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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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Derrien V, André E, Bernad S. Peroxidase activity of rice (Oryza sativa) hemoglobin: distinct role of tyrosines 112 and 151. J Biol Inorg Chem 2023; 28:613-626. [PMID: 37507628 DOI: 10.1007/s00775-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Five non-symbiotic hemoglobins (nsHb) have been identified in rice (Oryza sativa). Previous studies have shown that stress conditions can induce their overexpression, but the role of those globins is still unclear. To better understand the functions of nsHb, the reactivity of rice Hb1 toward hydrogen peroxide (H2O2) has been studied in vitro. Our results show that recombinant rice Hb1 dimerizes through dityrosine cross-links in the presence of H2O2. By site-directed mutagenesis, we suggest that tyrosine 112 located in the FG loop is involved in this dimerization. Interestingly, this residue is not conserved in the sequence of the five rice non-symbiotic hemoglobins. Stopped-flow spectrophotometric experiments have been performed to measure the catalytic constants of rice Hb and its variants using the oxidation of guaiacol. We have shown that Tyrosine112 is a residue that enhances the peroxidase activity of rice Hb1, since its replacement by an alananine leads to a decrease of guaiacol oxidation. In contrast, tyrosine 151, a conserved residue which is buried inside the heme pocket, reduces the protein reactivity. Indeed, the variant Tyr151Ala exhibits a higher peroxidase activity than the wild type. Interestingly, this residue affects the heme coordination and the replacement of the tyrosine by an alanine leads to the loss of the distal ligand. Therefore, even if the amino acid at position 151 does not participate to the formation of the dimer, this residue modulates the peroxidase activity and plays a role in the hexacoordinated state of the heme.
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Affiliation(s)
- Valérie Derrien
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France.
| | - Eric André
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France
| | - Sophie Bernad
- Institut de Chimie Physique, UMR8000, Université Paris-Saclay, CNRS, Avenue Jean Perrin. Bat 350, 91405, Orsay, France
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Lukas J, Družeta I, Kühl T. Comparative studies of soluble and immobilized Fe(III) heme-peptide complexes as alternative heterogeneous biocatalysts. Biol Chem 2022; 403:1099-1105. [PMID: 36257922 DOI: 10.1515/hsz-2022-0199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Fe(III) heme is known to possess low catalytic activity when exposed to hydrogen peroxide and a reducing substrate. Efficient non-covalently linked Fe(III) heme-peptide complexes may represent suitable alternatives as a new group of green catalysts. Here, we evaluated a set of heme-peptide complexes by determination of their peroxidase-like activity and the kinetics of the catalytic conversion in both, the soluble and the immobilized state. We show the impact of peptide length on binding of the peptides to Fe(III) heme and the catalytic activity. Immobilization of the peptide onto a polymer support maintains the catalytic performance of the Fe(III) heme-peptide complex. This study thus opens up a new perspective with regard to the development of heterogeneous biocatalysts with a peroxidase-like activity.
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Affiliation(s)
- Joey Lukas
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Ivona Družeta
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
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Lin YW. Biodegradation of aromatic pollutants by metalloenzymes: A structural-functional-environmental perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213774] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lin YW. Uranyl Binding to Proteins and Structural-Functional Impacts. Biomolecules 2020; 10:biom10030457. [PMID: 32187982 PMCID: PMC7175365 DOI: 10.3390/biom10030457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/29/2023] Open
Abstract
The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; ; Tel.: +86-734-8578079
- 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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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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Lin YW. Structure and function of heme proteins regulated by diverse post-translational modifications. Arch Biochem Biophys 2018; 641:1-30. [DOI: 10.1016/j.abb.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 01/08/2023]
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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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Samhan-Arias AK, Maia LB, Cordas CM, Moura I, Gutierrez-Merino C, Moura JJG. Peroxidase-like activity of cytochrome b 5 is triggered upon hemichrome formation in alkaline pH. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:373-378. [PMID: 28317253 DOI: 10.1016/j.bbapap.2017.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
Abstract
In alkaline media (pH12) a catalytic peroxidase activity of cytochrome b5 was found associated to a different conformational state. Upon incubation at this pH, cytochrome b5 electronic absorption spectrum was altered, with disappearance of characteristic bands of cytochrome b5 at pH7.0. The appearance of new electronic absorption bands and EPR measurements support the formation of a cytochrome b5 class B hemichrome with an acquired ability to bind polar ligands. This hemichrome is characterized by a negative formal redox potential and the same folding properties than cytochrome b5 at pH7. The acquired peroxidase-like activity of cytochrome b5 found at pH12, driven by a hemichrome formation, suggests a role of this protein in peroxidation products propagation.
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Affiliation(s)
- Alejandro K Samhan-Arias
- UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
| | - Luisa B Maia
- UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cristina M Cordas
- UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos Gutierrez-Merino
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura, 06006, Badajoz, Spain
| | - José J G Moura
- UCIBIO, REQUIMTE, Departamento de Quimica, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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Hu S, He B, Du KJ, Wang XJ, Gao SQ, Lin YW. Peroxidase Activity of a c-Type Cytochrome b5 in the Non-Native State is Comparable to that of Native Peroxidases. ChemistryOpen 2017. [PMID: 28638761 PMCID: PMC5474653 DOI: 10.1002/open.201700055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The design of artificial metalloenzymes has achieved tremendous progress, although few designs can achieve catalytic performances comparable to that of native enzymes. Moreover, the structure and function of artificial metalloenzymes in non‐native states has rarely been explored. Herein, we found that a c‐type cytochrome b5 (Cyt b5), N57C/S71C Cyt b5, with heme covalently attached to the protein matrix through two Cys–heme linkages, adopts a non‐native state with an open heme site after guanidine hydrochloride (Gdn⋅HCl)‐induced unfolding, which facilitates H2O2 activation and substrate binding. Stopped‐flow kinetic studies further revealed that c‐type Cyt b5 in the non‐native state exhibited impressive peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase. This study presents an alternative approach to the design of functional artificial metalloenzymes by exploring enzymatic functions in non‐native states.
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Affiliation(s)
- Shan Hu
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Bo He
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Xiao-Juan Wang
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering University of South China Hengyang 421001 P.R. China.,Laboratory of Protein Structure and Function University of South China Hengyang 421001 P.R. China
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Li LL, Yuan H, Liao F, He B, Gao SQ, Wen GB, Tan X, Lin YW. Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center. Dalton Trans 2017; 46:11230-11238. [DOI: 10.1039/c7dt02302b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial dye-decolorizing peroxidases (DyPs) have been rationally designed using myoglobin (Mb) as a protein scaffold by engineering Tyr/Trp in the heme center, such as F43Y/F138 W Mb, which exhibited catalytic performance comparable to some native DyPs.
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Affiliation(s)
- Le-Le Li
- 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
| | - 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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