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Freindorf M, Antonio JJ, Kraka E. Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. J Comput Chem 2024; 45:574-588. [PMID: 38041830 DOI: 10.1002/jcc.27267] [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: 08/12/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka (FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x-ray structures. ka (FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka (FeN), allowing one to compare trends in diverse protein groups. Moreover, ka (NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Juliana J Antonio
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Elfi Kraka
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
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2
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Mantle D, Yang G. Hydrogen sulfide and metal interaction: the pathophysiological implications. Mol Cell Biochem 2022; 477:2235-2248. [PMID: 35461429 DOI: 10.1007/s11010-022-04443-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/08/2022] [Indexed: 11/27/2022]
Abstract
Hydrogen sulfide (H2S), previously recognized as a toxic gas, has emerged as an important gaseous signaling molecule along with nitric oxide, carbon monoxide and also hydrogen. H2S can be endogenously produced in the mammalian body at a very low level for various pathophysiological processes. Notably, H2S can interact with several essential metals in the body such as iron, copper, nickel, and zinc to carry out specific functions. The interactions of H2S with metal-binding proteins have been shown to aid in its signal transduction and cellular metabolism. In addition, H2S is capable of providing a cytoprotective role against metal toxicity. As the research in the field of H2S signaling in biology and medicine increases, much progresses have been developed for detecting H2S via interaction with metals. In this review, the interaction of H2S with metals, specifically in regard to metal-driven metabolism of H2S, the protection against metal toxicity by H2S and the detection of H2S using metals will be discussed. Discovering the interactions of this gasotransmitter with metals is important for determining the mechanisms underlying the cellular functions of H2S as well as developing novel therapeutic avenues.
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Affiliation(s)
- Devin Mantle
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
| | - Guangdong Yang
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada.
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada.
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3
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Malych R, Füssy Z, Ženíšková K, Arbon D, Hampl V, Hrdý I, Sutak R. The response of Naegleria gruberi to oxidative stress. Metallomics 2022; 14:6527579. [PMID: 35150262 DOI: 10.1093/mtomcs/mfac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/06/2022] [Indexed: 11/14/2022]
Abstract
Aerobic organisms require oxygen for respiration but must simultaneously cope with oxidative damages inherently linked with this molecule. Unicellular amoeboflagellates of the genus Naegleria, containing both free-living species and opportunistic parasite, thrive in aerobic environments. However, they are also known to maintain typical features of anaerobic organisms. Here, we describe the mechanisms of oxidative damage mitigation in Naegleria gruberi and focus on the molecular characteristics of three noncanonical proteins interacting with oxygen and its derived reactive forms. We show that this protist expresses hemerythrin, protoglobin and an aerobic-type rubrerythrin, with spectral properties characteristic of the cofactors they bind. We provide evidence that protoglobin and hemerythrin interact with oxygen in vitro and confirm the mitochondrial localization of rubrerythrin by immunolabeling. Our proteomic analysis and immunoblotting following heavy metal treatment revealed upregulation of hemerythrin, while rotenone treatment resulted in an increase in rubrerythrin protein levels together with vast upregulation of alternative oxidase. Our study provided new insights into the mechanisms employed by N. gruberi to cope with different types of oxidative stress and allowed us to propose specific roles for three unique and understudied proteins: hemerythrin, protoglobin and rubrerythrin.
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Affiliation(s)
- Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kateřina Ženíšková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Dominik Arbon
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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4
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Luo Y, Wan G, Zhou X, Wang Q, Zhang Y, Bao J, Cong Y, Zhao Y, Li D. Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release. Front Mol Biosci 2021; 8:701826. [PMID: 34557519 PMCID: PMC8453165 DOI: 10.3389/fmolb.2021.701826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical role in the Hedgehog (Hh) signaling pathway by releasing the dually lipidated ligand HhN from the membrane, a prerequisite step to the downstream signaling cascade. In this study, we focus on the Disp from water bear, a primitive animal known as the most indestructible on Earth. Using a zebrafish model, we show that the water bear homolog possesses the function of Disp. We have solved its structure to a 6.5-Å resolution using single-particle cryogenic electron microscopy. Consistent with the evolutional conservation of the pathway, the water bear Disp structure is overall similar to the previously reported structures of the fruit fly and human homologs. Although not revealing much detail at this resolution, the water bear Disp shows a different conformation compared to published structures, suggesting that they represent different functional snapshots.
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Affiliation(s)
- Yitian Luo
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guoyue Wan
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Zhou
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiuwen Wang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunbin Zhang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Bao
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Cong
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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Breuer M. The FEBS Journal: hidden gems. FEBS J 2021; 288:6586-6588. [PMID: 34263998 DOI: 10.1111/febs.16087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Every quarter, The FEBS Journal presents some of its "hidden gems"-original research and review-type articles that provide a significant advance or discuss recent developments in the molecular or cellular life sciences. These articles are of high value to the scientific community, and we like to take the opportunity to promote these contributions from previous issues of the journal, as we feel their scientific content merits a boost in exposure.
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Affiliation(s)
- Manuel Breuer
- The FEBS Journal Editorial Office Suite B1, Cambridge, UK
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Kobayashi K, Kim J, Fukuda Y, Kozawa T, Inoue T. Fields, biochemistry fast autooxidation of a Bis-Histidyl-ligated globin from the anhydrobiotic tardigrade, ramazzottius varieornatus, by molecular oxygen. J Biochem 2021; 169:663-673. [PMID: 33479760 DOI: 10.1093/jb/mvab003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/27/2020] [Indexed: 01/11/2023] Open
Abstract
Tardigrades, a phylum of meiofaunal organisms, exhibit extraordinary tolerance to various environmental conditions, including extreme temperatures (-272 to 151 °C) and exposure to ionizing radiation. Proteins from anhydrobiotic tardigrades with homology to known proteins from other organisms are new potential targets for structural genomics. Recently, we reported spectroscopic and structural characterization of a hexacoordinated hemoglobin (Kumaglobin [Kgb]) found in an anhydrobiotic tardigrade. In the absence of its exogenous ligand, Kgb displays hexacoordination with distal and proximal histidines. In this work, we analyzed binding of the molecular oxygen ligand following reduction of heme in Kgb using a pulse radiolysis technique. Radiolytically generated hydrated electrons (eaq-) reduced the heme iron of Kgb within 20 µs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediate with a second-order rate constant of 3.0 × 106 M-1 s-1. The intermediate was rapidly (within 0.1 s) autooxidized to the ferric form. Redox potential measurements revealed an E'0 of -400 mV (vs. SHE) in the ferric/ferrous couple. Our results suggest that Kgb may serve as a physiological generator of O2·- via redox signaling and/or electron transfer.
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - JeeEun Kim
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
| | - Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
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Fukuda Y, Kim J, Inoue T. Structure of cytochrome b 5 unique to tardigrades. Protein Sci 2020; 29:1829-1835. [PMID: 32483879 PMCID: PMC7380671 DOI: 10.1002/pro.3896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
Cytochrome b5 is an essential electron transfer protein, which is ubiquitously found in living systems and involved in wide variety of biological processes. Tardigrades (also known as water bears), some of which are famous for desiccation resistance, have many proteins unique to them. Here, we report spectroscopic and structural characterization of a cytochrome b5 like protein from one of the desiccation‐tolerant tardigrades, Ramazzottius varieornatus strain YOKOZUNA‐1 (RvCytb5). A 1.4 Å resolution crystal structure revealed that RvCytb5 is a new cytochrome b5 protein specific to tardigrades. PDB Code(s): 7BWH;
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Affiliation(s)
- Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - JeeEun Kim
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
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