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Martinez Grundman JE, Johnson EA, Lecomte JTJ. Architectural digest: Thermodynamic stability and domain structure of a consensus monomeric globin. Biophys J 2023; 122:3117-3132. [PMID: 37353934 PMCID: PMC10432219 DOI: 10.1016/j.bpj.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Artificial proteins representing the consensus of a set of homologous sequences have attracted attention for their increased thermodynamic stability and conserved activity. Here, we applied the consensus approach to a b-type heme-binding protein to inspect the contribution of a dissociable cofactor to enhanced stability and the chemical consequences of creating a generic heme environment. We targeted the group 1 truncated hemoglobin (TrHb1) subfamily of proteins for their small size (∼120 residues) and ease of characterization. The primary structure, derived from a curated set of ∼300 representative sequences, yielded a highly soluble consensus globin (cGlbN) enriched in acidic residues. Optical and NMR spectroscopies revealed high-affinity heme binding in the expected site and in two orientations. At neutral pH, proximal and distal iron coordination was achieved with a pair of histidine residues, as observed in some natural TrHb1s, and with labile ligation on the distal side. As opposed to studied TrHb1s, which undergo additional folding upon heme binding, cGlbN displayed the same extent of secondary structure whether the heme was associated with the protein or not. Denaturation required guanidine hydrochloride and showed that apo- and holoprotein unfolded in two transitions-the first (occurring with a midpoint of ∼2 M) was shifted to higher denaturant concentration in the holoprotein (∼3.7 M) and reflected stabilization due to heme binding, while the second transition (∼6.2 M) was common to both forms. Thus, the consensus sequence stabilized the protein but exposed the existence of two separately cooperative subdomains within the globin architecture, masked as one single domain in TrHb1s with typical stabilities. The results suggested ways in which specific chemical or thermodynamic features may be controlled in artificial heme proteins.
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Affiliation(s)
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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2
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Yamanaka M, Mashima T, Ogihara M, Okamoto M, Uchihashi T, Hirota S. Construction of ferritin hydrogels utilizing subunit-subunit interactions. PLoS One 2021; 16:e0259052. [PMID: 34731167 PMCID: PMC8565734 DOI: 10.1371/journal.pone.0259052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022] Open
Abstract
Various proteins form nanostructures exhibiting unique functions, making them attractive as next-generation materials. Ferritin is a hollow spherical protein that incorporates iron ions. Here, we found that hydrogels are simply formed from concentrated apoferritin solutions by acid denaturation and subsequent neutralization. The water content of the hydrogel was approximately 80%. The apoferritin hydrogel did not decompose in the presence of 1 M HCl, 2-mercaptoethanol, or methanol but was dissolved in the presence of 1 M NaOH, by heating at 80°C, or by treatment with trypsin or 6 M guanidine hydrochloride. The Young’s modulus of the hydrogel was 20.4 ± 12.1 kPa according to local indentation experimentes using atomic force microscopy, indicating that the hydrogel was relatively stiff. Transition electron microscopy measurements revealed that a fibrous network was constructed in the hydrogel. The color of the hydrogel became yellow-brown upon incubation in the presence of Fe3+ ions, indicating that the hydrogel adsorbed the Fe3+ ions. The yellow-brown color of the Fe3+-adsorbed hydrogel did not change upon incubation in pure water, whereas it became pale by incubating it in the presence of 100 mM ethylenediaminetetraacetic acid (EDTA). The apoferritin hydrogel also adsorbed Co2+ and Cu2+ ions and released them in the presence of EDTA, while it adsorbed less Ni2+ ions; more Fe3+ ions adsorbed to the apoferritin hydrogel than other metal ions, indicating that the hydrogel keeps the iron storage characteristic of ferritin. These results demonstrate a new property of ferritin: the ability to form a hydrogel that can adsorb/desorb metal ions, which may be useful in designing future biomaterials.
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Affiliation(s)
- Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tsuyoshi Mashima
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Michio Ogihara
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Mei Okamoto
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- * E-mail:
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3
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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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4
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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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5
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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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6
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Wei C, Wang X, Gao S, Wen G, Lin Y. A Phenylalanine Derivative Containing a 4‐Pyridine Group Can Construct Both Single Crystals and a Selective Cu‐Ag Bimetallohydrogel. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Chuan‐Wan Wei
- School of Chemistry and Chemical Engineering University of South China 421001 Hengyang China
| | - Xiao‐Juan Wang
- School of Chemistry and Chemical Engineering University of South China 421001 Hengyang China
| | - Shu‐Qin Gao
- Laboratory of Protein Structure and Function University of South China 421001 Hengyang China
| | - Ge‐Bo Wen
- Laboratory of Protein Structure and Function University of South China 421001 Hengyang China
| | - Ying‐Wu Lin
- School of Chemistry and Chemical Engineering University of South China 421001 Hengyang China
- Laboratory of Protein Structure and Function University of South China 421001 Hengyang China
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7
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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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8
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Villarino L, Splan KE, Reddem E, Alonso‐Cotchico L, Gutiérrez de Souza C, Lledós A, Maréchal J, Thunnissen AWH, Roelfes G. An Artificial Heme Enzyme for Cyclopropanation Reactions. Angew Chem Int Ed Engl 2018; 57:7785-7789. [PMID: 29719099 PMCID: PMC6033091 DOI: 10.1002/anie.201802946] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Indexed: 12/12/2022]
Abstract
An artificial heme enzyme was created through self-assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows the heme bound inside the hydrophobic pore of the protein, where it appears inaccessible for substrates. However, good catalytic activity and moderate enantioselectivity was observed in an abiological cyclopropanation reaction. We propose that the dynamic nature of the structure of the LmrR protein is key to the observed activity. This was supported by molecular dynamics simulations, which showed transient formation of opened conformations that allow the binding of substrates and the formation of pre-catalytic structures.
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Affiliation(s)
- Lara Villarino
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Kathryn E. Splan
- Department of ChemistryMacalester College1600 Grand AvenueSaint PaulMN55105USA
| | - Eswar Reddem
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Lur Alonso‐Cotchico
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Cora Gutiérrez de Souza
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Agustí Lledós
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Jean‐Didier Maréchal
- Departament de QuímicaUniversitat Autònoma de BarcelonaEdifici C.n.08193 Cerdanyola del VallésBarcelonaSpain
| | - Andy‐Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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9
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Villarino L, Splan KE, Reddem E, Alonso-Cotchico L, Gutiérrez de Souza C, Lledós A, Maréchal JD, Thunnissen AMWH, Roelfes G. An Artificial Heme Enzyme for Cyclopropanation Reactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802946] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lara Villarino
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kathryn E. Splan
- Department of Chemistry; Macalester College; 1600 Grand Avenue Saint Paul MN 55105 USA
| | - Eswar Reddem
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Lur Alonso-Cotchico
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Cora Gutiérrez de Souza
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Agustí Lledós
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193 Cerdanyola del Vallés Barcelona Spain
| | - Andy-Mark W. H. Thunnissen
- Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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10
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Nagarajan D, Sukumaran S, Deka G, Krishnamurthy K, Atreya HS, Chandra N. Design of a heme-binding peptide motif adopting a β-hairpin conformation. J Biol Chem 2018; 293:9412-9422. [PMID: 29695501 DOI: 10.1074/jbc.ra118.001768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/19/2018] [Indexed: 11/06/2022] Open
Abstract
Heme-binding proteins constitute a large family of catalytic and transport proteins. Their widespread presence as globins and as essential oxygen and electron transporters, along with their diverse enzymatic functions, have made them targets for protein design. Most previously reported designs involved the use of α-helical scaffolds, and natural peptides also exhibit a strong preference for these scaffolds. However, the reason for this preference is not well-understood, in part because alternative protein designs, such as those with β-sheets or hairpins, are challenging to perform. Here, we report the computational design and experimental validation of a water-soluble heme-binding peptide, Pincer-1, composed of predominantly β-scaffold secondary structures. Such heme-binding proteins are rarely observed in nature, and by designing such a scaffold, we simultaneously increase the known fold space of heme-binding proteins and expand the limits of computational design methods. For a β-scaffold, two tryptophan zipper β-hairpins sandwiching a heme molecule were linked through an N-terminal cysteine disulfide bond. β-Hairpin orientations and residue selection were performed computationally. Heme binding was confirmed through absorbance experiments and surface plasmon resonance experiments (KD = 730 ± 160 nm). CD and NMR experiments validated the β-hairpin topology of the designed peptide. Our results indicate that a helical scaffold is not essential for heme binding and reveal the first designed water-soluble, heme-binding β-hairpin peptide. This peptide could help expand the search for and design space to cytoplasmic heme-binding proteins.
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Affiliation(s)
| | | | - Geeta Deka
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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11
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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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12
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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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13
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Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions. J Biol Inorg Chem 2017; 23:7-25. [DOI: 10.1007/s00775-017-1506-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/20/2017] [Indexed: 12/12/2022]
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14
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15
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Hu C, Yu Y, Wang J. Improving artificial metalloenzymes' activity by optimizing electron transfer. Chem Commun (Camb) 2017; 53:4173-4186. [DOI: 10.1039/c6cc09921a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This feature article discusses the strategies to optimize electron transfer efficiency, towards enhancing the activity of artificial metalloenzymes.
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Affiliation(s)
- Cheng Hu
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
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16
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Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0343-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Wu LB, Yuan H, Zhou H, Gao SQ, Nie CM, Tan X, Wen GB, Lin YW. An intramolecular disulfide bond designed in myoglobin fine-tunes both protein structure and peroxidase activity. Arch Biochem Biophys 2016; 600:47-55. [DOI: 10.1016/j.abb.2016.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 01/08/2023]
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Shu X, Su J, Du K, You Y, Gao S, Wen G, Tan X, Lin Y. Rational Design of Dual Active Sites in a Single Protein Scaffold: A Case Study of Heme Protein in Myoglobin. ChemistryOpen 2016; 5:192-196. [PMID: 27933225 PMCID: PMC5125789 DOI: 10.1002/open.201500224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 01/03/2023] Open
Abstract
Rational protein design has been proven to be a powerful tool for creating functional artificial proteins. Although many artificial metalloproteins with a single active site have been successfully created, those with dual active sites in a single protein scaffold are still relatively rare. In this study, we rationally designed dual active sites in a single heme protein scaffold, myoglobin (Mb), by retaining the native heme site and creating a copper-binding site remotely through a single mutation of Arg118 to His or Met. Isothermal titration calorimetry (ITC) and electron paramagnetic resonance (EPR) studies confirmed that a copper-binding site of [3-His] or [2-His-1-Met] motif was successfully created in the single mutant of R118H Mb and R118M Mb, respectively. UV/Vis kinetic spectroscopy and EPR studies further revealed that both the heme site and the designed copper site exhibited nitrite reductase activity. This study presents a new example for rational protein design with multiple active sites in a single protein scaffold, which also lays the groundwork for further investigation of the structure and function relationship of heme/non-heme proteins.
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Affiliation(s)
- Xiao‐Gang Shu
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Ji‐Hu Su
- Department of Modern PhysicsUniversity of Science and Technology of ChinaHefei230026P. R. China
| | - Ke‐Jie Du
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
| | - Yong You
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Shu‐Qin Gao
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Ge‐Bo Wen
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
| | - Xiangshi Tan
- Department of ChemistryShanghai Key Lab of Chemical Biology for Protein Research& Institute of Biomedical ScienceFudan UniversityShanghai200433P. R. China
| | - Ying‐Wu Lin
- School of Chemistry and Chemical EngineeringUniversity of South ChinaHengyang421001P. R. China
- Laboratory of Protein Structure and FunctionUniversity of South ChinaHengyang421001P. R. China
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Yan DJ, Yuan H, Li W, Xiang Y, He B, Nie CM, Wen GB, Lin YW, Tan X. How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin. Dalton Trans 2016; 44:18815-22. [PMID: 26458300 DOI: 10.1039/c5dt03040d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.
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Affiliation(s)
- Dao-Jing Yan
- 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.
| | - Wei Li
- Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Bo He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, 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. and Laboratory 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.
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Zhao Y, Du KJ, Gao SQ, He B, Wen GB, Tan X, Lin YW. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center. J Inorg Biochem 2016; 156:113-21. [DOI: 10.1016/j.jinorgbio.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 12/14/2022]
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21
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Lin YW. The broad diversity of heme-protein cross-links: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:844-59. [DOI: 10.1016/j.bbapap.2015.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/26/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
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22
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Hydrogen-bonding network in heme active site regulates the hydrolysis activity of myoglobin. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Du JF, Li W, Li L, Wen GB, Lin YW, Tan X. Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network. ChemistryOpen 2014; 4:97-101. [PMID: 25969804 PMCID: PMC4420578 DOI: 10.1002/open.201402108] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 01/03/2023] Open
Abstract
Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.
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Affiliation(s)
- Jun-Fang Du
- School of Chemistry and Chemical Engineering, University of South China Hengyang, 421001, (P. R. China))
| | - Wei Li
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University Liaocheng, 252059, (P. R. China)
| | - Ge-Bo Wen
- 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)
| | - Xiangshi Tan
- Department of Chemistry and Institute of Biomedical Science, Fudan University Shanghai, 200433, (P. R. China)
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24
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational design of heterodimeric protein using domain swapping for myoglobin. Angew Chem Int Ed Engl 2014; 54:511-5. [PMID: 25370865 DOI: 10.1002/anie.201409267] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/12/2022]
Abstract
Protein design is a useful method to create novel artificial proteins. A rational approach to design a heterodimeric protein using domain swapping for horse myoglobin (Mb) was developed. As confirmed by X-ray crystallographic analysis, a heterodimeric Mb with two different active sites was produced efficiently from two surface mutants of Mb, in which the charges of two amino acids involved in the dimer salt bridges were reversed in each mutant individually, with the active site of one mutant modified. This study shows that the method of constructing heterodimeric Mb with domain swapping is useful for designing artificial multiheme proteins.
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Affiliation(s)
- Ying-Wu Lin
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192 (Japan); School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001 (China)
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25
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Lin YW, Nagao S, Zhang M, Shomura Y, Higuchi Y, Hirota S. Rational Design of Heterodimeric Protein using Domain Swapping for Myoglobin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Lin YW, Shu XG, Du KJ, Nie CM, Wen GB. Computational insight into nitration of human myoglobin. Comput Biol Chem 2014; 52:60-5. [DOI: 10.1016/j.compbiolchem.2014.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 09/08/2014] [Accepted: 09/13/2014] [Indexed: 11/29/2022]
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27
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Sun MH, Liu SQ, Du KJ, Nie CM, Lin YW. A spectroscopic study of uranyl-cytochrome b5/cytochrome c interactions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:130-137. [PMID: 24051281 DOI: 10.1016/j.saa.2013.08.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 08/28/2013] [Accepted: 08/28/2013] [Indexed: 06/02/2023]
Abstract
Uranium is harmful to human health due to its radiation damage and the ability of uranyl ion (UO2(2+)) to interact with various proteins and disturb their biological functions. Cytochrome b5 (cyt b5) is a highly negatively charged heme protein and plays a key role in mediating cytochrome c (cyt c) signaling in apoptosis by forming a dynamic cyt b5-cyt c complex. In previous molecular modeling study in combination with UV-Vis studies, we found that UO2(2+) is capable of binding to cyt b5 at surface residues, Glu37 and Glu43. In this study, we further investigated the structural consequences of cyt b5 and cyt c, as well as cyt b5-cyt c complex, upon uranyl binding, by fluorescence spectroscopic and circular dichroism techniques. Moreover, we proposed a uranyl binding site for cyt c at surface residues, Glu66 and Glu69, by performing a molecular modeling study. It was shown that uranyl binds to cyt b5 (KD=10 μM), cyt c (KD=87 μM), and cyt b5-cyt c complex (KD=30 μM) with a different affinity, which slightly alters the protein conformation and disturbs the interaction of cyt b5-cyt c complex. Additionally, we investigated the functional consequences of uranyl binding to the protein surface, which decreases the inherent peroxidase activity of cyt c. The information of uranyl-cyt b5/cyt c interactions gained in this study likely provides a clue for the mechanism of uranyl toxicity.
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Affiliation(s)
- Mei-Hui Sun
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
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28
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Lin Y, Wang J, Lu Y. Functional tuning and expanding of myoglobin by rational protein design. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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Sun MH, Li W, Liu JH, Wen GB, Tan X, Lin YW. Structural and nitrite reductase activity comparisons of myoglobins with one to three distal histidines. RSC Adv 2013. [DOI: 10.1039/c3ra40839f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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