1
|
Wu Y, Huo C, Ming T, Liu Y, Su C, Qiu X, Lu C, Zhou J, Li Y, Zhang Z, Han J, Feng Y, Su X. Structural and Functional Insights into the Roles of Potential Metal-Binding Sites in Apostichopus japonicus Ferritin. Polymers (Basel) 2022; 14:5378. [PMID: 36559745 PMCID: PMC9785301 DOI: 10.3390/polym14245378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Ferritin is widely acknowledged as a conservative iron storage protein found in almost all living kingdoms. Apostichopus japonicus (Selenka) is among the oldest echinoderm fauna and has unique regenerative potential, but the catalytic mechanism of iron oxidation in A. japonicus ferritin (AjFER) remains elusive. We previously identified several potential metal-binding sites at the ferroxidase center, the three- and four-fold channels in AjFER. Herein, we prepared AjFER, AjFER-E25A/E60A/E105A, AjFER-D129A/E132A, and AjFER-E168A mutants, investigated their structures, and functionally characterized these ferritins with respect to Fe2+ uptake using X-ray techniques together with biochemical analytical methods. A crystallographic model of the AjFER-D129A/E132A mutant, which was solved to a resolution of 1.98 Å, suggested that the substitutions had a significant influence on the quaternary structure of the three-fold channel compared to that of AjFER. The structures of these ferritins in solution were determined based on the molecular envelopes of AjFER and its variants by small-angle X-ray scattering, and the structures were almost consistent with the characteristics of well-folded and globular-shaped proteins. Comparative biochemical analyses indicated that site-directed mutagenesis of metal-binding sites in AjFER presented relatively low rates of iron oxidation and thermostability, as well as weak iron-binding affinity, suggesting that these potential metal-binding sites play critical roles in the catalytic activity of ferritin. These findings provide profound insight into the structure-function relationships related to marine invertebrate ferritins.
Collapse
Affiliation(s)
- Yan Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
| | - Chunheng Huo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Yan Liu
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo 315800, China
| | - Chang Su
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic, Ningbo 315800, China
| | - Xiaoting Qiu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Ying Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
- College of Life Sciences, Tonghua Normal University, Tonghua 134000, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo 315832, China
- School of Marine Science, Ningbo University, Ningbo 315832, China
| |
Collapse
|
2
|
Lu C, Maity B, Peng X, Ito N, Abe S, Sheng X, Ueno T, Lu D. Design of a gold clustering site in an engineered apo-ferritin cage. Commun Chem 2022; 5:39. [PMID: 36697940 PMCID: PMC9814837 DOI: 10.1038/s42004-022-00651-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/18/2022] [Indexed: 01/28/2023] Open
Abstract
Water-soluble and biocompatible protein-protected gold nanoclusters (Au NCs) hold great promise for numerous applications. However, design and precise regulation of their structure at an atomic level remain challenging. Herein, we have engineered and constructed a gold clustering site at the 4-fold symmetric axis channel of the apo-ferritin cage. Using a series of X-ray crystal structures, we evaluated the stepwise accumulation process of Au ions into the cage and the formation of a multinuclear Au cluster in our designed cavity. We also disclosed the role of key residues in the metal accumulation process. X-ray crystal structures in combination with quantum chemical (QC) calculation revealed a unique Au clustering site with up to 12 Au atoms positions in the cavity. Moreover, the structure of the gold nanocluster was precisely tuned by the dosage of the Au precursor. As the gold concentration increases, the number of Au atoms position at the clustering site increases from 8 to 12, and a structural rearrangement was observed at a higher Au concentration. Furthermore, the binding affinity order of the four Au binding sites on apo-ferritin was unveiled with a stepwise increase of Au precursor concentration.
Collapse
Affiliation(s)
- Chenlin Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100-084, China
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Xue Peng
- Department of Chemical Engineering, Tsinghua University, Beijing, 100-084, China
| | - Nozomi Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, and, National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100-084, China.
| |
Collapse
|
3
|
Ming T, Wu Y, Huan H, Jiang Q, Su C, Lu C, Zhou J, Li Y, Su X. Integrative proteomics and metabolomics profiling of the protective effects of Phascolosoma esculent ferritin on BMSCs in Cd(II) injury. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111995. [PMID: 33529923 DOI: 10.1016/j.ecoenv.2021.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/05/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Ferritin is the major intracellular iron storage protein and is essential for iron homeostasis and detoxification. Cadmium affects cellular homeostasis and induces cell toxicity via sophisticated mechanisms. Here, we aimed to explore the mechanisms of cytoprotective effect of Phascolosoma esculenta ferritin (PeFer) on Cd(II)-induced bone marrow mesenchymal stem cell (BMSC) injury. Herein, the effects of different treated groups on apoptosis and cell cycle were assessed using flow cytometric analysis. We further investigated the alterations of the three groups using integrative 2-DE-based proteomics and 1H NMR-based metabolomics profiles. The results indicate that PeFer reduces BMSC apoptosis induced by Cd(II) and delays G0/G1 cell cycle progression. A total of 19 proteins and 70 metabolites were significantly different among BMSC samples of the three groups. Notably, multiomics analysis revealed that Cd(II) might perturb the ER stress-mediated apoptosis pathway and disrupt biological processes related to the TCA cycle, amino acid metabolism, purine and pyrimidine metabolism, thereby suppressing the cell growth rate and initiating apoptosis; however, the addition of PeFer might protect BMSCs against cell apoptosis to improve cell survival by enhancing energy metabolism. This study provides a better understanding of the underlying molecular mechanisms of the protective effect of PeFer in BMSCs against Cd(II) injury.
Collapse
Affiliation(s)
- Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Yan Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Hengshang Huan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Qinqin Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Chang Su
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic College, Ningbo, Zhejiang 315800, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.
| |
Collapse
|
4
|
Ming T, Huan H, Su C, Huo C, Wu Y, Jiang Q, Qiu X, Lu C, Zhou J, Li Y, Su X. Structural comparison of two ferritins from the marine invertebrate Phascolosoma esculenta. FEBS Open Bio 2021; 11:793-803. [PMID: 33448656 PMCID: PMC7931202 DOI: 10.1002/2211-5463.13080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 11/06/2022] Open
Abstract
For marine invertebrates with no adaptive immune system, ferritin is a major intracellular iron-storage protein with a critical role in innate immunity. Here, we present the crystal structures of two novel ferritins [Fer147 and Phascolosoma esculenta ferritin (PeFer)] from the marine invertebrate P. esculenta, which resides in muddy-bottom coastal regions. Fer147 and PeFer exhibit the 4-3-2 symmetry of cage-like hollow shells containing 24 subunits, similar to other known ferritins. Fer147 and PeFer contain both the conserved ferroxidase center and threefold channels. Subtle structural differences in the putative nucleation sites suggest possible routes of metal ion movement in the protein shells. However, the marked variation in the electrostatic potential of the threefold channels in Fer147 and the fourfold channels in PeFer suggests significant diversity between Fer147 and PeFer in terms of metal ion aggregation and cation exclusion. In summary, the presented crystal structures may serve as references for studies of the iron-storage mechanism of additional ferritins from marine invertebrates.
Collapse
Affiliation(s)
- Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| | - Hengshang Huan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,College of Food and Pharmaceutical Sciences, Ningbo University, China
| | - Chang Su
- Zhejiang Collaborative Innovation Center for High Value Utilization of Byproducts from Ethylene Project, Ningbo Polytechnic College, China
| | - Chunheng Huo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| | - Yan Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,College of Food and Pharmaceutical Sciences, Ningbo University, China
| | - Qinqin Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,College of Food and Pharmaceutical Sciences, Ningbo University, China
| | - Xiaoting Qiu
- College of Food and Pharmaceutical Sciences, Ningbo University, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, China.,School of Marine Sciences, Ningbo University, China
| |
Collapse
|
5
|
Hishikawa Y, Maity B, Ito N, Abe S, Lu D, Ueno T. Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage. CHEM LETT 2020. [DOI: 10.1246/cl.200217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuki Hishikawa
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Nozomi Ito
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|