX synthesis can be largely induced by conditions that lead to reduction-oxidation (redox) imbalances, particularly the state of the NADH/NAD+ couple together with an oxidative environment. In this work, we review the multiple known conditions that elicit ASX synthesis expanding on the data that we formerly examined. When considered alongside the Mitchell's chemiosmotic hypothesis, the study served to rationalize the induction of ASX synthesis and other adaptive cellular processes under a much broader set of conditions. Our aim was to propose an underlying mechanism that explains how a broad range of divergent conditions converge to induce ASX synthesis in P. rhodozyma. The mechanism that links the induction of ASX synthesis with the occurrence of NADH/NAD+ imbalances may help in understanding how other organisms detect any of a broad array of stimuli or gene mutations, and then adaptively respond to activate numerous compensatory cellular processes.
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Affiliation(s)
- Luis B Flores-Cotera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Cipriano Chávez-Cabrera
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Anahi Martínez-Cárdenas
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
| | - Sergio Sánchez
- Department of Molecular Biology and Biotechnology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México city 04510, México
| | - Oscar Ulises García-Flores
- Department of Biotechnology and Bioengineering, Cinvestav-IPN, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, México city 07360, México
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Zou W, Zhu Q, Fettinger JC, Power PP. Dimeric Copper and Lithium Thiolates: Comparison of Copper Thiolates with Their Lithium Congeners. Inorg Chem 2021; 60:17641-17648. [PMID: 34812614 DOI: 10.1021/acs.inorgchem.1c02226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The direct reactions of the large terphenyl thiols HSAriPr4 (AriPr4= -C6H3-2,6-(C6H3-2,6-iPr2)2) and HSAriPr6 (AriPr6= -C6H3-2,6-(C6H2-2,4,6-iPr3)2) with stoichiometric amounts of mesitylcopper(I) in THF at ca. 80 °C afforded the first well-characterized dimeric copper thiolato species {CuSAriPr4}2 (1) and {CuSAriPr6}2 (2) with elimination of mesitylene. The complexes 1 and 2 were characterized by NMR and electronic spectroscopy as well as by X-ray crystallography. They have dimeric Cu2S2 core structures in which the two copper atoms are bridged by the sulfurs from the thiolato ligands and feature short Cu--Cu distances near 2.4 Å as well as a weak copper-flanking aryl ring interaction from a terphenyl substituent. The structures of the planar Cu2S2 cores bear a resemblance to the CuA site in nitrous oxide reductase in which two cysteines also bridge two copper atoms. The related dimeric Li2S2 structural motif was also observed in the lithium congeners {LiSAriPr4}2 (3) and {LiSAriPr6}2 (4) which were synthesized directly from the thiols and n-BuLi in hexanes. However, despite the very similar effective ionic radii of the Li+ (0.59 Å) and Cu+ (0.60 Å) ions, the Li--Li structures display very much longer (by more than ca. 0.5 Å) separations than the corresponding Cu--Cu distances in 1 and 2, which may be due to weaker dispersion interactions.
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Affiliation(s)
- Wenxing Zou
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Qihao Zhu
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - James C Fettinger
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Philip P Power
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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35
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Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase. Nat Commun 2021; 12:6903. [PMID: 34824221 PMCID: PMC8617209 DOI: 10.1038/s41467-021-27174-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022] Open
Abstract
Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.
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36
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Etim UJ, Bai P, Gazit OM, Zhong Z. Low-Temperature Heterogeneous Oxidation Catalysis and Molecular Oxygen Activation. CATALYSIS REVIEWS 2021. [DOI: 10.1080/01614940.2021.1919044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ubong J. Etim
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, China
| | - Peng Bai
- College of Chemical Engineering, China University of Petroleum, Qingdao, China
| | - Oz M. Gazit
- Wolfson Faculty of Chemical Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Ziyi Zhong
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, China
- Technion Israel Institute of Technology (IIT), Haifa, Israel
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37
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Meyer RL, Miró P, Brennessel WW, Matson EM. O 2 Activation with a Sterically Encumbered, Oxygen-Deficient Polyoxovanadate-Alkoxide Cluster. Inorg Chem 2021; 60:13833-13843. [PMID: 34161731 DOI: 10.1021/acs.inorgchem.1c00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The isolation of the oxygen-deficient, polyoxovanadate-alkoxide (POV-alkoxide) cluster, [nBu4N][V6O6(OMe)12(MeCN)], and its subsequent reactivity with oxygen (O2), has demonstrated the utility of these assemblies as molecular models for heterogeneous metal oxide catalysts. However, the mechanism through which this cluster activates and reduces O2 to generate the oxygenated species is poorly understood. Currently it is speculated that this POV-alkoxide mediates the four-electron O-O bond cleavage through an O2 bridged dimeric intermediate, a mechanism which is not viable for O2 reduction at solid-state metal oxide surfaces. Here, we report the successful activation and reduction of O2 by the calix-functionalized POV-alkoxide cluster, [nBu4N][(calix)V6O6(OMe)8](MeCN)] (calix = 4-tert-butylcalix[4]arene). The steric hindrance imparted to the open vanadium site by the calix motif eliminates the possibility of cooperative, bimolecular O2 activation, allowing for a comparison of the reactivity of this system with that of the nonfunctionalized POV-alkoxide described previously. Rigorous characterization of the calix-substituted assembly, enabled by its newfound solubility in organic solvent, reveals that the incorporation of the tetradentate aryloxide ligand into the POV-alkoxide scaffold perturbs the electronic communication between the site-differentiated vanadium(III) ion and the cluster core. Collectively, our results provide insight into the physiochemical factors that are important during the O2 reduction reaction at oxygen-deficient sites in reduced POV-alkoxide clusters.
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Affiliation(s)
- Rachel L Meyer
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Pere Miró
- Department of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - William W Brennessel
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Ellen M Matson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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Suzuki Y, Taguchi K, Kure T, Sakai H, Enoki Y, Otagiri M, Matsumoto K. Liposome-encapsulated methemoglobin as an antidote against cyanide poisoning. J Control Release 2021; 337:59-70. [PMID: 34273418 DOI: 10.1016/j.jconrel.2021.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022]
Abstract
Cyanide induces acute lethal poisoning resulting from inhibition of cytochrome c oxidase located in the complex IV (Complex IV) of mitochondria. However, current therapies for cyanide poisoning using hydroxocobalamin and nitrous acid compounds remain a clinical issue. Here, we show that liposome-encapsulated methemoglobin (metHb@Lipo), nanosized biomimetic red blood cells, replicate the antidotal mechanism of nitrous acid compounds against cyanide poisoning, achieving superior efficacy and fast action with no adverse effects. The structure of metHb@Lipo, which consists of concentrated methemoglobin in its aqueous core and a lipid membrane resembling the red blood cell membrane, provides favorable characteristics as a cyanide antidote, such as binding properties and membrane permeability. Upon cyanide exposure, metHb@Lipo maintained the mitochondrial function in PC12 cells, resulting in a cell viability comparable to treatment with nitrous acid compounds. In a mouse model of cyanide poisoning, metHb@Lipo treatment dramatically improved mortality with a rapid recovery from the symptoms of cyanide poisoning compared to treatment with nitrous acid compounds. Furthermore, metHb@Lipo also possesses satisfactory pharmacokinetic properties without long-term bioaccumulation and toxicity. Our findings showed a novel concept to develop drugs for cyanide poisoning and provide a promising possibility for biomimetic red blood cell preparations for pharmaceutical applications.
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Affiliation(s)
- Yuto Suzuki
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Kazuaki Taguchi
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Tomoko Kure
- Department of Chemistry, Nara Medical University, Shijo-cho 840, Kashihara, Nara 634-8521, Japan
| | - Hiromi Sakai
- Department of Chemistry, Nara Medical University, Shijo-cho 840, Kashihara, Nara 634-8521, Japan
| | - Yuki Enoki
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
| | - Masaki Otagiri
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto City, Kumamoto 860-0082, Japan; DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto City, Kumamoto 860-0082, Japan
| | - Kazuaki Matsumoto
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
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Arima H, Wada M, Nakazono T, Wada T. Tuning Oxygen Reduction Catalysis of Dinuclear Cobalt Polypyridyl Complexes by the Bridging Structure. Inorg Chem 2021; 60:9402-9415. [PMID: 33988979 DOI: 10.1021/acs.inorgchem.1c00293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The four-electron oxygen reduction reaction (4e--ORR) is the mainstay in chemical energy conversion. Elucidation of factors influencing the catalyst's reaction rate and selectivity is important in the development of more active catalysts of 4e--ORR. In this study, we investigated chemical and electrochemical 4e--ORR catalyzed by Co2(μ-O2) complexes bridged by xanthene (1) and anthracene (3) and by a Co2(OH)2 complex bridged by anthraquinone (2). In the chemical ORR using Fe(CpMe)2 as a reductant in acidic PhCN, we found that 1 showed the highest initial turnover frequency (TOFinit = 6.8 × 102 s-1) and selectivity for 4e--ORR (96%) in three complexes. The detailed kinetic analyses have revealed that the rate-determining steps (RDSs) in the catalytic cycles of 1-3 have the O2 addition to [CoII2(OH2)2]4+ as an intermediate in common. In the only case that complex 1 was used as a catalyst, kcat depended on proton concentration because the reaction rate of the O2 addition to [CoII2(OH2)2]4+ was so fast as compared to that of the concerted PCET process of 1. Through X-ray, Raman, and electrochemical analyses and stoichiometric reactions, we found the face-to-face structure of 1 characterized by a slightly flexible xanthene was advantageous in capturing O2 and stabilizing the Co2(μ-O2) structure, thus increasing both the reaction rate and selectivity for 4e--ORR.
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Affiliation(s)
- Hiroaki Arima
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Misato Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Takashi Nakazono
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Tohru Wada
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme‐Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Linhua Tai
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Danyang Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaoyun Pang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Sin Man Lam
- LipidALL Technologies Company Limited Changzhou 213022 Jiangsu Province China
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101 China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Guohong Peng
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Straβe 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Key Laboratory of Biomacromolecules CAS Center for Excellence in Biomacromolecules Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
- Center for Biological Imaging Institute of Biophysics Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
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41
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Zhu G, Zeng H, Zhang S, Juli J, Tai L, Zhang D, Pang X, Zhang Y, Lam SM, Zhu Y, Peng G, Michel H, Sun F. The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew Chem Int Ed Engl 2021; 60:13323-13330. [PMID: 33665933 PMCID: PMC8251803 DOI: 10.1002/anie.202016785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 02/03/2023]
Abstract
The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Å resolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.
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Affiliation(s)
- Guoliang Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Hui Zeng
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Shuangbo Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jana Juli
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Linhua Tai
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Danyang Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xiaoyun Pang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Yan Zhang
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
| | - Sin Man Lam
- LipidALL Technologies Company LimitedChangzhou213022Jiangsu ProvinceChina
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesNo.1 West Beichen Road, Chaoyang DistrictBeijing100101China
| | - Yun Zhu
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Guohong Peng
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Hartmut Michel
- Department of Molecular Membrane BiologyMax Planck Institute of BiophysicsMax-von Laue-Straβe 360438Frankfurt am MainGermany
| | - Fei Sun
- National Key Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
- Center for Biological ImagingInstitute of BiophysicsChinese Academy of Sciences15 Datun Road, Chaoyang DistrictBeijing100101China
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42
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Wang S, Zhu E, Huang Y, Heinz H. Direct correlation of oxygen adsorption on platinum-electrolyte interfaces with the activity in the oxygen reduction reaction. SCIENCE ADVANCES 2021; 7:eabb1435. [PMID: 34108201 PMCID: PMC8189588 DOI: 10.1126/sciadv.abb1435] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/22/2021] [Indexed: 05/24/2023]
Abstract
The oxygen reduction reaction (ORR) on platinum catalysts is essential in fuel cells. Quantitative predictions of the relative ORR activity in experiments, in the range of 1 to 50 times, have remained challenging because of incomplete mechanistic understanding and lack of computational tools to account for the associated small differences in activation energies (<2.3 kilocalories per mole). Using highly accurate molecular dynamics (MD) simulation with the Interface force field (0.1 kilocalories per mole), we elucidated the mechanism of adsorption of molecular oxygen on regular and irregular platinum surfaces and nanostructures, followed by local density functional theory (DFT) calculations. The relative ORR activity is determined by oxygen access to platinum surfaces, which greatly depends on specific water adlayers, while electron transfer occurs at a similar slow rate. The MD methods facilitate quantitative predictions of relative ORR activities of any platinum nanostructures, are applicable to other catalysts, and enable effective MD/DFT approaches.
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Affiliation(s)
- Shiyi Wang
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Enbo Zhu
- Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - Yu Huang
- Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
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Borisov VB, Siletsky SA, Paiardini A, Hoogewijs D, Forte E, Giuffrè A, Poole RK. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets. Antioxid Redox Signal 2021; 34:1280-1318. [PMID: 32924537 PMCID: PMC8112716 DOI: 10.1089/ars.2020.8039] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022]
Abstract
Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria formally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, peroxynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase. Since cytochrome bd is a uniquely bacterial enzyme, future research should focus on harnessing fundamental knowledge of its structure and function to the development of novel and effective antibacterial agents.
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Affiliation(s)
- Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Sergey A. Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - David Hoogewijs
- Department of Medicine/Physiology, University of Fribourg, Fribourg, Switzerland
| | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
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44
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Ariyageadsakul P, Baeck KK. Wavepacket propagations for the early time dynamics of proton-coupled electron transfer in the charge-transfer state of NH 3Cl complex. J Chem Phys 2021; 154:154305. [PMID: 33887927 DOI: 10.1063/5.0046247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A charge-transfer (CT) excited state of NH3Cl, generated by photo-detachment of an electron from the anionic NH3Cl- precursor, can be represented as H2N+-H-Cl- and proceeds to two chemical reactions: one reaction generating NH2 and HCl resulting from a proton transfer (PT) and the other reaction producing NH3 and a Cl atom resulting from an electron transfer (ET); both are coupled to form a typical proton-coupled electron transfer (PCET) process. The early time dynamics of this CT were studied using time-dependent wavepacket propagation on three nonadiabatically coupled electronic states in a reduced three-dimensional space. The electronic states were treated using the XMS-CASPT2/aug-cc-pVTZ ab initio methodology. The population dynamics of the three coupled electronic states were analyzed in detail to reveal the initial stage of the PCET process up to ∼100 fs, while the branching ratio, χ = PT/(ET+PT), was determined after wavepacket propagations of up to 2000 fs. Another main result is the dependence of χ on the vibration levels of the initial precursor anion and the isotope substitution of the connecting H atom with deuterium and tritium. Our study reveals the detailed microscopic features of the PCET process embedded in the CT state of the NH3Cl complex and certain systematic dependences of the branching ratio χ on the above factors.
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Affiliation(s)
- Pinit Ariyageadsakul
- Department of Chemistry, Gangneung-Wonju National University, Gangneung, Gangwon-do 25457, Republic of Korea
| | - Kyoung Koo Baeck
- Department of Chemistry, Gangneung-Wonju National University, Gangneung, Gangwon-do 25457, Republic of Korea
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45
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Mishra S, Bhandari A, Singh D, Gupta R, Olmstead MM, Patra AK. Bis(μ-thiolato)-dicopper Containing Fully Spin Delocalized Mixed Valence Copper-Sulfur Clusters and Their Electronic Structural Properties with Relevance to the Cu A Site. Inorg Chem 2021; 60:5779-5790. [PMID: 33829770 DOI: 10.1021/acs.inorgchem.1c00075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With aromatic and aliphatic thiol-S donor Schiff base ligands, the copper-sulfur clusters, [(L1)8CuI6CuII2](ClO4)2·DMF·0.5CH3OH (1) and [(L2)12CuI5CuII11(μ4-S)(μ4-O)6](ClO4)·4H2O, respectively, have been reported ( Chem. Commun. 2017, 53, 3334); HL1/HL2 are 2-(((3-methylthiophen-2-yl)methylene)amino)benzene/ethanethiol). Complex 1 comprises a wheel shaped Cu8S8 framework, made up of interlinked Cu2{μ-S(R)}2 units. To understand the properties with relevance to the CuA site and to check whether self-assembly generates similar type clusters to 1, three complexes, [(L3)8CuI6CuII2](ClO4)2·(C2H5)2O·2.5H2O (2), [(L3Cl)8CuI6CuII2](ClO4)2·1.25(C2H5)2O·1.25CH3OH·2H2O (3), and [(L3CF3)8CuI6CuII2](ClO4)2·2(C2H5)2O·H2O (4) have been synthesized with supporting ligands HL3X (HL3 = 2-((furan-2-ylmethylene)amino)benzenethiol when X = -H; X = -Cl or -CF3 para to thiol-S are HL3Cl and HL3CF3 ligands, respectively). The X-ray structures of 3 and 4 feature a similar Cu8S8 architecture to 1. The spectroscopic properties and the X-ray structures revealed that 2-4 are fully spin delocalized mixed valence (MV) of class-III type clusters. The structural parameters of the N2Cu2{μ-S(R)}2 units of 3 and 4 closely resemble those of the MV binuclear CuA site. With the aid of UV-vis-NIR, EPR, and spectroelectrochemical studies, the electronic properties of these complexes have been described in comparison with the MV model complexes and CuA site.
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Affiliation(s)
- Saikat Mishra
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
| | - Anirban Bhandari
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
| | - Devender Singh
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Rajeev Gupta
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | - Marilyn M Olmstead
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Apurba K Patra
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
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46
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Potential Role of L-Carnitine in Autism Spectrum Disorder. J Clin Med 2021; 10:jcm10061202. [PMID: 33805796 PMCID: PMC8000371 DOI: 10.3390/jcm10061202] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
L-carnitine plays an important role in the functioning of the central nervous system, and especially in the mitochondrial metabolism of fatty acids. Altered carnitine metabolism, abnormal fatty acid metabolism in patients with autism spectrum disorder (ASD) has been documented. ASD is a complex heterogeneous neurodevelopmental condition that is usually diagnosed in early childhood. Patients with ASD require careful classification as this heterogeneous clinical category may include patients with an intellectual disability or high functioning, epilepsy, language impairments, or associated Mendelian genetic conditions. L-carnitine participates in the long-chain oxidation of fatty acids in the brain, stimulates acetylcholine synthesis (donor of the acyl groups), stimulates expression of growth-associated protein-43, prevents cell apoptosis and neuron damage and stimulates neurotransmission. Determination of L-carnitine in serum/plasma and analysis of acylcarnitines in a dried blood spot may be useful in ASD diagnosis and treatment. Changes in the acylcarnitine profiles may indicate potential mitochondrial dysfunctions and abnormal fatty acid metabolism in ASD children. L-carnitine deficiency or deregulation of L-carnitine metabolism in ASD is accompanied by disturbances of other metabolic pathways, e.g., Krebs cycle, the activity of respiratory chain complexes, indicative of mitochondrial dysfunction. Supplementation of L-carnitine may be beneficial to alleviate behavioral and cognitive symptoms in ASD patients.
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47
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Ramzan R, Kadenbach B, Vogt S. Multiple Mechanisms Regulate Eukaryotic Cytochrome C Oxidase. Cells 2021; 10:cells10030514. [PMID: 33671025 PMCID: PMC7997345 DOI: 10.3390/cells10030514] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
Cytochrome c oxidase (COX), the rate-limiting enzyme of mitochondrial respiration, is regulated by various mechanisms. Its regulation by ATP (adenosine triphosphate) appears of particular importance, since it evolved early during evolution and is still found in cyanobacteria, but not in other bacteria. Therefore the "allosteric ATP inhibition of COX" is described here in more detail. Most regulatory properties of COX are related to "supernumerary" subunits, which are largely absent in bacterial COX. The "allosteric ATP inhibition of COX" was also recently described in intact isolated rat heart mitochondria.
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Affiliation(s)
- Rabia Ramzan
- Cardiovascular Research Laboratory, Biochemical-Pharmacological Center, Philipps-University Marburg, Karl-von-Frisch-Strasse 1, D-35043 Marburg, Germany;
| | - Bernhard Kadenbach
- Fachbereich Chemie, Philipps-University, D-35032 Marburg, Germany
- Correspondence:
| | - Sebastian Vogt
- Department of Heart Surgery, Campus Marburg, University Hospital of Giessen and Marburg, D-35043 Marburg, Germany;
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48
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Kato M, Fujibayashi N, Abe D, Matsubara N, Yasuda S, Yagi I. Impact of Heterometallic Cooperativity of Iron and Copper Active Sites on Electrocatalytic Oxygen Reduction Kinetics. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04753] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Masaru Kato
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
| | | | | | | | - Satoshi Yasuda
- Research Group for Nanoscale Structure and Function of Advanced Materials, Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ichizo Yagi
- Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
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49
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Xin JW, Chai ZX, Zhang CF, Yang YM, Zhang Q, Zhu Y, Cao HW, YangJi C, Zhong JC, Ji QM. Comparative Analysis of Skeleton Muscle Proteome Profile between Yak and Cattle Provides Insight into High-Altitude Adaptation. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666200127151931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background::
Mechanisms underlying yak adaptation to high-altitude environments have
been investigated at the levels of morphology, anatomy, physiology, genome and transcriptome, but
have not been explored at the proteome level.
Objective:
The protein profiles were compared between yak and cattle to explore molecular mechanisms
underlying yak adaptation to high altitude conditions.
Methods:
In the present study, an antibody microarray chip was developed, which included 6,500
mouse monoclonal antibodies. Immunoprecipitation and mass spectrometry were performed on 12
selected antibodies which showed that the chip was highly specific. Using this chip, muscle tissue proteome
was compared between yak and cattle, and 12 significantly Differentially Expressed Proteins (DEPs)
between yak and cattle were identified. Their expression levels were validated using Western blot.
Results:
ompared with cattle, higher levels of Rieske Iron-Sulfur Protein (RISP), Cytochrome C oxidase
subunit 4 isoform 1, mitochondrial (COX4I1), ATP synthase F1 subunit beta (ATP5F1B), Sarcoplasmic/
Endoplasmic Reticulum Calcium ATPase1 (SERCA1) and Adenosine Monophosphate Deaminase1
(AMPD1) in yak might improve oxygen utilization and energy metabolism. Pyruvate Dehydrogenase
protein X component (PDHX) and Acetyltransferase component of pyruvate dehydrogenase
complex (DLAT) showed higher expression levels and L-lactate dehydrogenase A chain (LDHA)
showed lower expression level in yak, which might help yak reduce the accumulation of lactic acid. In
addition, higher expression levels of Filamin C (FLNC) and low levels of AHNAK and Four and a half
LIM domains 1 (FHL1) in yak might reduce the risks of pulmonary arteries vasoconstriction, remodeling
and hypertension.
Conclusion:
Overall, the present study reported the differences in protein profile between yak and cattle,
which might be helpful to further understand molecular mechanisms underlying yak adaptation to
high altitude environments.
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Affiliation(s)
- Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yu-Mei Yang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Cidan YangJi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Jin-Cheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiu-Mei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
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50
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Noodleman L, Han Du WG, McRee D, Chen Y, Goh T, Götz AW. Coupled transport of electrons and protons in a bacterial cytochrome c oxidase-DFT calculated properties compared to structures and spectroscopies. Phys Chem Chem Phys 2021; 22:26652-26668. [PMID: 33231596 DOI: 10.1039/d0cp04848h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After a general introduction to the features and mechanisms of cytochrome c oxidases (CcOs) in mitochondria and aerobic bacteria, we present DFT calculated physical and spectroscopic properties for the catalytic reaction cycle compared with experimental observations in bacterial ba3 type CcO, also with comparisons/contrasts to aa3 type CcOs. The Dinuclear Complex (DNC) is the active catalytic reaction center, containing a heme a3 Fe center and a near lying Cu center (called CuB) where by successive reduction and protonation, molecular O2 is transformed to two H2O molecules, and protons are pumped from an inner region across the membrane to an outer region by transit through the CcO integral membrane protein. Structures, energies and vibrational frequencies for Fe-O and O-O modes are calculated by DFT over the catalytic cycle. The calculated DFT frequencies in the DNC of CcO are compared with measured frequencies from Resonance Raman spectroscopy to clarify the composition, geometry, and electronic structures of different intermediates through the reaction cycle, and to trace reaction pathways. X-ray structures of the resting oxidized state are analyzed with reference to the known experimental reaction chemistry and using DFT calculated structures in fitting observed electron density maps. Our calculations lead to a new proposed reaction pathway for coupling the PR → F → OH (ferryl-oxo → ferric-hydroxo) pathway to proton pumping by a water shift mechanism. Through this arc of the catalytic cycle, major shifts in pKa's of the special tyrosine and a histidine near the upper water pool activate proton transfer. Additional mechanisms for proton pumping are explored, and the role of the CuB+ (cuprous state) in controlling access to the dinuclear reaction site is proposed.
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Affiliation(s)
- Louis Noodleman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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