1
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Lin YW. Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions. J Inorg Biochem 2024; 257:112595. [PMID: 38759262 DOI: 10.1016/j.jinorgbio.2024.112595] [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: 03/25/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China.
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2
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Chen ZY, Yuan H, Wang H, Sun LJ, Yu L, Gao SQ, Tan X, Lin YW. Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin. Chembiochem 2024; 25:e202300678. [PMID: 38015421 DOI: 10.1002/cbic.202300678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 11/29/2023]
Abstract
Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.
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Affiliation(s)
- Ze-Yuan Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
- Hengyang Medical School, University of South China, Hengyang, 421001, China
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3
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Daniel DJP, Shanmugasundaram S, Chandra Mohan KS, Siva Bharathi V, Abraham JK, Anbazhagan P, Pavadai P, Ram Kumar Pandian S, Sundar K, Kunjiappan S. Elucidating the role of phytocompounds from Brassica oleracea var. italic (Broccoli) on hyperthyroidism: an in-silico approach. In Silico Pharmacol 2024; 12:6. [PMID: 38187876 PMCID: PMC10766920 DOI: 10.1007/s40203-023-00180-2] [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: 10/21/2023] [Accepted: 11/10/2023] [Indexed: 01/09/2024] Open
Abstract
Thyroid hormone (TH) plays a crucial role in regulating the metabolism in every cell and all organs in of the human body. TH also control the rate of calorie burning, body weight, and function of the heartbeat. Therefore, the aim of the present study is to investigate the role of phytocompounds from Brassica oleracea var. italic (Broccoli) against irregularities of TH biosynthesis (hyperthyroidism) through in silico molecular modelling. Initially, the genetic network was built with graph theoretical network analysis to find the right target to control excessive TH production. Based on the network analysis, the three-dimensional crystal structure of the mammalian enzyme lactoperoxidase (PDB id: 5ff1) was retrieved from the protein data bank (PDB), and the active site was predicted using BIOVIA Discovery studio. Sixty-three phytocompounds were selected from the IMPPAT database and other literature. Selected sixty-six phytocompounds were docked against lactoperoxidase enzyme and compared with the standard drug methimazole. Based on the docking scores and binding energies, the top three compounds, namely brassicoside (- 10.00 kcal × mol-1), 24-methylene-25-methylcholesterol (- 9.50 kcal × mol-1), 5-dehydroavenasterol (- 9.40 kcal × mol-1) along with standard drug methimazole (- 4.10 kcal × mol-1) were selected for further ADMET and molecular dynamics simulation analysis. The top-scored compounds were for their properties such as ADMET, physicochemical and drug-likeness. The molecular dynamics simulation analyses proved the stability of lactoperoxidase-ligand complexes. The intermolecular interaction assessed by the dynamic conditions paved the way to discover the bioactive compounds brassicoside, 24-methylene-25-methylcholesterol, and 5-dehydroavenasterol prevent the excessive production of thyroid hormones. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00180-2.
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Affiliation(s)
- Derina J. Pearlin Daniel
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Shruthi Shanmugasundaram
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Karunya Sri Chandra Mohan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Velayutham Siva Bharathi
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Jins K. Abraham
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Parthiban Anbazhagan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, M S R Nagar, Bengaluru, 560054 Karnataka India
| | - Sureshbabu Ram Kumar Pandian
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Krishnan Sundar
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
| | - Selvaraj Kunjiappan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, 626126 Tamil Nadu India
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4
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Liu JJ, Wang ZY, Jiang BB, Gao SQ, Lin YW. Protective effect of thymoquinone on glycation of human myoglobin induced by d-ribose. Int J Biol Macromol 2023; 253:127016. [PMID: 37741485 DOI: 10.1016/j.ijbiomac.2023.127016] [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: 06/21/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Nonenzymatic glycation and the subsequent accumulation of advanced glycation end-products (AGEs) in proteins are factors underlying long-term pathogenesis in diabetes. The study of protein glycation is crucial for elucidating their relationship with diabetes mellitus and related disorders. This study explores the interaction between d-ribose and human myoglobin (HMb), as well as the protective effect of thymoquinone (TQ) on glycation. A time-dependent in-vitro glycation study was performed to investigate the mechanism of d-ribose-induced structural interference of HMb in the absence and presence of TQ. Spectroscopic and proteomic analysis indicated that the presence of TQ significantly reduced the total amount of AGEs while maintaining structural characteristics of HMb. 14 glycated sites on HMb were further identified via liquid chromatography-tandem mass spectrometry (LC-MS/MS) after incubation with d-ribose for 12 h, predominantly interacting with lysine residues. TQ was found to disrupt this interaction, reducing the glycated sites from 14 to 12 sites and the percentage of glycated peptides from 26.50 % to 12.97 %. Additionally, there was a significant decrease in the degree of glycation at the same sites. In summary, our findings suggest that TQ has the potential to act as an anti-glycation agent and provide a comprehensive understanding underlying the inhibition mechanism of glycation.
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Affiliation(s)
- Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Hunan Normal University, Ministry of Education, Changsha, Hunan 410081, China.
| | - Zhan-Yi Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Bin-Bin Jiang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
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Ghorbel M, Haddaji N, Feki K, Tounsi S, Chihaoui M, Alghamdi A, Mseddi K, Brini F. Identification of a putative kinase interacting domain in the durum wheat catalase 1 (TdCAT1) protein. Heliyon 2023; 9:e18916. [PMID: 37609422 PMCID: PMC10440534 DOI: 10.1016/j.heliyon.2023.e18916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Catalases are crucial antioxidant enzymes that regulate plants responses to different biotic and abiotic stresses. It has been previously shown that the activities of durum wheat catalase proteins (TdCAT1) were stimulated in the presence of divalent cations Mn2+, Mg2+, Fe2+, Zn2+, and Ca2+. In addition, TdCAT1s can interact with calmodulins in calcium-independent manner, and this interaction stimulates its catalytic activity in a calcium-dependent manner. Moreover, this activity is further enhanced by Mn2+ cations. The current study showed that wheat catalase presents different phosphorylation targets. Besides, we demonstrated that catalase is able to interact with Mitogen Activated Proteins kinases via a conserved domain. This interaction activates wheat catalase independently of its phosphorylation status but is more promoted by Mn2+, Fe2+ and Ca2+ divalent cations. Interestingly, we have demonstrated that durum wheat catalase activity is differentially regulated by Mitogen Activated Proteins kinases and Calmodulins in the presence of calcium. Moreover, the V0 of the reaction increase gradually following the increasing quantities of Mn2+ divalent cations. Such results have never been described before and suggest i) complex regulatory mechanisms exerted on wheat catalase, ii) divalent cations (Mn2+; Mg2+; Ca2+ and Fe2+) act as key cofactors in these regulatory mechanisms.
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Affiliation(s)
- Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Kaouthar Feki
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
| | - Sana Tounsi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
| | - Mejda Chihaoui
- Computer Science Departement, Applied College- University of Ha'il, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Ahmad Alghamdi
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Khalil Mseddi
- Department of Biology, Faculty of Science of Sfax, University of Sfax, Sfax, 3000, Tunisia
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
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6
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Baker A, Lin CC, Lett C, Karpinska B, Wright MH, Foyer CH. Catalase: A critical node in the regulation of cell fate. Free Radic Biol Med 2023; 199:56-66. [PMID: 36775107 DOI: 10.1016/j.freeradbiomed.2023.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Catalase (CAT) is an extensively studied if somewhat enigmatic enzyme that is at the heart of eukaryotic antioxidant systems with a canonical role in peroxisomal function. The CAT family of proteins exert control over a wide range of plant growth and defence processes. CAT proteins are subject to many types of post-translational modification (PTM), which modify activity, ligand binding, stability, compartmentation and function. The CAT interactome involves many cytosolic and nuclear proteins that appear to be essential for protein functions. Hence, the CAT network of roles extends far beyond those associated with peroxisomal metabolism. Some pathogen effector proteins are able to redirect CAT to the nucleus and recent evidence indicates CAT can traffic to the nucleus in the absence of exogenous proteins. While the mechanisms that target CAT to the nucleus are not understood, CAT activity in the cytosol and nucleus is promoted by interactions with nucleoredoxin. Here we discuss recent findings that have been pivotal in generating a step change in our understanding of CAT functions in plant cells.
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Affiliation(s)
- Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Chi-Chuan Lin
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Casey Lett
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Megan H Wright
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Christine H Foyer
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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7
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Tang S, Pan AQ, Wang XJ, Gao SQ, Tan XS, Lin YW. O 2 Carrier Myoglobin Also Exhibits β-Lactamase Activity That Is Regulated by the Heme Coordination State. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238478. [PMID: 36500571 PMCID: PMC9737100 DOI: 10.3390/molecules27238478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Heme proteins perform a variety of biological functions and also play significant roles in the field of bio-catalysis. The β-lactamase activity of heme proteins has rarely been reported. Herein, we found, for the first time, that myoglobin (Mb), an O2 carrier, also exhibits novel β-lactamase activity by catalyzing the hydrolysis of ampicillin. The catalytic proficiency ((kcat/KM)/kuncat) was determined to be 6.25 × 1010, which is much higher than the proficiency reported for designed metalloenzymes, although it is lower than that of natural β-lactamases. Moreover, we found that this activity could be regulated by an engineered disulfide bond, such as Cys46-Cys61 in F46C/L61C Mb or by the addition of imidazole to directly coordinate to the heme center. These results indicate that the heme active site is responsible for the β-lactamase activity of Mb. Therefore, the study suggests the potential of heme proteins acting as β-lactamases, which broadens the diversity of their catalytic functions.
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Affiliation(s)
- Shuai Tang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Ai-Qun Pan
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China Medical School, Hengyang 421001, China
| | - Xiang-Shi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
- Lab of Protein Structure and Function, University of South China Medical School, Hengyang 421001, China
- Correspondence: ; Tel.: +86-734-8282375
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Hansberg W. Monofunctional Heme-Catalases. Antioxidants (Basel) 2022; 11:2173. [PMID: 36358546 PMCID: PMC9687031 DOI: 10.3390/antiox11112173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 09/17/2023] Open
Abstract
The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H2O2) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one of the issues examined. Part of the answer is a gate valve system that is instrumental to drive out solvent molecules from the final section of the main channel. A second issue relates to how the enzyme deals with an unproductive reactive compound I (Cpd I) intermediate. Peroxidatic two and one electron donors and the transfer of electrons to the active site from NADPH and other compounds are reviewed. The new ascribed catalase reactions are revised, indicating possible measurement pitfalls. A third issue concerns the heme b to heme d oxidation, why this reaction occurs only in some large-size subunit catalases (LSCs), and the possible role of singlet oxygen in this and other modifications. The formation of a covalent bond between the proximal tyrosine with the vicinal residue is analyzed. The last issue refers to the origin and function of the additional C-terminal domain (TD) of LSCs. The TD has a molecular chaperone activity that is traced to a gene fusion between a Hsp31-type chaperone and a small-size subunit catalase (SSC).
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Affiliation(s)
- Wilhelm Hansberg
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
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9
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Qi YL, Wang HR, Chen LL, Duan YT, Yang SY, Zhu HL. Recent advances in small-molecule fluorescent probes for studying ferroptosis. Chem Soc Rev 2022; 51:7752-7778. [PMID: 36052828 DOI: 10.1039/d1cs01167g] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferroptosis is an iron-dependent, non-apoptotic form of programmed cell death driven by excessive lipid peroxidation (LPO). Mounting evidence suggests that the unique modality of cell death is involved in the development and progression of several diseases including cancer, cardiovascular diseases (CVDs), neurodegenerative disorders, etc. However, the pathogenesis and signalling pathways of ferroptosis are not fully understood, possibly due to the lack of robust tools for the highly selective and sensitive imaging of ferroptosis analytes in complex living systems. Up to now, various small-molecule fluorescent probes have been applied as promising chemosensors for studying ferroptosis through tracking the biomolecules or microenvironment-related parameters in vitro and in vivo. In this review, we comprehensively reviewed the recent development of small-molecule fluorescent probes for studying ferroptosis, with a focus on the analytes, design strategies and bioimaging applications. We also provided new insights to overcome the major challenges in this emerging field.
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Affiliation(s)
- Ya-Lin Qi
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China. .,Henan Provincial Key Laboratory of Pediatric Hematology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.,Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA.
| | - Hai-Rong Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Li-Li Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yong-Tao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China. .,Henan Provincial Key Laboratory of Pediatric Hematology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China
| | - Sheng-Yu Yang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA.
| | - Hai-Liang Zhu
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China. .,Henan Provincial Key Laboratory of Pediatric Hematology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450018, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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10
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Yuan Z, De La Cruz LK, Yang X, Wang B. Carbon Monoxide Signaling: Examining Its Engagement with Various Molecular Targets in the Context of Binding Affinity, Concentration, and Biologic Response. Pharmacol Rev 2022; 74:823-873. [PMID: 35738683 DOI: 10.1124/pharmrev.121.000564] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Carbon monoxide (CO) has been firmly established as an endogenous signaling molecule with a variety of pathophysiological and pharmacological functions, including immunomodulation, organ protection, and circadian clock regulation, among many others. In terms of its molecular mechanism(s) of action, CO is known to bind to a large number of hemoproteins with at least 25 identified targets, including hemoglobin, myoglobin, neuroglobin, cytochrome c oxidase, cytochrome P450, soluble guanylyl cyclase, myeloperoxidase, and some ion channels with dissociation constant values spanning the range of sub-nM to high μM. Although CO's binding affinity with a large number of targets has been extensively studied and firmly established, there is a pressing need to incorporate such binding information into the analysis of CO's biologic response in the context of affinity and dosage. Especially important is to understand the reservoir role of hemoglobin in CO storage, transport, distribution, and transfer. We critically review the literature and inject a sense of quantitative assessment into our analyses of the various relationships among binding affinity, CO concentration, target occupancy level, and anticipated pharmacological actions. We hope that this review presents a picture of the overall landscape of CO's engagement with various targets, stimulates additional research, and helps to move the CO field in the direction of examining individual targets in the context of all of the targets and the concentration of available CO. We believe that such work will help the further understanding of the relationship of CO concentration and its pathophysiological functions and the eventual development of CO-based therapeutics. SIGNIFICANCE STATEMENT: The further development of carbon monoxide (CO) as a therapeutic agent will significantly rely on the understanding of CO's engagement with therapeutically relevant targets of varying affinity. This review critically examines the literature by quantitatively analyzing the intricate relationships among targets, target affinity for CO, CO level, and the affinity state of carboxyhemoglobin and provide a holistic approach to examining the molecular mechanism(s) of action for CO.
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Affiliation(s)
- Zhengnan Yuan
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Ladie Kimberly De La Cruz
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia
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11
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Suprun EV, Budnikov HC. Bioelectrochemistry as a Field of Analysis: Historical Aspects and Current Status. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822060168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Feng Y, Liu XC, Li L, Gao SQ, Wen GB, Lin YW. Naturally Occurring I81N Mutation in Human Cytochrome c Regulates Both Inherent Peroxidase Activity and Interactions with Neuroglobin. ACS OMEGA 2022; 7:11510-11518. [PMID: 35415373 PMCID: PMC8992277 DOI: 10.1021/acsomega.2c01256] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 05/24/2023]
Abstract
Human cytochrome c (hCyt c) is a crucial heme protein and plays an indispensable role in energy conversion and intrinsic apoptosis pathways. The sequence and structure of Cyt c were evolutionarily conserved and only a few naturally occurring mutants were detected in humans. Among those variable sites, position 81 was proposed to act as a peroxidase switch in the initiation stages of apoptosis. In this study, we show that Ile81 not only suppresses the intrinsic peroxidase activity but also is essential for Cyt c to interact with neuroglobin (Ngb), a potential protein partner. The kinetic assays showed that the peroxidase activity of the naturally occurring variant I81N was enhanced up to threefold under pH 5. The local stability of the Ω-loop D (residues 70-85) in the I81N variant was decreased. Moreover, the Alphafold2 program predicted that Ile81 forms stable contact with human Ngb. Meanwhile, the Ile81 to Asn81 missense mutation abolishes the interaction interface, resulting in a ∼40-fold decrease in binding affinity. These observations provide an insight into the structure-function relationship of the conserved Ile81 in vertebrate Cyt c.
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Affiliation(s)
- Yu Feng
- School
of Chemistry and Chemical Engineering, University
of South China, Hengyang 421001, China
| | - Xi-Chun Liu
- School
of Chemistry and Chemical Engineering, University
of South China, Hengyang 421001, China
| | - Lianzhi Li
- School
of Chemistry and Chemical Engineering, Liaocheng
University, Liaocheng 252059, China
| | - Shu-Qin Gao
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School
of Chemistry and Chemical Engineering, University
of South China, Hengyang 421001, China
- Key
Lab of Protein Structure and Function of Universities in Hunan Province, University of South China, Hengyang 421001, China
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13
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Elkholi IE, Elsherbiny ME, Emara M. Myoglobin: From physiological role to potential implications in cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188706. [PMID: 35247507 DOI: 10.1016/j.bbcan.2022.188706] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/18/2022] [Accepted: 02/26/2022] [Indexed: 10/19/2022]
Abstract
Myoglobin (MB) belongs to the well-studied globin proteins superfamily. It has been extensively studied for its physiological roles in oxygen storage and transport for about a century now. However, the last two decades shed the light on unexpected aspects for MB research. Myoglobin has been suggested as a scavenger for nitric oxide and reactive oxygen species (ROS). Furthermore, MB was found to be expressed and regulated in different tissues, beyond the muscle lineage, including cancers. Current evidence suggest that MB is directly regulated by hypoxia and might be contributing to the metabolic rewiring in cancer tissues. In this article, we first discuss the MB physiological roles and then focus on the latter potential roles and regulatory networks of MB in cancer.
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Affiliation(s)
- Islam E Elkholi
- Center for Aging and Associated Diseases (CAAD), Zewail City of Science, Technology, and Innovation, 6th of October City, Giza 12578, Egypt; Montreal Clinical Research Institute (IRCM), Montréal, QC H2W 1R7, Canada; Molecular Biology Programs, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza, Egypt
| | - Marwan Emara
- Center for Aging and Associated Diseases (CAAD), Zewail City of Science, Technology, and Innovation, 6th of October City, Giza 12578, Egypt.
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14
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Patenaude BF, Berda EB, Pazicni S. Probing secondary coordination sphere interactions within porphyrin-cored polymer nanoparticles. Polym Chem 2022. [DOI: 10.1039/d1py01005k] [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
A suite of zinc porphyrin-cored polymeric nanoparticles were synthesized and characterized to study secondary coordination sphere interactions. We show that with proper design these materials catalyze the reaction of cyanide with N,N-dimethylformamide.
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Affiliation(s)
- Brian F. Patenaude
- Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, USA
| | - Erik B. Berda
- Department of Chemistry, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, USA
- Materials Science Program, University of New Hampshire, 23 Academic Way, Durham, New Hampshire 03824, USA
| | - Samuel Pazicni
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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15
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Liu JJ, You Y, Gao SQ, Tang S, Chen L, Wen GB, Lin YW. Identification of the Protein Glycation Sites in Human Myoglobin as Rapidly Induced by d-Ribose. Molecules 2021; 26:molecules26195829. [PMID: 34641382 PMCID: PMC8512392 DOI: 10.3390/molecules26195829] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Protein glycation is an important protein post-translational modification and is one of the main pathogenesis of diabetic angiopathy. Other than glycated hemoglobin, the protein glycation of other globins such as myoglobin (Mb) is less studied. The protein glycation of human Mb with ribose has not been reported, and the glycation sites in the Mb remain unknown. This article reports that d-ribose undergoes rapid protein glycation of human myoglobin (HMb) at lysine residues (K34, K87, K56, and K147) on the protein surface, as identified by ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). Moreover, glycation by d-ribose at these sites slightly decreased the rate of the met heme (FeIII) in reaction with H2O2 to form a ferryl heme (FeIV=O). This study provides valuable insight into the protein glycation by d-ribose and provides a foundation for studying the structure and function of glycated heme proteins.
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Affiliation(s)
- Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (J.-J.L.); (S.T.); (L.C.)
| | - Yong You
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China; (Y.Y.); (S.-Q.G.); (G.-B.W.)
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China; (Y.Y.); (S.-Q.G.); (G.-B.W.)
| | - Shuai Tang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (J.-J.L.); (S.T.); (L.C.)
| | - Lei Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (J.-J.L.); (S.T.); (L.C.)
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China; (Y.Y.); (S.-Q.G.); (G.-B.W.)
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; (J.-J.L.); (S.T.); (L.C.)
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China; (Y.Y.); (S.-Q.G.); (G.-B.W.)
- Correspondence: ; Tel.: +86-734-8282375
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16
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Guo WJ, Xu JK, Liu JJ, Lang JJ, Gao SQ, Wen GB, Lin YW. Biotransformation of Lignin by an Artificial Heme Enzyme Designed in Myoglobin With a Covalently Linked Heme Group. Front Bioeng Biotechnol 2021; 9:664388. [PMID: 34136471 PMCID: PMC8201792 DOI: 10.3389/fbioe.2021.664388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
The conversion of Kraft lignin in plant biomass into renewable chemicals, aiming at harvesting aromatic compounds, is a challenge process in biorefinery. Comparing to the traditional chemical methods, enzymatic catalysis provides a gentle way for the degradation of lignin. Alternative to natural enzymes, artificial enzymes have been received much attention for potential applications. We herein achieved the biodegradation of Kraft lignin using an artificial peroxidase rationally designed in myoglobin (Mb), F43Y/T67R Mb, with a covalently linked heme cofactor. The artificial enzyme of F43Y/T67R Mb has improved catalytic efficiencies at mild acidic pH for phenolic and aromatic amine substrates, including Kraft lignin and the model lignin dimer guaiacylglycerol-β-guaiacyl ether (GGE). We proposed a possible catalytic mechanism for the biotransformation of lignin catalyzed by the enzyme, based on the results of kinetic UV-Vis studies and UPLC-ESI-MS analysis, as well as molecular modeling studies. With the advantages of F43Y/T67R Mb, such as the high-yield by overexpression in E. coli cells and the enhanced protein stability, this study suggests that the artificial enzyme has potential applications in the biodegradation of lignin to provide sustainable bioresource.
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Affiliation(s)
- Wen-Jie Guo
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Kun Xu
- Key Lab of Sustainable Development of Polar Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Lab for Marine Drugs and Byproducts of Pilot National Lab for Marine Science and Technology, Qingdao, China
| | - Jing-Jing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
| | - Jia-Jia Lang
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, China
- Laboratory of Protein Structure and Function, University of South China Medical School, Hengyang, China
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17
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Mori F, Natali L, Danesi R, Nannizzi S, Farina C. Post-translational modifications and antioxidant properties of different therapeutic human serum albumins. Int J Biol Macromol 2021; 183:927-935. [PMID: 33971232 DOI: 10.1016/j.ijbiomac.2021.05.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/05/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
Human serum albumin (HSA) is widely used for the treatment of diverse clinical conditions to restore plasma volume, manage burns and treat hypoproteinemia.Although the HSA preparations should ideally preserve its functionality, the structural integrity and antioxidant properties of HSA may be compromised as a result of the manufacturing process. The present study examined seven commercially available HSA preparations for clinical use to investigate their post-translational modifications (PTMs) and antioxidant activity, including DPPH radical-scavenging, peroxyl radical antioxidant and metal binding activities, by means of mass spectrometry and Ellman's assay. The results confirmed that most of the PTMs of HSA and especially the oxidation of the free thiol residue varied between the different commercial albumins and the percentage of these PTMs were higher than those of physiological HSA. Moreover, HSA-DA isoform was increased at the end of the stability time and new oxidative modifications occurred in these samples. In conclusion, the bioprocesses for production of commercial albumins are responsible of their wide heterogeneity, being the ethanol fractionation and their storage conditions the more critical phases. Nonetheless, the Kedrion albumin shows a high content of free thiol and a lower concentration of PTMs than other commercial albumins.
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Affiliation(s)
- Filippo Mori
- Kedrion S.p.A., Research and Innovation Department, Via di Fondovalle, Loc., Bolognana 55027, Gallicano (LU), Italy.
| | - Letizia Natali
- Kedrion S.p.A., Research and Innovation Department, Via di Fondovalle, Loc., Bolognana 55027, Gallicano (LU), Italy
| | - Romano Danesi
- University of Pisa, Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, Via Roma 55, Pisa, Italy
| | - Silvia Nannizzi
- Kedrion S.p.A., Research and Innovation Department, Via di Fondovalle, Loc., Bolognana 55027, Gallicano (LU), Italy
| | - Claudio Farina
- Kedrion S.p.A., Research and Innovation Department, Via di Fondovalle, Loc., Bolognana 55027, Gallicano (LU), Italy
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18
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Wang Y, Li S, Rentfrow G, Chen J, Zhu H, Suman SP. Myoglobin Post-Translational Modifications Influence Color Stability of Beef Longissimus Lumborum. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.11689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Post-translational modifications (PTM) of proteins play critical roles in biological processes. PTM of muscle proteins influence meat quality. Nonetheless, myoglobin (Mb) PTM and their impact on fresh beef color stability have not been characterized yet. Therefore, our objectives were to identify Mb PTM in beef longissimus lumborum muscle during postmortem aging and to characterize their influence on color stability. The longissimus lumborum muscles from 9 (n = 9) beef carcasses (24 h postmortem) were subjected to wet aging for 0, 7, 14, and 21 d. At the end of each wet-aging period, steaks were fabricated. One steak for analyses of PTM was immediately frozen at −80°C, whereas other steaks were assigned to refrigerated storage in the darkness under aerobic packaging. Instrumental color and biochemical attributes were evaluated on day 0, 3, or 6 of storage. Mb PTM were analyzed using two-dimensional electrophoresis and tandem mass spectrometry. Surface redness (a* value), color stability, and Mb concentration decreased (P < 0.05) upon aging. Gel image analyses identified 6 Mb spots with similar molecular weight (17 kDa) but different isoelectric pH. Tandem mass spectrometry identified multiple PTM (phosphorylation, methylation, carboxymethylation, acetylation, and 4-hydroxynonenal alkylation) in these 6 isoforms. The amino acids susceptible to phosphorylation were serine (S), threonine (T), and tyrosine, whereas other PTM were detected in lysine (K), arginine (R), and histidine residues. Additionally, distal histidine (position 64), critical to heme stability, was found to be alkylated. Overall, Mb PTM increased with aging. The aging-induced PTM, especially those occurring close to hydrophobic heme pocket, could disrupt Mb tertiary structure, influence heme affinity, and compromise oxygen binding capacity, leading to decreased color stability of fresh beef. Furthermore, PTM at K45, K47, and K87 were unique to Mb from non-aged beef, whereas PTM at R31, T51, K96, K98, S121, R139, and K147 were unique to Mb from aged counterparts, indicating that these Mb PTM could be used as novel biomarkers for fresh beef color stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Gregg Rentfrow
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
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19
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Shumyantseva VV, Agafonova LE, Bulko TV, Kuzikov AV, Masamrekh RA, Yuan J, Pergushov DV, Sigolaeva LV. Electroanalysis of Biomolecules: Rational Selection of Sensor Construction. BIOCHEMISTRY (MOSCOW) 2021; 86:S140-S151. [PMID: 33827405 DOI: 10.1134/s0006297921140108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.
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Affiliation(s)
- Victoria V Shumyantseva
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia. .,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Lubov E Agafonova
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia
| | - Tatiana V Bulko
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia
| | - Alexey V Kuzikov
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Rami A Masamrekh
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Jiayin Yuan
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, 10691, Sweden
| | - Dmitry V Pergushov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 117991, Russia
| | - Larisa V Sigolaeva
- Laboratory of Bioelectrochemistry, Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119992, Russia.,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 117991, Russia
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20
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Suprun EV. Direct electrochemistry of proteins and nucleic acids: The focus on 3D structure. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2021.106983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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21
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Liu Y, Chen Z, Shao Z, Guo R. Single gold nanoparticle-driven heme cofactor nanozyme as an unprecedented oxidase mimetic. Chem Commun (Camb) 2021; 57:3399-3402. [PMID: 33686388 DOI: 10.1039/d1cc00279a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The catalytic diversity of heme enzymes is a perpetuating pursuit for biomimetic chemistry, but heme nanozymes exhibit catalytic activity only reminiscent of peroxidases. Miraculously, the oxidase-like catalytic function of a heme cofactor is elicited with the help of gold nanoparticles (AuNPs) by maintaining heme with a low-valence state (ferrous) in a confined configuration.
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Affiliation(s)
- Yan Liu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, P. R. China.
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22
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Crosslinking of human plasma C-reactive protein to human serum albumin via disulfide bond oxidation. Redox Biol 2021; 41:101925. [PMID: 33714740 PMCID: PMC7966873 DOI: 10.1016/j.redox.2021.101925] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 01/08/2023] Open
Abstract
Inter- and intra-molecular crosslinks can generate protein dysfunction, and are associated with protein aggregate accumulation in aged and diseased tissues. Crosslinks formed between multiple amino acid side chains can be reversible or irreversible. Disulfides formed either enzymatically, or as a result of oxidant-mediated reactions, are a major class of reversible crosslinks. Whilst these are commonly generated via oxidation of Cys thiol groups, they are also formed by ‘oxidant-mediated thiol-disulfide reactions’ via initial disulfide oxidation to a thiosulfinate or zwitterionic peroxide, and subsequent reaction with another thiol including those on other proteins. This generates new intermolecular protein-protein crosslinks. Here we demonstrate that photooxidation, or reaction with the biological oxidants HOCl and ONOOH, of the single disulfide present in the major human plasma inflammatory protein, C-reactive protein (CRP) can give rise to reversible disulfide bond formation with human serum albumin (HSA). This occurs in an oxidant dose-, or illumination-time-, dependent manner. These CRP-HSA crosslinks are formed both in isolated protein systems, and in fresh human plasma samples containing high, but not low, levels of CRP. The inter-protein crosslinks which involve Cys36 of CRP and Cys34 of HSA, have been detected by both immunoblotting and mass spectrometry (MS). The yield of protein-protein crosslinks depends on the nature and extent of oxidant exposure, and can be reversed by dithiothreitol and tris(2-carboxyethyl)phosphine hydrochloride. These data indicate that oxidation of disulfide bonds in proteins can be a source of novel inter-protein crosslinks, which may help rationalize the accumulation of crosslinked proteins in aged and diseased tissues. C-reactive protein (CRP) is a major acute phase inflammatory protein in human plasma. Oxidation of the single Cys36-Cys97 disulfide in CRP generates reactive intermediates. The oxidized disulfide reacts with Cys34 of human serum albumin to forms a new crosslink. The inter-protein CRP-HSA crosslink has been characterized by immunoblotting and LS-MS/MS. This novel crosslink may be a long-lived plasma marker of inflammation-induced damage.
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23
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Tifoun N, De las Heras JM, Guillaume A, Bouleau S, Mignotte B, Le Floch N. Insights into the Roles of the Sideroflexins/SLC56 Family in Iron Homeostasis and Iron-Sulfur Biogenesis. Biomedicines 2021; 9:103. [PMID: 33494450 PMCID: PMC7911444 DOI: 10.3390/biomedicines9020103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/25/2023] Open
Abstract
Sideroflexins (SLC56 family) are highly conserved multi-spanning transmembrane proteins inserted in the inner mitochondrial membrane in eukaryotes. Few data are available on their molecular function, but since their first description, they were thought to be metabolite transporters probably required for iron utilization inside the mitochondrion. Such as numerous mitochondrial transporters, sideroflexins remain poorly characterized. The prototypic member SFXN1 has been recently identified as the previously unknown mitochondrial transporter of serine. Nevertheless, pending questions on the molecular function of sideroflexins remain unsolved, especially their link with iron metabolism. Here, we review the current knowledge on sideroflexins, their presumed mitochondrial functions and the sparse-but growing-evidence linking sideroflexins to iron homeostasis and iron-sulfur cluster biogenesis. Since an imbalance in iron homeostasis can be detrimental at the cellular and organismal levels, we also investigate the relationship between sideroflexins, iron and physiological disorders. Investigating Sideroflexins' functions constitutes an emerging research field of great interest and will certainly lead to the main discoveries of mitochondrial physio-pathology.
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Affiliation(s)
- Nesrine Tifoun
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - José M. De las Heras
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Arnaud Guillaume
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Sylvina Bouleau
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
| | - Bernard Mignotte
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- École Pratique des Hautes Études, PSL University, 75014 Paris, France
| | - Nathalie Le Floch
- LGBC, UVSQ, Université Paris-Saclay, 78000 Versailles, France; (N.T.); (J.M.D.l.H.); (A.G.); (S.B.); (B.M.)
- GCGP Department, IUT de Vélizy/Rambouillet, UVSQ, Université Paris-Saclay, 78120 Rambouillet, France
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24
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Peoc'h K, Puy V, Fournier T. Haem oxygenases play a pivotal role in placental physiology and pathology. Hum Reprod Update 2020; 26:634-649. [PMID: 32347305 DOI: 10.1093/humupd/dmaa014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Haem oxygenases (HO) catabolise haem, which is the prosthetic group of numerous haemoproteins. Thus, multiple primary cellular pathways and functions rely on haem availability. HO exists in two isoforms, both expressed in the placenta, namely HO-1 and HO-2, the first being inducible. Haem oxygenases, particularly HO-1, have garnered specific interest in the field of physiological and pathological placental function. These enzymes mediate haem degradation by cleaving the alpha methene bridge to produce biliverdin, which is subsequently converted to bilirubin, carbon monoxide and iron. HO-1 has anti-inflammatory and antioxidant activities. SEARCH METHODS An initial literature analysis was performed using PubMed on 3 October 2018 using key terms such as 'haem oxygenase and pregnancy', 'haem oxygenase and placenta', 'HO-1 and pregnancy', 'HO-1 and placenta', 'HO and placenta', 'HO and pregnancy', 'genetic variant and HO', 'CO and pregnancy', 'CO and placenta', 'Bilirubin and pregnancy', 'Iron and pregnancy' and 'PPAR and Haem', selecting consensus conferences, recommendations, meta-analyses, practical recommendations and reviews. A second literature analysis was performed, including notable miscarriages, foetal loss and diabetes mellitus, on 20 December 2019. The three authors studied the publications independently to decipher whether they should be included in the manuscript. OBJECTIVE AND RATIONALE This review aimed to summarise current pieces of knowledge of haem oxygenase location, function and regulation in the placenta, either in healthy pregnancies or those associated with miscarriages and foetal loss, pre-eclampsia, foetal growth restriction and diabetes mellitus. OUTCOMES HO-1 exerts some protective effects on the placentation, probably by a combination of factors, including its interrelation with the PGC-1α/PPAR pathway and the sFlt1/PlGF balance, and through its primary metabolites, notably carbon monoxide and bilirubin. Its protective role has been highlighted in numerous pregnancy conditions, including pre-eclampsia, foetal growth restriction, gestational diabetes mellitus and miscarriages. WIDER IMPLICATIONS HO-1 is a crucial enzyme in physiological and pathological placentation. This protective enzyme is currently considered a potential therapeutic target in various pregnancy diseases.
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Affiliation(s)
- Katell Peoc'h
- Université de Paris, Laboratory of Excellence GR-Ex, Centre de Recherche sur l'Inflammation, INSERM U1149, UFR de Médecine Bichat, 75018 Paris, France
- Assistance Publique des Hôpitaux de Paris, APHP Nord, Paris, France
| | - Vincent Puy
- Reproductive Biology Unit CECOS, Paris-Saclay University, Antoine Béclère Hospital, APHP, Clamart 92140, France
- Laboratoire de Développement des Gonades, UMRE008 Stabilité Génétique Cellules Souches et Radiations, Université de Paris, Université Paris-Saclay, CEA, F-92265 Fontenay-aux-Roses, France
| | - Thierry Fournier
- Université de Paris, INSERM, UMR-S 1139, 3PHM, F-75006, Paris, France
- Fondation PremUp, F-75014, Paris, France
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25
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Abstract
Ammonia-oxidizing bacteria (AOB) convert ammonia (NH3) to nitrite (NO2-) as their primary metabolism and thus provide a blueprint for the use of NH3 as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH2OH) to NO2-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH2OH and were both originally reported to produce NO2-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH2OH oxidation. Under aerobic conditions substoichiometric production of NO2- was observed along with production of nitrous oxide (N2O). Under anaerobic conditions, however, N2O was the exclusive product of NH2OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O2, thus producing NO2- abiotically. Because N2O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO2- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO2- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH2OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH2OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.
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Affiliation(s)
- Rachael E. Coleman
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M. Lancaster
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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Effects of histamine and sodium hypochlorite on prooxidand state in the rats erytrocytes. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2020. [DOI: 10.2478/cipms-2020-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
We studied the simultaneous influence of histamine and sodium hypochlorite (SH) on lipid peroxidation processes, as well as the level of structural changes in membranes (via the content of sialic acid) in rat erythrocytes. We established that histamine affects lipid peroxidation processes with the formation of lipid hydroperoxides, damages proteins and reduces the content of sialic acids, which leads to changes in the surface charge of red blood cells. However, the simultaneous action of histamine and low SH concentration has a positive effect in that it corrects the pro-oxidant state of erythrocytes. Hence, the content of lipid hydroperoxides, TBA-active products, carbonyl groups of proteins and sialic acids were mainly reduced after the simultaneous action of histamine and SH at all studied concentrations during the rehabilitation period.
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Palma JM, Mateos RM, López-Jaramillo J, Rodríguez-Ruiz M, González-Gordo S, Lechuga-Sancho AM, Corpas FJ. Plant catalases as NO and H 2S targets. Redox Biol 2020; 34:101525. [PMID: 32505768 PMCID: PMC7276441 DOI: 10.1016/j.redox.2020.101525] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/20/2022] Open
Abstract
Catalase is a powerful antioxidant metalloenzyme located in peroxisomes which also plays a central role in signaling processes under physiological and adverse situations. Whereas animals contain a single catalase gene, in plants this enzyme is encoded by a multigene family providing multiple isoenzymes whose number varies depending on the species, and their expression is regulated according to their tissue/organ distribution and the environmental conditions. This enzyme can be modulated by reactive oxygen and nitrogen species (ROS/RNS) as well as by hydrogen sulfide (H2S). Catalase is the major protein undergoing Tyr-nitration [post-translational modification (PTM) promoted by RNS] during fruit ripening, but the enzyme from diverse sources is also susceptible to undergo other activity-modifying PTMs. Data on S-nitrosation and persulfidation of catalase from different plant origins are given and compared here with results from obese children where S-nitrosation of catalase occurs. The cysteine residues prone to be S-nitrosated in catalase from plants and from bovine liver have been identified. These evidences assign to peroxisomes a crucial statement in the signaling crossroads among relevant molecules (NO and H2S), since catalase is allocated in these organelles. This review depicts a scenario where the regulation of catalase through PTMs, especially S-nitrosation and persulfidation, is highlighted.
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Affiliation(s)
- José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Dept. Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Rosa M Mateos
- Imflammation, Nutrition, Metabolism and Oxidative Stress Study Group (INMOX), Biomedical Research and Innovation Institute of Cádiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain; Area of Biochemistry and Molecular Biology, Department of Biomedicine, Biotechnology and Public Health, University of Cádiz, Cádiz, Spain
| | | | - Marta Rodríguez-Ruiz
- Laboratório de Fisiologia do Desenvolvimiento Vegetal; Instituto de Biociências-Universidad de São Paulo; Cidade Universitária-São Paulo-SP, Brazil
| | - Salvador González-Gordo
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Dept. Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - Alfonso M Lechuga-Sancho
- Imflammation, Nutrition, Metabolism and Oxidative Stress Study Group (INMOX), Biomedical Research and Innovation Institute of Cádiz (INiBICA), Research Unit, Puerta del Mar University Hospital, Cádiz, Spain; Department of Child and Mother Health and Radiology, Medical School, University of Cádiz, Cádiz, Spain
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Dept. Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, Spain
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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Shumyantseva VV, Bulko TV, Kuzikov AV, Masamrekh RA, Pergushov DV, Schacher FH, Sigolaeva LV. Electrochemical fingerprint of cytochrome c on a polymer/MWCNT nanocomposite electrode. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond. Int J Mol Sci 2020; 21:ijms21072512. [PMID: 32260401 PMCID: PMC7177771 DOI: 10.3390/ijms21072512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/23/2022] Open
Abstract
Protein design is able to create artificial proteins with advanced functions, and computer simulation plays a key role in guiding the rational design. In the absence of structural evidence for cytoglobin (Cgb) with an intramolecular disulfide bond, we recently designed a de novo disulfide bond in myoglobin (Mb) based on structural alignment (i.e., V21C/V66C Mb double mutant). To provide deep insight into the regulation role of the Cys21-Cys66 disulfide bond, we herein perform molecular dynamics (MD) simulation of the fluoride–protein complex by using a fluoride ion as a probe, which reveals detailed interactions of the fluoride ion in the heme distal pocket, involving both the distal His64 and water molecules. Moreover, we determined the kinetic parameters of fluoride binding to the double mutant. The results agree with the MD simulation and show that the formation of the Cys21-Cys66 disulfide bond facilitates both fluoride binding to and dissociating from the heme iron. Therefore, the combination of theoretical and experimental studies provides valuable information for understanding the structure and function of heme proteins, as regulated by a disulfide bond. This study is thus able to guide the rational design of artificial proteins with tunable functions in the future.
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Kim H, Sharma SK, Schaefer AW, Solomon EI, Karlin KD. Heme-Cu Binucleating Ligand Supports Heme/O 2 and Fe II-Cu I/O 2 Reactivity Providing High- and Low-Spin Fe III-Peroxo-Cu II Complexes. Inorg Chem 2019; 58:15423-15432. [PMID: 31657921 DOI: 10.1021/acs.inorgchem.9b02521] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The focus of this study is in the description of synthetic heme/copper/O2 chemistry employing a heme-containing binucleating ligand which provides a tridentate chelate for copper ion binding. The addition of O2 (-80 °C, tetrahydrofuran (THF) solvent) to the reduced heme compound (PImH)FeII (1), gives the oxy-heme adduct, formally a heme-superoxide complex FeIII-(O2•-) (2) (resonance Raman spectroscopy (rR): νO-O, 1171 cm-1 (Δ18O2, -61 cm-1); νFe-O, 575 cm-1 (Δ18O2, -24 cm-1)). Simple warming of 2 to room temperature regenerates reduced complex 1; this reaction is reversible, as followed by UV-vis spectroscopy. Complex 2 is electron paramagnetic resonance (EPR)-silent and exhibits upfield-shifted pyrrole resonances (δ 9.12 ppm) in 2H NMR spectroscopy, indicative of a six-coordinate low-spin heme. The coordination of the tethered imidazolyl arm to the heme-superoxide complex as an axial base ligand is suggested. We also report the new fully reduced heme-copper complex [(PImH)FeIICuI]+ (3), where the copper ion is bound to the tethered tridentate portion of PImH. This reacts with O2 to give a distinctive low-temperature-stable, high-spin (S = 2, overall) peroxo-bridged complex [(PImH)FeIII-(O22-)-CuII]+ (3a): λmax, 420 (Soret), 545, 565 nm; δpyrr, 93 ppm; νO-O, 799 cm-1 (Δ18O2, -48 cm-1); νFe-O, 524 cm-1 (Δ18O2, -23 cm-1). To 3a, the addition of dicyclohexylimidazole (DCHIm), which serves as a heme axial base, leads to low-spin (S = 0 overall) species complex [(DCHIm)(PImH)FeIII-(O22-)-CuII]+ (3b): λmax, 425 (Soret), 538 nm; δpyrr, 10.2 ppm; νO-O, 817 cm-1 (Δ18O2, -55 cm-1); νFe-O, 610 cm-1 (Δ18O2, -26 cm-1). These investigations into the characterization of the O2-adducts from (PImH)FeII (1) with/without additional copper chelation advance our understanding of the dioxygen reactivity of heme-only and heme/Cu-ligand heterobinuclear system, thus potentially relevant to O2 reduction in heme-copper oxidases or fuel-cell chemistry.
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Affiliation(s)
- Hyun Kim
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Savita K Sharma
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Andrew W Schaefer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Edward I Solomon
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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32
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Lin YW. Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters. Molecules 2019; 24:E2743. [PMID: 31362341 PMCID: PMC6696605 DOI: 10.3390/molecules24152743] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China.
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33
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Suprun EV. Protein post-translational modifications – A challenge for bioelectrochemistry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ehudin MA, Senft L, Franke A, Ivanović-Burmazović I, Karlin KD. Formation and Reactivity of New Isoporphyrins: Implications for Understanding the Tyr-His Cross-Link Cofactor Biogenesis in Cytochrome c Oxidase. J Am Chem Soc 2019; 141:10632-10643. [PMID: 31150209 DOI: 10.1021/jacs.9b01791] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of dioxygen to water utilizing a heterobinuclear active site composed of a heme moiety and a mononuclear copper center coordinated to three histidine residues, one of which is covalently cross-linked to a tyrosine residue via a post-translational modification (PTM). Although this tyrosine-histidine moiety has functional and structural importance, the pathway behind this net oxidative C-N bond coupling is still unknown. A novel route employing an iron(III) meso-substituted isoporphyrin derivative, isoelectronic with Cmpd-I ((Por•+)FeIV═O), is for the first time proposed to be a key intermediate in the Tyr-His cofactor biogenesis. Newly synthesized iron(III) meso-substituted isoporphyrins were prepared with azide, cyanide, and substituted imidazole functionalities, by adding nucleophiles to an iron(III) π-dication species formed via addition of trifluoroacetic acid to F8Cmpd-I (F8 = (tetrakis(2,6-difluorophenyl)porphyrinate)). Isoporphyrin derivatives were characterized at cryogenic temperatures via ESI-MS and UV-vis, 2H NMR, and EPR spectroscopies. Addition of 1,3,5-trimethoxybenzene or 4-methoxyphenol to the imidazole-substituted isoporphyrin led to formation of the organic product containing the imidazole coupled to aromatic substrate via a new C-N bond, as detected via cryo-ESI-MS. Experimental evidence for the formation of an imidazole-substituted isoporphyrin and its promising reactivity to form the imidazole-phenol coupled product yields viability to the herein proposed pathway behind the PTM (i.e., biogenesis) leading to the key covalent Tyr-His cross-link in CcO.
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Affiliation(s)
- Melanie A Ehudin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Laura Senft
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Alicja Franke
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy , Friedrich-Alexander University Erlangen-Nuremberg , 91058 Erlangen , Germany
| | - Kenneth D Karlin
- Department of Chemistry , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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35
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Lin Y. Rational design of heme enzymes for biodegradation of pollutants toward a green future. Biotechnol Appl Biochem 2019; 67:484-494. [DOI: 10.1002/bab.1788] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang People's Republic of China
- Laboratory of Protein Structure and Function University of South China Hengyang People's Republic of China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes University of South China Hengyang People's Republic of China
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36
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Liu C, Yuan H, Liao F, Wei CW, Du KJ, Gao SQ, Tan X, Lin YW. Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases. Chem Commun (Camb) 2019; 55:6610-6613. [PMID: 31119219 DOI: 10.1039/c9cc02714a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The X-ray crystal structure of F43Y/T67R myoglobin revealed unique Tyr-heme double cross-links between Tyr43 and the heme 4-vinyl group, which represents a novel post-translational modification of heme proteins. Moreover, with the feature of a distal His-Arg pair, the designed artificial enzyme exhibited a peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase.
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Affiliation(s)
- Can Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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A Density Functional Theory-Based Scheme to Compute the Redox Potential of a Transition Metal Complex: Applications to Heme Compound. Molecules 2019; 24:molecules24040819. [PMID: 30823577 PMCID: PMC6412623 DOI: 10.3390/molecules24040819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 12/23/2022] Open
Abstract
We estimated the redox potential of a model heme compound by using the combination of our density functionals with a computational scheme, which corrects the solvation energy to the normal solvent model. Among many density functionals, the LC-BOP12 functional gave the smallest mean absolute error of 0.16 V in the test molecular sets. The application of these methods revealed that the redox potential of a model heme can be controlled within 200 mV by changing the protonation state and even within 20 mV by the flipping of the ligand histidine. In addition, the redox potential depends on the inverse of the dielectric constant, which controls the surroundings. The computational results also imply that a system with a low dielectric constant avoids the charged molecule by controlling either the redox potential or the protonation system.
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Sahu DK, Singha D, Sahu K. Sensing of iron(III)-biomolecules by surfactant-free fluorescent copper nanoclusters. SENSING AND BIO-SENSING RESEARCH 2019. [DOI: 10.1016/j.sbsr.2018.100250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Liu HX, Li L, Yang XZ, Wei CW, Cheng HM, Gao SQ, Wen GB, Lin YW. Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin. RSC Adv 2019; 9:4172-4179. [PMID: 35520156 PMCID: PMC9062612 DOI: 10.1039/c8ra10390a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022] Open
Abstract
Human neuroglobin (Ngb) forms an intramolecular disulfide bond between Cys46 and Cys55, with a third Cys120 near the protein surface, which is a promising protein model for heme protein design. In order to protect the free Cys120 and to enhance the protein stability, we herein developed a strategy by designing an additional disulfide bond between Cys120 and Cys15 via A15C mutation. The design was supported by molecular modeling, and the formation of Cys15–Cys120 disulfide bond was confirmed experimentally by ESI-MS analysis. Molecular modeling, UV-Vis and CD spectroscopy showed that the additional disulfide bond caused minimal structural alterations of Ngb. Meanwhile, the disulfide bond of Cys15–Cys120 was found to enhance both Gdn·HCl-induced unfolding stability (increased by ∼0.64 M) and pH-induced unfolding stability (decreased by ∼0.69 pH unit), as compared to those of WT Ngb with a single native disulfide bond of Cys46–Cys55. Moreover, the half denaturation temperature (Tm) of A15C Ngb was determined to be higher than 100 °C. In addition, the disulfide bond of Cys15–Cys120 has slight effects on protein function, such as an increase in the rate of O2 release by ∼1.4-fold. This study not only suggests a crucial role of the artificial disulfide in protein stabilization, but also lays the groundwork for further investigation of the structure and function of Ngb, as well as for the design of other functional heme proteins, based on the scaffold of A15C Ngb with an enhanced stability. A disulfide bond of Cys120 and Cys15 was rationally designed in human neuroglobin (Ngb) by A15C mutation, which caused minimal structural alterations, whereas enhanced both chemical and pH stability, with a thermal stability higher than 100 °C.![]()
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Xin-Zhi Yang
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hui-Min Cheng
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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Liu HX, Li L, He B, Gao SQ, Wen GB, Lin YW. Neuroglobin is capable of self-oxidation of methionine64 introduced at the heme axial position. Dalton Trans 2018; 47:10847-10852. [PMID: 30027178 DOI: 10.1039/c8dt02397b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Neuroglobin (Ngb), with its physiological role not fully understood, was found to be capable of self-oxidation of methionine64 introduced at the heme axial position (H64M Ngb), adopting a high-spin heme state and producing both methionine sulfoxide (SO-Met) and sulfone (SO2-Met), which represents the structure and function of cytochrome c in a non-native state.
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Affiliation(s)
- Hai-Xiao Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
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Cheng HM, Yuan H, Wang XJ, Xu JK, Gao SQ, Wen GB, Tan X, Lin YW. Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen. J Inorg Biochem 2018; 182:141-149. [PMID: 29477977 DOI: 10.1016/j.jinorgbio.2018.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022]
Abstract
The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O2, as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H2O2. This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.
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Affiliation(s)
- Hui-Min Cheng
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Jia-Kun Xu
- Yellow Sea Fisheries Research Institute, Qingdao 266071, China
| | - Shu-Qin Gao
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Lab of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Lab of Protein Structure and Function, University of South China, Hengyang 421001, China.
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42
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Liu C, Xu J, Gao SQ, He B, Wei CW, Wang XJ, Wang Z, Lin YW. Green and efficient biosynthesis of indigo from indole by engineered myoglobins. RSC Adv 2018; 8:33325-33330. [PMID: 35548150 PMCID: PMC9086478 DOI: 10.1039/c8ra07825d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 11/21/2022] Open
Abstract
Myoglobin (Mb) was redesigned to a green and efficient biocatalysts for the biosynthesis of indigo from indole, exhibiting improved yield, catalytic efficiency and chemoselectivity (as high as ∼80%).
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Affiliation(s)
- Can Liu
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Jiakun Xu
- Yellow Sea Fisheries Research Institute
- Qingdao 266071
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Zhonghua Wang
- College of Chemistry and Chemical Engineering
- China West Normal University
- Nanchong 637002
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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43
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Muneeswaran G, Pandiaraj M, Kartheeswaran S, Sankaralingam M, Muthukumar K, Karunakaran C. Molecular dynamics simulation approach to explore atomistic molecular mechanism of peroxidase activity of apoptotic cytochrome c mutants. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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44
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Yin LL, Yuan H, Du KJ, He B, Gao SQ, Wen GB, Tan X, Lin YW. Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin. Chem Commun (Camb) 2018; 54:4356-4359. [DOI: 10.1039/c8cc01646a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.
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Affiliation(s)
- Lu-Lu Yin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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