1
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Jin H, Merz KM. Modeling Zinc Complexes Using Neural Networks. J Chem Inf Model 2024; 64:3140-3148. [PMID: 38587510 PMCID: PMC11040731 DOI: 10.1021/acs.jcim.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 04/09/2024]
Abstract
Understanding the energetic landscapes of large molecules is necessary for the study of chemical and biological systems. Recently, deep learning has greatly accelerated the development of models based on quantum chemistry, making it possible to build potential energy surfaces and explore chemical space. However, most of this work has focused on organic molecules due to the simplicity of their electronic structures as well as the availability of data sets. In this work, we build a deep learning architecture to model the energetics of zinc organometallic complexes. To achieve this, we have compiled a configurationally and conformationally diverse data set of zinc complexes using metadynamics to overcome the limitations of traditional sampling methods. In terms of the neural network potentials, our results indicate that for zinc complexes, partial charges play an important role in modeling the long-range interactions with a neural network. Our developed model outperforms semiempirical methods in predicting the relative energy of zinc conformers, yielding a mean absolute error (MAE) of 1.32 kcal/mol with reference to the double-hybrid PWPB95 method.
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Affiliation(s)
- Hongni Jin
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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2
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Zhang L, Wang H, Qu X. Biosystem-Inspired Engineering of Nanozymes for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211147. [PMID: 36622946 DOI: 10.1002/adma.202211147] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Nanozymes with intrinsic enzyme-mimicking activities have shown great potential to become surrogates of natural enzymes in many fields by virtue of their advantages of high catalytic stability, ease of functionalization, and low cost. However, due to the lack of predictable descriptors, most of the nanozymes reported in the past have been obtained mainly through trial-and-error strategies, and the catalytic efficacy, substrate specificity, as well as practical application effect under physiological conditions, are far inferior to that of natural enzymes. To optimize the catalytic efficacies and functions of nanozymes in biomedical settings, recent studies have introduced biosystem-inspired strategies into nanozyme design. In this review, recent advances in the engineering of biosystem-inspired nanozymes by leveraging the refined catalytic structure of natural enzymes, simulating the behavior changes of natural enzymes in the catalytic process, and mimicking the specific biological processes or living organisms, are introduced. Furthermore, the currently involved biomedical applications of biosystem-inspired nanozymes are summarized. More importantly, the current opportunities and challenges of the design and application of biosystem-inspired nanozymes are discussed. It is hoped that the studies of nanozymes based on bioinspired strategies will be beneficial for constructing the new generation of nanozymes and broadening their biomedical applications.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Huan Wang
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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3
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Siva M, Das K, Guha S, Sivagnanam S, Das G, Saha A, Stewart A, Maity B, Das P. Liposomes Containing Zinc-Based Chemotherapeutic Drug Block Proliferation and Trigger Apoptosis in Breast Cancer Cells. ACS APPLIED BIO MATERIALS 2023; 6:5310-5323. [PMID: 37988654 DOI: 10.1021/acsabm.3c00587] [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] [Indexed: 11/23/2023]
Abstract
Platinum-based chemotherapeutic drugs are effective in killing malignant cells but often trigger drug resistance or off-target side effects. Unlike platinum, zinc is used as an endogenous cofactor for several cellular enzymes and may, thus, display increased biocompatibility. In this present study, we have rationally designed and synthesized two substituted phenanthro[9,10-d]imidazole-based ligands L1 and L2 with pyridine and quinoline substitution at the 2 position and their corresponding Zn(II) complexes; (L1)2Zn and (L2)2Zn, which are characterized by standard analytical and spectroscopic methods. (L2)2Zn, but not (L1)2Zn has intrinsic fluorescence, indicating its potential utility in imaging applications. To facilitate cellular uptake, we generated liposomal formations with a phospholipid DMPC (1,2-Dimyristoyl-sn-glycero-3-phosphocholine) through molecular self-assembly. These liposomal formulations Lip-(L1)2Zn and Lip-(L2)2Zn were able to enter breast cancer cells, induce DNA fragmentation, arrest the cell cycle at the G0/G1 phase, decrease proliferation, and promote apoptosis by activating the DNA damage response. Importantly, both Lip-(L1)2Zn and Lip-(L2)2Zn decreased the size of breast cancer cell-based spheroids, indicating they may be capable of suppressing tumor growth. Our work represents an important proof-of-concept exercise demonstrating that successful liposomal formation of phenanthro[9,10-d]imidazole-based Zn(II) complexes with inherent optical properties have great promise for the development of imaging probes and efficient anticancer drugs.
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Affiliation(s)
- Mallayasamy Siva
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Kiran Das
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI campus, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
| | - Subhabrata Guha
- Department of Signal Transduction and Biogenic Amines, Chittaranajan National Cancer Institute, 37, S.P.Mukherjee Road, Kolkata, West Bengal 700 026, India
| | - Subramaniyam Sivagnanam
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Gaurav Das
- Department of Signal Transduction and Biogenic Amines, Chittaranajan National Cancer Institute, 37, S.P.Mukherjee Road, Kolkata, West Bengal 700 026, India
| | - Abhijit Saha
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
| | - Adele Stewart
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Biswanath Maity
- Department of Systems Biology, Centre of Biomedical Research (CBMR), SGPGI campus, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
| | - Priyadip Das
- Department of Chemistry, SRM Institute of Science and Technology, SRM Nagar, Potheri, Kattankulathur, Tamil Nadu 603203, India
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4
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Yang L, Dong S, Gai S, Yang D, Ding H, Feng L, Yang G, Rehman Z, Yang P. Deep Insight of Design, Mechanism, and Cancer Theranostic Strategy of Nanozymes. NANO-MICRO LETTERS 2023; 16:28. [PMID: 37989794 PMCID: PMC10663430 DOI: 10.1007/s40820-023-01224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/23/2023] [Indexed: 11/23/2023]
Abstract
Since the discovery of enzyme-like activity of Fe3O4 nanoparticles in 2007, nanozymes are becoming the promising substitutes for natural enzymes due to their advantages of high catalytic activity, low cost, mild reaction conditions, good stability, and suitable for large-scale production. Recently, with the cross fusion of nanomedicine and nanocatalysis, nanozyme-based theranostic strategies attract great attention, since the enzymatic reactions can be triggered in the tumor microenvironment to achieve good curative effect with substrate specificity and low side effects. Thus, various nanozymes have been developed and used for tumor therapy. In this review, more than 270 research articles are discussed systematically to present progress in the past five years. First, the discovery and development of nanozymes are summarized. Second, classification and catalytic mechanism of nanozymes are discussed. Third, activity prediction and rational design of nanozymes are focused by highlighting the methods of density functional theory, machine learning, biomimetic and chemical design. Then, synergistic theranostic strategy of nanozymes are introduced. Finally, current challenges and future prospects of nanozymes used for tumor theranostic are outlined, including selectivity, biosafety, repeatability and stability, in-depth catalytic mechanism, predicting and evaluating activities.
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Affiliation(s)
- Lu Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Shuming Dong
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Shili Gai
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China.
- Yantai Research Institute, Harbin Engineering University, Yantai, 264000, People's Republic of China.
| | - Dan Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - He Ding
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Lili Feng
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Guixin Yang
- Key Laboratory of Green Chemical Engineering and Technology of Heilongjiang Province, College of Material Science and Chemical Engineering, Harbin University of Science and Technology, Harbin, 150040, People's Republic of China
| | - Ziaur Rehman
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Piaoping Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China.
- Yantai Research Institute, Harbin Engineering University, Yantai, 264000, People's Republic of China.
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5
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Song Y, Li S, Gong H, Yip RCS, Chen H. Biopharmaceutical applications of microbial polysaccharides as materials: A review. Int J Biol Macromol 2023; 239:124259. [PMID: 37003381 DOI: 10.1016/j.ijbiomac.2023.124259] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Biological characteristics of natural polymers make microbial polysaccharides an excellent choice for biopharmaceuticals. Due to its easy purifying procedure and high production efficiency, it is capable of resolving the existing application issues associated with some plant and animal polysaccharides. Furthermore, microbial polysaccharides are recognized as prospective substitutes for these polysaccharides based on the search for eco-friendly chemicals. In this review, the microstructure and properties of microbial polysaccharides are utilized to highlight their characteristics and potential medical applications. From the standpoint of pathogenic processes, in-depth explanations are provided on the effects of microbial polysaccharides as active ingredients in the treatment of human diseases, anti-aging, and drug delivery. In addition, the scholarly developments and commercial applications of microbial polysaccharides as medical raw materials are also discussed. The conclusion is that understanding the use of microbial polysaccharides in biopharmaceuticals is essential for the future development of pharmacology and therapeutic medicine.
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Affiliation(s)
- Yige Song
- Marine College, Shandong University, NO. 180 Wenhua West Road, Gao Strict, Weihai 264209, PR China
| | - Shuxin Li
- SDU-ANU Joint Science College, Shandong University, NO. 180 Wenhua West Road, Gao Strict, Weihai 264209, PR China
| | - Hao Gong
- SDU-ANU Joint Science College, Shandong University, NO. 180 Wenhua West Road, Gao Strict, Weihai 264209, PR China
| | - Ryan Chak Sang Yip
- Center for Nanomedicine, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hao Chen
- Marine College, Shandong University, NO. 180 Wenhua West Road, Gao Strict, Weihai 264209, PR China.
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6
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Hambrook JR, Hanington PC. A cercarial invadolysin interferes with the host immune response and facilitates infection establishment of Schistosoma mansoni. PLoS Pathog 2023; 19:e1010884. [PMID: 36730464 PMCID: PMC9928134 DOI: 10.1371/journal.ppat.1010884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/14/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Schistosoma mansoni employs immune evasion and immunosuppression to overcome immune responses mounted by its snail and human hosts. Myriad immunomodulating factors underlie this process, some of which are proteases. Here, we demonstrate that one protease, an invadolysin we have termed SmCI-1, is released from the acetabular glands of S. mansoni cercaria and is involved in creating an immunological milieu favorable for survival of the parasite. The presence of SmCI-1 in the cercarial stage of S. mansoni is released during transformation into the schistosomula. SmCI-1 functions as a metalloprotease with the capacity to cleave collagen type IV, gelatin and fibrinogen. Additionally, complement component C3b is cleaved by this protease, resulting in inhibition of the classical and alternative complement pathways. Using SmCI-1 knockdown cercariae, we demonstrate that SmCI-1 protects schistosomula from complement-mediated lysis in human plasma. We also assess the effect of SmCI-1 on cytokine release from human peripheral blood mononuclear cells, providing compelling evidence that SmCI-1 promotes an anti-inflammatory microenvironment by enhancing production of IL-10 and suppressing the production of inflammatory cytokines like IL-1B and IL-12p70 and those involved in eosinophil recruitment and activation, like Eotaxin-1 and IL-5. Finally, we utilize the SmCI-1 knockdown cercaria in a mouse model of infection, revealing a role for SmCI-1 in S. mansoni survival.
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Affiliation(s)
- Jacob R. Hambrook
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
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7
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Cobalt containing bimetallic ZIFs and their derivatives as OER electrocatalysts: A critical review. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Assunção AGL. The F-bZIP-regulated Zn deficiency response in land plants. PLANTA 2022; 256:108. [PMID: 36348172 PMCID: PMC9643250 DOI: 10.1007/s00425-022-04019-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
This review describes zinc sensing and transcriptional regulation of the zinc deficiency response in Arabidopsis, and discusses how their evolutionary conservation in land plants facilitates translational approaches for improving the Zn nutritional value of crop species. Zinc is an essential micronutrient for all living organisms due to its presence in a large number of proteins, as a structural or catalytic cofactor. In plants, zinc homeostasis mechanisms comprise uptake from soil, transport and distribution throughout the plant to provide adequate cellular zinc availability. Here, I discuss the transcriptional regulation of the response to zinc deficiency and the zinc sensing mechanisms in Arabidopsis, and their evolutionary conservation in land plants. The Arabidopsis F-group basic region leucine-zipper (F-bZIP) transcription factors bZIP19 and bZIP23 function simultaneously as sensors of intracellular zinc status, by direct binding of zinc ions, and as the central regulators of the zinc deficiency response, with their target genes including zinc transporters from the ZRT/IRT-like Protein (ZIP) family and nicotianamine synthase enzymes that produce the zinc ligand nicotianamine. I note that this relatively simple mechanism of zinc sensing and regulation, together with the evolutionary conservation of F-bZIP transcription factors across land plants, offer important research opportunities. One of them is to use the F-bZIP-regulated zinc deficiency response as a tractable module for evolutionary and comparative functional studies. Another research opportunity is translational research in crop plants, modulating F-bZIP activity as a molecular switch to enhance zinc accumulation. This should become a useful plant-based solution to alleviate effects of zinc deficiency in soils, which impact crop production and crop zinc content, with consequences for human nutrition globally.
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Affiliation(s)
- Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
- CIBIO-InBIO, Research Centre in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.
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9
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Dong K, Xu C, Ren J, Qu. X. Chiral Nanozymes for Enantioselective Biological Catalysis. Angew Chem Int Ed Engl 2022; 61:e202208757. [DOI: 10.1002/anie.202208757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Kai Dong
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 China
- College of Chinese Medicinal Materials Jilin Agricultural University Changchun Jilin 130118 China
| | - Chen Xu
- College of Chinese Medicinal Materials Jilin Agricultural University Changchun Jilin 130118 China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Xiaogang Qu.
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
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10
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Dong K, Xu C, Ren J, Qu X. Chiral Nanozymes for Enantioselective Biological Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kai Dong
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Laboratory of Rare Earth Resource Utilization CHINA
| | - Chen Xu
- Jilin Agricultural University College of Chinese Medicinal Materials, CHINA
| | - Jinsong Ren
- Changchun Institute of Applied Chemistry Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization renmin street, #5625 130022 Changchun CHINA
| | - Xiaogang Qu
- Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences State Key Laboratory of Rare Earth Resource Utilization CHINA
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11
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Liao F, Lilay GH, Castro PH, Azevedo H, Assunção AGL. Regulation of the Zinc Deficiency Response in the Legume Model Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:916168. [PMID: 35845702 PMCID: PMC9279927 DOI: 10.3389/fpls.2022.916168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
The zinc deficiency response in Arabidopsis thaliana is regulated by F-group basic region leucine-zipper (F-bZIP) transcription factors, and there is evidence of evolutionary conservation of this regulatory network in land plants. Fundamental knowledge on the zinc homeostasis regulation in crop species will contribute to improving their zinc nutritional value. Legumes are protein-rich crops, used worldwide as part of traditional diets and as animal forage, being therefore a good target for micronutrient biofortification. Here, we identified F-bZIP transcription factors in representative legume species and functionally characterized the two F-bZIPs from Medicago truncatula. Results indicate that MtFbZIP1 is the functional homolog of A. thaliana bZIP19 and bZIP23, while MtFbZIP2 does not play a role in the zinc deficiency response. Additionally, analysis of M. truncatula genes from the Zrt/Irt-like protein (ZIP) family of zinc transporters or encoding nicotianamine synthase enzymes that produce the zinc ligand nicotianamine, support the conservation of the F-bZIP-regulated zinc deficiency response in M. truncatula. Phylogenetic analysis of F-bZIP homologs enriched in legume species reinforces the branching into two groups, with MtFbZIP1 and MtFbZIP2 mapping in Groups 1 and 2, respectively. This phylogeny combined with the functional characterization of MtFbZIPs supports the suggested conservation of the zinc deficiency response associated with Group 1 F-bZIPs, and the more variable evolutionary paths associated with Group 2. Overall, we provide novel insight on the mechanisms of response to zinc deficiency in M. truncatula, which contributes to developing strategies for improving zinc content in legume crops.
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Affiliation(s)
- Feixue Liao
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Grmay Hailu Lilay
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Pedro Humberto Castro
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Biodiversity and Land Planning, Vairão, Portugal
| | - Herlander Azevedo
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Biodiversity and Land Planning, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Ana G. L. Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- CIBIO-InBIO Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
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12
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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13
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Pellei M, Del Bello F, Porchia M, Santini C. Zinc coordination complexes as anticancer agents. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214088] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Biswal HS, Kumar Sahu A, Frontera A, Bauzá A. Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. J Chem Inf Model 2021; 61:3945-3954. [PMID: 34375103 PMCID: PMC8525862 DOI: 10.1021/acs.jcim.1c00594] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 01/09/2023]
Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S. Biswal
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via—Jatni, Khurda, 752050 Bhubaneswar, India
- Training
School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School
of Chemical Sciences, National Institute
of Science Education and Research (NISER), Bhimpur-Padanpur, Via—Jatni, Khurda, 752050 Bhubaneswar, India
- Training
School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department
of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department
of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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15
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Voos K, Schönauer E, Alhayek A, Haupenthal J, Andreas A, Müller R, Hartmann RW, Brandstetter H, Hirsch AKH, Ducho C. Phosphonate as a Stable Zinc-Binding Group for "Pathoblocker" Inhibitors of Clostridial Collagenase H (ColH). ChemMedChem 2021; 16:1257-1267. [PMID: 33506625 PMCID: PMC8251769 DOI: 10.1002/cmdc.202000994] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 01/05/2023]
Abstract
Microbial infections are a significant threat to public health, and resistance is on the rise, so new antibiotics with novel modes of action are urgently needed. The extracellular zinc metalloprotease collagenase H (ColH) from Clostridium histolyticum is a virulence factor that catalyses tissue damage, leading to improved host invasion and colonisation. Besides the major role of ColH in pathogenicity, its extracellular localisation makes it a highly attractive target for the development of new antivirulence agents. Previously, we had found that a highly selective and potent thiol prodrug (with a hydrolytically cleavable thiocarbamate unit) provided efficient ColH inhibition. We now report the synthesis and biological evaluation of a range of zinc-binding group (ZBG) variants of this thiol-derived inhibitor, with the mercapto unit being replaced by other zinc ligands. Among these, an analogue with a phosphonate motif as ZBG showed promising activity against ColH, an improved selectivity profile, and significantly higher stability than the thiol reference compound, thus making it an attractive candidate for future drug development.
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Affiliation(s)
- Katrin Voos
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
| | - Esther Schönauer
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Alaa Alhayek
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Jörg Haupenthal
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
| | - Anastasia Andreas
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf Müller
- Department of Microbial Natural ProductsHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Rolf W. Hartmann
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Hans Brandstetter
- Department of Biosciences andChristian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationDivision of Structural BiologyUniversity of SalzburgBillrothstrasse 115020SalzburgAustria
| | - Anna K. H. Hirsch
- Department of Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Campus E8 166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus E8 166123SaarbrückenGermany
| | - Christian Ducho
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2 366123SaarbrückenGermany
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16
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The less conserved metal-binding site in human CRISP1 remains sensitive to zinc ions to permit protein oligomerization. Sci Rep 2021; 11:5498. [PMID: 33750840 PMCID: PMC7943821 DOI: 10.1038/s41598-021-84926-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/18/2021] [Indexed: 12/30/2022] Open
Abstract
Cysteine-rich secretory proteins (CRISPs) are a subgroup of the CRISP, antigen 5 and PR-1 (CAP) superfamily that is characterized by the presence of a conserved CAP domain. Two conserved histidines in the CAP domain are proposed to function as a Zn2+-binding site with unknown function. Human CRISP1 is, however, one of the few family members that lack one of these characteristic histidine residues. The Zn2+-dependent oligomerization properties of human CRISP1 were investigated using a maltose-binding protein (MBP)-tagging approach in combination with low expression levels in XL-1 Blue bacteria. Moderate yields of soluble recombinant MBP-tagged human CRISP1 (MBP-CRISP1) and the MBP-tagged CAP domain of CRISP1 (MBP-CRISP1ΔC) were obtained. Zn2+ specifically induced oligomerization of both MBP-CRISP1 and MBP-CRISP1ΔC in vitro. The conserved His142 in the CAP domain was essential for this Zn2+ dependent oligomerization process, confirming a role of the CAP metal-binding site in the interaction with Zn2+. Furthermore, MBP-CRISP1 and MBP-CRISP1ΔC oligomers dissociated into monomers upon Zn2+ removal by EDTA. Condensation of proteins is characteristic for maturing sperm in the epididymis and this process was previously found to be Zn2+-dependent. The Zn2+-induced oligomerization of human recombinant CRISP1 may shed novel insights into the formation of functional protein complexes involved in mammalian fertilization.
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17
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Du J, Zou Z, Xu C. Enhanced oxygen and hydrogen evolution reaction by zinc doping in cobalt–nickel sulfide heteronanorods. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202000038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jing Du
- State Key Laboratory of Applied Organic Chemistry, Laboratory of Special Function Materials and Structure Design of the Ministry of Education College of Chemistry and Chemical Engineering Lanzhou University Lanzhou China
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education) Nankai University Tianjin China
| | - Zehua Zou
- State Key Laboratory of Applied Organic Chemistry, Laboratory of Special Function Materials and Structure Design of the Ministry of Education College of Chemistry and Chemical Engineering Lanzhou University Lanzhou China
| | - Cailing Xu
- State Key Laboratory of Applied Organic Chemistry, Laboratory of Special Function Materials and Structure Design of the Ministry of Education College of Chemistry and Chemical Engineering Lanzhou University Lanzhou China
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18
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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19
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Chakraborty T, Mukherjee S, Parveen R, Chandra A, Samanta D, Das D. A combined experimental and theoretical rationalization of an unusual zinc(ii)-mediated conversion of 18-membered Schiff-base macrocycles to 18-membered imine–amine macrocycles with imidazolidine side rings: an investigation of their bio-relevant catalytic activities. NEW J CHEM 2021. [DOI: 10.1039/d0nj05635a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Macrocyclic Zn(ii)-based Schiff base complexes exhibit significant phosphatase-like activity as well as high potential anticancer activity against breast cancer cells.
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Affiliation(s)
| | - Somali Mukherjee
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
| | - Rumana Parveen
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
| | - Arpita Chandra
- In Vitro Carcinogenesis and Cellular Chemotherapy
- Chittaranjan National Cancer Institute
- Kolkata-700026
- India
| | - Debabrata Samanta
- Department of Chemistry
- Dukhulal Nibaran Chandra College
- Aurangabad
- India
| | - Debasis Das
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
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20
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Zheng B, Bai T, Ling J, Sun J. Direct N-substituted N-thiocarboxyanhydride polymerization towards polypeptoids bearing unprotected carboxyl groups. Commun Chem 2020; 3:144. [PMID: 36703352 PMCID: PMC9814353 DOI: 10.1038/s42004-020-00393-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Synthesis of poly(α-amino acid)s bearing carboxyl groups is a critical pathway to prepare biomaterials to simulate functional proteins. The traditional approaches call for carboxyl-protected monomers to prevent degradation of monomers or wrong linkage. In this contribution, we synthesize N-carboxypentyl glycine N-thiocarboxyanhydride (CPG-NTA) and iminodiacetic acid N-thiocarboxyanhydride (IDA-NTA) without protection. Initiated by amines, CPG-NTA directly polymerizes into polyCPG bearing unprotected carboxyl groups with controlled molecular weight (2.8-9.3 kg mol-1) and low dispersities (1.08-1.12). Block and random copolymerizations of CPG-NTA with N-ethyl glycine N-thiocarboxyanhydride (NEG-NTA) demonstrate its versatile construction of complicated polypeptoids. On the contrary, IDA-NTA transforms amines into cyclic IDA dimer-capped species with carboxyl end group in decent yields (>89%) regio-selectively. Density functional theory calculation elucidates that IDA repeating unit is prone to cyclize to be the six-membered ring product with low ΔG. The polymer is a good adhesive reagent to various materials with adhesive strength of 33-229 kPa.
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Affiliation(s)
- Botuo Zheng
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Tianwen Bai
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jun Ling
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Innovation Center for Minimally Invasive Techniques and Devices, Zhejiang University, Hangzhou, 310016, China.
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21
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Grasso G. THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS. MASS SPECTROMETRY REVIEWS 2020; 39:574-585. [PMID: 31898821 DOI: 10.1002/mas.21621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates and how environmental factors can affect enzyme activities. In this scenario, mass spectrometric methods occupy a very important role in elucidating different aspects of ZnMPs-substrates interaction. These range from identification of cleavage sites to quantitation of kinetic parameters. In this work, an overview of all the main achievements regarding the application of mass spectrometric methods to investigating ZnMPs-substrates interactions is presented. A general experimental protocol is also described which may prove useful to the study of similar interactions. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Giuseppe Grasso
- Department of Chemical Sciences, Università degli Studi di Catania, Viale Andrea Doria 6, Catania, 95125, Italy
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22
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Muripiti V, Gondru R, Patri SV. Review of Zinc(II) Scaffolds: Efficient Role in Gene Delivery. ChemistrySelect 2020. [DOI: 10.1002/slct.202001557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Venkanna Muripiti
- Department of Chemistry National Institute of Technology Warangal Warangal 506004 Telangana India
| | - Ramesh Gondru
- Environmental Monitoring & Exposure Assessment (Air) Laboratory ICMR-National Institute for Research in Environmental Health (NIREH) Bhopal 462030 Madhya Pradesh India
| | - Srilakshmi V. Patri
- Department of Chemistry National Institute of Technology Warangal Warangal 506004 Telangana India
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23
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Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B, Zanjani ZS, Fornili A, Cianciotto NP, Garnett JA. Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLoS Pathog 2020; 16:e1008342. [PMID: 32365117 PMCID: PMC7224574 DOI: 10.1371/journal.ppat.1008342] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 05/14/2020] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function. Legionella pneumophila is the causative agent of Legionnaires' disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival of L. pneumophila in the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence that L. pneumophila can bind mucins on its surface, but this is not dependent on ChiA. This demonstrates that additional peripheral mucin binding proteins are also expressed in L. pneumophila. We also show that the ChiA C-terminal chitinase domain has novel Zn2+-dependent peptidase activity against mammalian mucin-like proteins, namely MUC5AC and the C1-esterase inhibitor, and that ChiA promotes bacterial penetration of mucin gels. Our findings suggest that ChiA can facilitate passage of L. pneumophila through the alveolar mucosa, can modulate the host complement system and that ChiA may be a promising target for vaccine development.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
| | - Lubov S. Grigoryeva
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Katherine H. Richardson
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Paula Corsini
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard C. White
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Rosie Shaw
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Theo J. Portlock
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Benjamin Dorgan
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Zeinab S. Zanjani
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arianna Fornili
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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24
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Lim SY, Park S, Im SW, Ha H, Seo H, Nam KT. Chemically Deposited Amorphous Zn-Doped NiFeOxHy for Enhanced Water Oxidation. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03544] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sung Yul Lim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518000, People’s Republic of China
| | - Sunghak Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Sang Won Im
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Heonjin Ha
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Hongmin Seo
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea
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25
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Michaelis M, Fayyaz A, Parambath M, Koeppen S, Ciacchi LC, Hanley QS, Perry CC. Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14230-14237. [PMID: 31609123 DOI: 10.1021/acs.langmuir.9b03085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC50), binding affinity (Ki), and binding free energy (ΔGads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | | | | | - Susan Koeppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Material Science (BCCMS), Center for Environmental Research and Sustainable Technology (UFT) and MAPEX Centre for Materials and Processes , University of Bremen , D-28359 Bremen , Germany
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26
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Prejanò M, Romeo I, Sgrizzi L, Russo N, Marino T. Why hydroxy-proline improves the catalytic power of the peptidoglycan N-deacetylase enzyme: insight from theory. Phys Chem Chem Phys 2019; 21:23338-23345. [PMID: 31617504 DOI: 10.1039/c9cp03804c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature exploits different strategies for enhancing the catalytic activity of enzymes, often resorting to producing beneficial mutations. The case of post-translational proline hydroxylation mutation in the active site of polysaccharide deacetylase (PDA) Bc1960 from Bacillus cereus is an interesting example of how small chemical modifications can cause significant improvements in enzymatic activity. In the present study the deacetylation mechanism promoted by both OH-proline (2Hyp) and standard proline (Pro) containing PDA is investigated using density functional theory. Although the mechanism presented for the two examined enzymes is in agreement with protease catalysis in metalloenzymes, the analysis along the potential energy surface (PES) reveals that the intermediate and product benefit energetically from the presence of the hydroxyl group on the proline. Our calculations provide evidence that for PDA-2Hyp, the hydrogen bond network established by the -OH group on the Cα of the proline with its closest neighbors stabilizes the transition states and, consequently, the reaction takes advantage of this. These results further contribute towards explaining the different catalytic activity experimentally observed for the polysaccharide deacetylase enzymes.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende, CS, Italy.
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27
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Kidd M, Ferket P, Qureshi M. Zinc metabolism with special reference to its role in immunity. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps19960022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- M.T. Kidd
- Department of Poultry Science, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - P.R. Ferket
- Department of Poultry Science, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - M.A. Qureshi
- Department of Poultry Science, North Carolina State University, Raleigh, North Carolina 27695, USA
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28
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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29
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Zinc(II) complexes of indole thiosemicarbazones: DNA/protein binding, molecular docking and in vitro cytotoxicity studies. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.05.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Understanding (R) Specific Carbonyl Reductase from Candida parapsilosis ATCC 7330 [CpCR]: Substrate Scope, Kinetic Studies and the Role of Zinc. Catalysts 2019. [DOI: 10.3390/catal9090702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
CpCR, an (R) specific carbonyl reductase, so named because it gave (R)-alcohols on asymmetric reduction of ketones and ketoesters, is a recombinantly expressed enzyme from Candida parapsilosis ATCC 7330. It turns out to be a better aldehyde reductase and catalyses cofactor (NADPH) specific reduction of aliphatic and aromatic aldehydes. Kinetics studies against benzaldehyde and 2,4-dichlorobenzaldehyde show that the enzyme affinity and rate of reaction change significantly upon substitution on the benzene ring of benzaldehyde. CpCR, an MDR (medium chain reductase/dehydrogenase) containing both structural and catalytic Zn atoms, exists as a dimer, unlike the (S) specific reductase (SRED) from the same yeast which can exist in both dimeric and tetrameric forms. Divalent metal salts inhibit the enzyme even at nanomolar concentrations. EDTA chelation decreases CpCR activity. However, chelation done after the enzyme is pre-incubated with the NADPH retains most of the activity implying that Zn removal is largely prevented by the formation of the enzyme-cofactor complex.
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31
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Azim N, Gardner QA, Rashid N, Akhtar M. Mechanistic studies on Pyrobaculum calidifontis porphobilinogen synthase (5-aminolevulinic acid dehydratase). Bioorg Chem 2019; 91:103117. [PMID: 31377385 DOI: 10.1016/j.bioorg.2019.103117] [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: 03/19/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
Abstract
Porphobilinogen synthase (PBG synthase) gene from Pyrobaculum calidifontis was cloned and expressed in E. coli. The recombinant enzyme was purified as an octamer and was found by mass spectrometry to have a subunit Mr of 37676.59 (calculated, 37676.3). The enzyme showed high thermal stability and retained almost all of its activity after incubation at 70 °C for 16 h in the presence of β-mercaptoethanol (β-ME) and zinc chloride. However, in the absence of the latter the enzyme was inactivated after 16 h although it regained full activity in the presence of β-ME and zinc chloride. The protein contained 4 mol of tightly bound zinc per octamer. Further, 4 mol of low affinity zinc could be incorporated following incubation with exogenous zinc salts. The enzyme was inactivated by incubation with levulinic acid followed by treatment with sodium borohydride. Tryptic digest of the modified enzyme and mass spectrometric analysis showed that Lys257 was the site of modification, which has previously been shown to be the site for the binding of 5-aminolevulinic acid giving rise to the propionate-half of porphobilinogen. P. calidifontis PBG synthase was inactivated by 5-chlorolevulinic acid and the residue modified was shown to be the central cysteine (Cys127) of the zinc-binding cysteine-triad, comprising Cys125, 127, 135. The present results in conjunction with earlier findings on zinc containing PBG synthases, are discussed which advocate that the catalytic role of zinc in the activation of the 5-aminolevulinic acid molecule forming the acetate-half of PBG is possible.
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Affiliation(s)
- Naseema Azim
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | | | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan; Biological Sciences, University of Southampton SO17 1BJ, UK.
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32
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Howe C, Moparthi VK, Ho FM, Persson K, Stensjö K. The Dps4 from Nostoc punctiforme ATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria. PLoS One 2019; 14:e0218300. [PMID: 31369577 PMCID: PMC6675082 DOI: 10.1371/journal.pone.0218300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 11/18/2022] Open
Abstract
Dps proteins (DNA-binding proteins from starved cells) have been found to detoxify H2O2. At their catalytic centers, the ferroxidase center (FOC), Dps proteins utilize Fe2+ to reduce H2O2 and therefore play an essential role in the protection against oxidative stress and maintaining iron homeostasis. Whereas most bacteria accommodate one or two Dps, there are five different Dps proteins in Nostoc punctiforme, a phototrophic and filamentous cyanobacterium. This uncommonly high number of Dps proteins implies a sophisticated machinery for maintaining complex iron homeostasis and for protection against oxidative stress. Functional analyses and structural information on cyanobacterial Dps proteins are rare, but essential for understanding the function of each of the NpDps proteins. In this study, we present the crystal structure of NpDps4 in its metal-free, iron- and zinc-bound forms. The FOC coordinates either two iron atoms or one zinc atom. Spectroscopic analyses revealed that NpDps4 could oxidize Fe2+ utilizing O2, but no evidence for its use of the oxidant H2O2 could be found. We identified Zn2+ to be an effective inhibitor of the O2-mediated Fe2+ oxidation in NpDps4. NpDps4 exhibits a FOC that is very different from canonical Dps, but structurally similar to the atypical one from DpsA of Thermosynechococcus elongatus. Sequence comparisons among Dps protein homologs to NpDps4 within the cyanobacterial phylum led us to classify a novel FOC class: the His-type FOC. The features of this special FOC have not been identified in Dps proteins from other bacterial phyla and it might be unique to cyanobacterial Dps proteins.
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Affiliation(s)
- Christoph Howe
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Vamsi K. Moparthi
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Felix M. Ho
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karina Persson
- Department of Chemistry, Umeå University, Umeå, Sweden
- * E-mail: (KS); (KP)
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail: (KS); (KP)
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33
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Cardoso JCR, Ferreira V, Zhang X, Anjos L, Félix RC, Batista FM, Power DM. Evolution and diversity of alpha-carbonic anhydrases in the mantle of the Mediterranean mussel (Mytilus galloprovincialis). Sci Rep 2019; 9:10400. [PMID: 31320702 PMCID: PMC6639325 DOI: 10.1038/s41598-019-46913-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/05/2019] [Indexed: 01/17/2023] Open
Abstract
The α-carbonic anhydrases (α-CAs) are a large and ancient group of metazoan-specific enzymes. They generate bicarbonate from metabolic carbon dioxide and through calcium carbonate crystal formation play a key role in the regulation of mineralized structures. To better understand how α-CAs contribute to shell mineralization in the marine Mediterranean mussel (Mytilus galloprovincialis) we characterized them in the mantle. Phylogenetic analysis revealed that mollusc α-CA evolution was affected by lineage and species-specific events. Ten α-CAs were found in the Mediterranean mussel mantle and the most abundant form was named, MgNACR, as it grouped with oyster nacreins (NACR). Exposure of the Mediterranean mussel to reduced water salinity (18 vs 37 ppt), caused a significant reduction (p < 0.05) in mantle esterase activity and MgNACR transcript abundance (p < 0.05). Protonograms revealed multiple proteins in the mantle with α-CA hydratase activity and mapped to a protein with a similar size to that deduced for monomeric MgNACR. Our data indicate that MgNACR is a major α-CA enzyme in mantle and that by homology with oyster nacreins likely regulates mussel shell production. We propose that species-dependent α-CA evolution may contribute to explain the diversity of bivalve shell structures and their vulnerability to environmental changes.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Vinicius Ferreira
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Xushuai Zhang
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Liliana Anjos
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Frederico M Batista
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, UK
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
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34
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Liu B, Hou Y, Wang X, Ma X, Fang S, Huang T, Chen Y, Bai Z, Lin S, Zhang R, Hu K. Structural basis of the mechanism of β-methyl epimerization by enzyme MarH. Org Biomol Chem 2019; 17:9605-9614. [PMID: 31681917 DOI: 10.1039/c9ob01996k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Structures of free MarH and MarH in complex with l-Trp, the analogue of substrate, were determined and the mechanism of MarH-catalyzed stereospecific β-methyl epimerization was proposed.
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35
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Yadav U, Rai TK, Sethi SC, Chandraker A, Khan MA, Komath SS. Characterising N-acetylglucosaminylphosphatidylinositol de-N-acetylase (CaGpi12), the enzyme that catalyses the second step of GPI biosynthesis in Candida albicans. FEMS Yeast Res 2018; 18:5045028. [PMID: 29945236 DOI: 10.1093/femsyr/foy067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/23/2018] [Indexed: 01/01/2023] Open
Abstract
Candida albicans N-acetylglucosaminylphosphatidylinositol de-N-acetylase (CaGpi12) recognises N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI) from Saccharomyces cerevisiae and is able to complement ScGPI12 function. Both N- and C-terminal ends of CaGpi12 are important for its function. CaGpi12 was biochemically characterised using rough endoplasmic reticulum microsomes prepared from BWP17 strain of C. albicans. CaGpi12 is optimally active at 30°C and pH 7.5. It is a metal-dependent enzyme that is stimulated by divalent cations but shows no preference for Zn2+ unlike the mammalian homologue. It irreversibly loses activity upon incubation with a metal chelator. Two conserved motifs, HPDDE and HXXH, are both important for its function in the cell. CaGPI12 is essential for growth and viability of C. albicans. Its loss causes reduction of GlcNAc-PI de-N-acetylase activity, cell wall defects and filamentation defects. The filamentation defects could be specifically correlated to an upregulation of the HOG1 pathway.
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Affiliation(s)
- Usha Yadav
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Tarun Kumar Rai
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | | | - Anupriya Chandraker
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Mohd Ashraf Khan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
| | - Sneha Sudha Komath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi-110 067, India
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36
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Hamdan F, Tahoori F, Balalaie S. Synthesis of novel cyclopeptides containing heterocyclic skeletons. RSC Adv 2018; 8:33893-33926. [PMID: 35548835 PMCID: PMC9086729 DOI: 10.1039/c8ra03899f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/14/2018] [Indexed: 01/13/2023] Open
Abstract
Cyclopeptides can be considered as naturally biologically active compounds. Over the last several decades, many attempts have been made to synthesize complex naturally occurring cyclopeptides, and great progress has been achieved to advance the field of total synthesis. Moreover, cyclopeptides containing heterocyclic skeletons have been recently developed into powerful reactions and approaches. This review aims to highlight recent advances in the synthesis of cyclopeptides containing heterocyclic skeletons such as triazole, oxazole, thiazole, and tetrazole.
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Affiliation(s)
- Fatima Hamdan
- Peptide Chemistry Research Center, K. N. Toosi University of Technology P. O. Box 15875-4416 Tehran Iran
| | - Fatemeh Tahoori
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO) Karaj Iran
| | - Saeed Balalaie
- Peptide Chemistry Research Center, K. N. Toosi University of Technology P. O. Box 15875-4416 Tehran Iran
- Medical Biology Research Center, Kermanshah University of Medical Sciences Kermanshah Iran
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37
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Synthesis and characterization of phenoxo-bridged dinuclear zinc(II) halide complexes: Role of electron withdrawing group on phosphatase activity. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Ghosh M, Ta S, Banerjee M, Mahiuddin M, Das D. Exploring the Scope of Photo-Induced Electron Transfer-Chelation-Enhanced Fluorescence-Fluorescence Resonance Energy Transfer Processes for Recognition and Discrimination of Zn 2+, Cd 2+, Hg 2+, and Al 3+ in a Ratiometric Manner: Application to Sea Fish Analysis. ACS OMEGA 2018; 3:4262-4275. [PMID: 30023890 PMCID: PMC6044824 DOI: 10.1021/acsomega.8b00266] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/04/2018] [Indexed: 05/14/2023]
Abstract
A rhodamine-based smart probe (RHES) has been developed for trace-level detection and discrimination of multiple cations, viz. Al3+, Zn2+, Cd2+, and Hg2+ in a ratiometric manner involving photo-induced electron transfer-chelation-enhanced fluorescence-fluorescence resonance energy transfer processes. The method being very fast and highly selective allows their bare eye visualization at a physiological pH. The optimized geometry and spectral properties of RHES and its cation adducts have been analyzed by time-dependent density functional theory calculations. RHES detects as low as 1.5 × 10-9 M Al3+, 1.2 × 10-9 M Zn2+, 6.7 × 10-9 M Cd2+, and 1.7 × 10-10 M Hg2+, whereas the respective association constants are 1.33 × 105 M-1, 2.11 × 104 M-1, 1.35 × 105 M-1, and 4.09 × 105 M-1. The other common ions do not interfere. The probe is useful for intracellular imaging of Zn2+, Cd2+, and Hg2+ in squamous epithelial cells. RHES is useful for the determination of the ions in sea fish and real samples.
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Affiliation(s)
| | | | | | | | - Debasis Das
- E-mail: . Phone: +91-342-2533913. Fax: +91-342-2530452 (D.D.)
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39
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Robinson AC, Schlessman JL, García-Moreno E B. Dielectric Properties of a Protein Probed by Reversal of a Buried Ion Pair. J Phys Chem B 2018; 122:2516-2524. [PMID: 29466010 DOI: 10.1021/acs.jpcb.7b12121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Thirty years ago, Hwang and Warshel suggested that a microenvironment preorganized to stabilize an ion pair would be incapable of reorganizing to stabilize the reverse ion pair. The implications were that (1) proteins have a limited capacity to reorganize, even under the influence of strong interactions, such as those present when ionizable groups are buried in the hydrophobic interior of a protein, and (2) the inability of proteins to tolerate the reversal of buried ion pairs demonstrates the limitations inherent to continuum electrostatic models of proteins. Previously we showed that when buried individually in the interior of staphylococcal nuclease, Glu23 and Lys36 have p Ka values near pH 7, but when buried simultaneously, they establish a strong interaction of ∼5 kcal/mol and have p Ka values shifted toward more normal values. Here, using equilibrium thermodynamic measurements, crystal structures, and NMR spectroscopy experiments, we show that although the reversed, individual substitutions-Lys23 and Glu36-also have p Ka values near 7, when buried together, they neither establish a strong interaction nor promote reorganization of their microenvironment. These experiments both confirm Warshel's original hypothesis and expand it by showing that it applies to reorganization, as demonstrated by our artificial ion pairs, as well as to preorganization as is commonly argued for motifs that stabilize naturally occurring ion pairs in polar microenvironments. These data constitute a challenging benchmark useful to test the ability of structure-based algorithms to reproduce the compensation between self-energy, Coulomb and polar interactions in hydrophobic environments of proteins.
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Affiliation(s)
- Aaron C Robinson
- Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Jamie L Schlessman
- Chemistry Department , U.S. Naval Academy , Annapolis , Maryland 21402 , United States
| | - Bertrand García-Moreno E
- Department of Biophysics , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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40
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Wang TP, Su YC, Chen Y, Severance S, Hwang CC, Liou YM, Lu CH, Lin KL, Zhu RJ, Wang EC. Corroboration of Zn( ii)–Mg( ii)-tertiary structure interplays essential for the optimal catalysis of a phosphorothiolate thiolesterase ribozyme. RSC Adv 2018; 8:32775-32793. [PMID: 35547718 PMCID: PMC9086351 DOI: 10.1039/c8ra05083j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
The TW17 ribozyme, a catalytic RNA selected from a pool of artificial RNA, is specific for the Zn2+-dependent hydrolysis of a phosphorothiolate thiolester bond. Here, we describe the organic synthesis of both guanosine α-thio-monophosphate and the substrates required for selecting and characterizing the TW17 ribozyme, and for deciphering the catalytic mechanism of the ribozyme. By successively substituting the substrate originally conjugated to the RNA pool with structurally modified substrates, we demonstrated that the TW17 ribozyme specifically catalyzes phosphorothiolate thiolester hydrolysis. Metal titration studies of TW17 ribozyme catalysis in the presence of Zn2+ alone, Zn2+ and Mg2+, and Zn2+ and [Co(NH3)6]3+ supported our findings that Zn2+ is absolutely required for ribozyme catalysis, and indicated that optimal ribozyme catalysis involves the presence of outer-sphere and one inner-sphere Mg2+. A survey of the TW17 ribozyme activity at various pHs revealed that the activity of the ribozyme critically depends on the alkaline conditions. Moreover, a GNRA tetraloop-containing ribozyme constructed with active catalysis in trans provided catalysis and multiple substrate turnover efficiencies significantly higher than ribozymes lacking a GNRA tetraloop. This research supports the essential roles of Zn2+, Mg2+, and a GNRA tetraloop in modulating the TW17 ribozyme structure for optimal ribozyme catalysis, leading also to the formulation of a proposed reaction mechanism for TW17 ribozyme catalysis. Zn(ii) and Mg(ii) and GAGA tetraloop in the ion atmosphere of the TW17 ribozyme is critical to optimal ribozyme catalysis at alkaline pH.![]()
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Affiliation(s)
- Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
- Kaohsiung Medical University Hospital
| | - Yu-Chih Su
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Yi Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Scott Severance
- Department of Molecular and Cellular Sciences
- Liberty University College of Osteopathic Medicine
- Lynchburg
- USA
| | - Chi-Ching Hwang
- Department of Biochemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Yi-Ming Liou
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Chia-Hui Lu
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Kun-Liang Lin
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Rui Jing Zhu
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
| | - Eng-Chi Wang
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
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41
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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42
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Zhang H, Jiang Y, Yan H, Cui Z, Yin C. Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration. J Chem Inf Model 2017; 57:2763-2775. [DOI: 10.1021/acs.jcim.7b00485] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Hai Yan
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Ziheng Cui
- Beijing
Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Chunhua Yin
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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43
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Craig WR, Baker TW, Marts AR, DeGenova DT, Martin DP, Reed GC, McCarrick RM, Crowder MW, Cohen SM, Tierney DL. Substituent Effects on the Coordination Chemistry of Metal-Binding Pharmacophores. Inorg Chem 2017; 56:11721-11728. [PMID: 28898098 DOI: 10.1021/acs.inorgchem.7b01661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combination of XAS, UV-vis, NMR, and EPR was used to examine the binding of a series of α-hydroxythiones to CoCA. All three appear to bind preferentially in their neutral, protonated forms. Two of the three clearly bind in a monodentate fashion, through the thione sulfur alone. Thiomaltol (TM) appears to show some orientational preference, on the basis of the NMR, while it appears that thiopyromeconic acid (TPMA) retains rotational freedom. In contrast, allothiomaltol (ATM), after initially binding in its neutral form, presumably through the thione sulfur, forms a final complex that is five-coordinate via bidentate coordination of ATM. On the basis of optical titrations, we speculate that this may be due to the lower initial pKa of ATM (8.3) relative to those of TM (9.0) and TPMA (9.5). Binding through the thione is shown to reduce the hydroxyl pKa by ∼0.7 pH unit on metal binding, bringing only ATM's pKa close to the pH of the experiment, facilitating deprotonation and subsequent coordination of the hydroxyl. The data predict the presence of a solvent-exchangeable proton on TM and TPMA, and Q-band 2-pulse ESEEM experiments on CoCA + TM suggest that the proton is present. ESE-detected EPR also showed a surprising frequency dependence, giving only a subset of the expected resonances at X-band.
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Affiliation(s)
- Whitney R Craig
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Tessa W Baker
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Amy R Marts
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Daniel T DeGenova
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - David P Martin
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Garrett C Reed
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - David L Tierney
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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Martin JE, Edmonds KA, Bruce KE, Campanello GC, Eijkelkamp BA, Brazel EB, McDevitt CA, Winkler ME, Giedroc DP. The zinc efflux activator SczA protects Streptococcus pneumoniae serotype 2 D39 from intracellular zinc toxicity. Mol Microbiol 2017; 104:636-651. [PMID: 28249108 DOI: 10.1111/mmi.13654] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 12/19/2022]
Abstract
Zinc is an essential trace element that serves as a catalytic cofactor in metalloenzymes and a structural element in proteins involved in general metabolism and cellular defenses of pathogenic bacteria. Despite its importance, high zinc levels can impair cellular processes, inhibiting growth of many pathogenic bacteria, including the major respiratory pathogen Streptococcus pneumoniae. Zinc intoxication is prevented in S. pneumoniae by expression of the zinc exporter CzcD, whose expression is activated by the novel TetR-family transcriptional zinc-sensing regulator SczA. How zinc bioavailability triggers activation of SczA is unknown. It is shown here through functional studies in S. pneumoniae that an unannotated homodimeric TetR from S. agalactiae (PDB 3KKC) is the bona fide zinc efflux regulator SczA, and binds two zinc ions per protomer. Mutagenesis analysis reveals two metal binding sites, termed A and B, located on opposite sides of the SczA C-terminal regulatory domain. In vivo, the A- and B-site SczA mutant variants impact S. pneumoniae resistance to zinc toxicity and survival in infected macrophages. A model is proposed for S. pneumoniae SczA function in which both A- and B-sites were required for transcriptional activation of czcD expression, with the A-site serving as the evolutionarily conserved intracellular sensing site in SczAs.
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Affiliation(s)
- Julia E Martin
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, 47405-7005, USA
| | | | - Bart A Eijkelkamp
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Erin B Brazel
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Christopher A McDevitt
- Research Centre for Infectious Diseases, School of Biological Sciences, the University of Adelaide, SA, 5005, Australia
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, 47405-7005, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7005, USA
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Chi Y, Rahkola JT, Kendrick AA, Holliday MJ, Paukovich N, Roberts TS, Janoff EN, Eisenmesser EZ. Streptococcus pneumoniae IgA1 protease: A metalloprotease that can catalyze in a split manner in vitro. Protein Sci 2017; 26:600-610. [PMID: 28028839 PMCID: PMC5326571 DOI: 10.1002/pro.3110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/01/2016] [Accepted: 12/21/2016] [Indexed: 01/07/2023]
Abstract
IgA1 proteases (IgA1P) from diverse pathogenic bacteria specifically cleave human immunoglobulin A1 (IgA1) at the hinge region, thereby thwarting protective host immune responses. Streptococcus pneumoniae (S. pneumoniae) IgA1P shares no sequence conservation with serine or cysteine types of IgA1Ps or other known proteins, other than a conserved HExxH Zn-binding motif (1604-1608) found in metalloproteases. We have developed a novel expression system to produce the mature S. pneumoniae IgA1P and we have discovered that this form is both attached to the bacterial cell surface and released in its full form. Our data demonstrate that the S. pneumoniae IgA1P comprises two distinct regions that associate to form an active metalloprotease, the first such example of a metalloprotease that can be split in vitro and recombined to form an active enzyme. By capitalizing on this novel domain architecture, we show that the N-terminal region of S. pneumoniae IgA1P comprises the primary binding region for IgA1, although the C-terminal region of S. pneumoniae IgA1P is necessary for cleavage of IgA1. Our findings lend insight into the protein domain architecture of the S. pneumoniae IgA1P and function of this important virulence factor for S. pneumoniae infection.
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Affiliation(s)
- Ying‐Chih Chi
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
| | - Jeremy T. Rahkola
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado DenverAuroraCO
- Denver Veterans Affairs Medical CenterDenverCO
| | - Agnieszka A. Kendrick
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
| | - Michael J. Holliday
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
| | - Natasia Paukovich
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
| | - Thomas S. Roberts
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
| | - Edward N. Janoff
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado DenverAuroraCO
- Denver Veterans Affairs Medical CenterDenverCO
| | - Elan Z. Eisenmesser
- Departments of Biochemistry and Molecular GeneticsUniversity of Colorado DenverAuroraCO
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Heier JL, Mikolajczak DJ, Böttcher C, Koksch B. Substrate specificity of an actively assembling amyloid catalyst. Biopolymers 2017; 108. [PMID: 27858968 DOI: 10.1002/bip.23003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023]
Abstract
In the presence of Zn2+ , the catalytic, amyloid-forming peptide Ac-IHIHIQI-NH2 , was found to exhibit enhanced selectivity for hydrophobic p-nitrophenyl ester substrates while in the process of self-assembly. As opposed to the substrate p-nitrophenyl acetate, which was more effectively hydrolyzed with Ac-IHIHIQI-NH2 in its fully fibrillar state, the hydrophobic substrate Z-L-Phe-ONp was converted with a second-order rate constant more than 11-times greater when the catalyst was actively assembling. Under such conditions, Z-L-Phe-ONp hydrolysis proceeded at a greater velocity than the more hydrophilic and otherwise more labile ester Boc-L-Asn-ONp. When assembling, the catalyst also showed increased selectivity for the L-enantiomer of Z-Phe-ONp. These findings suggest the occurrence of increased interactions of hydrophobic moieties of the substrate with exposed hydrophobic surfaces of the assembling peptides and present valuable features for future de novo design consideration.
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Affiliation(s)
- Jason L Heier
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
| | - Dorian J Mikolajczak
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
| | - Christoph Böttcher
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Research Center for Electron Microscopy Berlin, Germany
| | - Beate Koksch
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
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47
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Chakrabarti B, Bairagya HR, Mukhopadhyay BP, Sekar K. New biochemical insight of conserved water molecules at catalytic and structural Zn 2+ ions in human matrix metalloproteinase-I: a study by MD-simulation. J Mol Model 2017; 23:57. [PMID: 28161785 DOI: 10.1007/s00894-017-3210-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/09/2017] [Indexed: 12/01/2022]
Abstract
Human matrix metalloproteinase (MMP)-1 or collagenase-1 plays a significant role in embryonic development, tissue remodeling, and is also involved in several diseases like arthritis, metastasis, etc. Molecular dynamics simulation studies on hMMP-1 X-ray structures (PDB Id. 1CGE, 1CGF, 1CGL, 1HFC, and 2TCL) suggest that the three conserved water molecules (WH/1, WI, WS) are coordinated with catalytic zinc (ZnC), and one water molecule (W) is associated at structural zinc ion (ZnS). Transition of the coordination geometry around ZnC from tetrahedral to octahedral and tetrahedral to trigonal bipyramidal at ZnS are also observed during the dynamics. Recognition of two zinc ions through water mediated bridges (ZnC - WH (W1)…W2….H183 - ZnS) and stabilization of secondary coordination zone around the metal ions indicates the possibility of ZnC…ZnS coupled catalytic mechanism in hMMP-I. This study not only reveals a functionally important role of conserved water molecules in hMMP-I but also highlights the involvement of other non catalytic residues, such as S172 and D170 in the catalytic mechanism. The results obtained in this study could be relevant for importance of conserved water mediated recognition site of the sequence residue id. 202(RWTNNFREY)210, interaction of W(tryptophan)203 to zinc bound histidine, their influence on the water molecules that are involved in bridging between ZnC and ZnS, and structure-based design of specific hMMP inhibitors. Graphical abstract Water mediated recognition of structural and catalytic zinc ions of hMMP-1 structure (MD simulatated conformation).
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Affiliation(s)
- Bornali Chakrabarti
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, 713209, India
| | - Hridoy R Bairagya
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, 713209, India.,Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, UK
| | - Bishnu P Mukhopadhyay
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, 713209, India.
| | - K Sekar
- Department of Computational and Data Sciences Indian Institute of Science, Laboratory for Structural Biology and Bio-computing, Bangalore, 560 012, India
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Poddar R, Jain A, Kidwai M. Bis[(l)prolinate-N,O]Zn: A water-soluble and recycle catalyst for various organic transformations. J Adv Res 2017; 8:245-270. [PMID: 28289549 PMCID: PMC5338870 DOI: 10.1016/j.jare.2016.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/28/2016] [Accepted: 12/20/2016] [Indexed: 11/17/2022] Open
Abstract
Under the green chemistry perspective, bis[(l)prolinate-N,O]Zn (also called zinc-proline or Zn[(l)-pro]2) has proven its competence as a promising alternative in a plethora of applications such as catalyst or promoter. Owing to its biodegradable and non-toxic nature of bis[(l)prolinate-N,O]Zn, it is being actively investigated as a water soluble green catalyst for synthetic chemistry. Bis[(l)prolinate-N,O]Zn are readily utilized under mild conditions and have high selectivity and reactivity with broad range of substrate acceptance to make it better reaction medium for a wide variety of organic transformations. This Review summarizes the till date literature on its synthesis, characterization, and its catalytic role in various organic reactions.
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Affiliation(s)
- Roona Poddar
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Arti Jain
- Department of Chemistry, Daulat Ram College, University of Delhi, Delhi 110007, India
| | - Mazaahir Kidwai
- Department of Chemistry, University of Delhi, Delhi 110007, India
- Corresponding author. Fax: +91 1127666235.
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Soudek P, Ursu M, Petrová Š, Vaněk T. Improving crop tolerance to heavy metal stress by polyamine application. Food Chem 2016; 213:223-229. [DOI: 10.1016/j.foodchem.2016.06.087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 05/30/2016] [Accepted: 06/24/2016] [Indexed: 01/09/2023]
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50
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New zinc(II) complexes of the Non-steroidal Anti-Inflammatory Drug (indomethacin) and various nitrogen donor ligands. Synthesis, characterization and biological activity. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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