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Wang H, Wang X, Yang Y, Zhu Y, Wang S, Chen Q, Yan D, Dong X, Li M, Lu S. Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population. BMC Genomics 2024; 25:582. [PMID: 38858624 PMCID: PMC11165779 DOI: 10.1186/s12864-024-10484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). RESULTS A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10- 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. CONCLUSIONS The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Faculty of Animal Science, Xichang University, Xichang, Sichuan, 615000, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yongli Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixuan Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Shuyan Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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2
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Zheng H, Zhang H, Zhong J, Gucwa M, Zhang Y, Ma H, Deng L, Mao L, Minor W, Wang N. PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules. RESEARCH SQUARE 2024:rs.3.rs-3908734. [PMID: 38463967 PMCID: PMC10925427 DOI: 10.21203/rs.3.rs-3908734/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Metal ions are vital components in many proteins for the inference and engineering of protein function, with coordination complexity linked to structural (4-residue predominate), catalytic (3-residue predominate), or regulatory (2-residue predominate) roles. Computational tools for modeling metal ions in protein structures, especially for transient, reversible, and concentration-dependent regulatory sites, remain immature. We present PinMyMetal (PMM), a sophisticated hybrid machine learning system for predicting zinc ion localization and environment in macromolecular structures. Compared to other predictors, PMM excels in predicting regulatory sites (median deviation of 0.34 Å), demonstrating superior accuracy in locating catalytic sites (median deviation of 0.27 Å) and structural sites (median deviation of 0.14 Å). PMM assigns a certainty score to each predicted site based on local structural and physicochemical features independent of homolog presence. Interactive validation through our server, CheckMyMetal, expands PMM's scope, enabling it to pinpoint and validates diverse functional zinc sites from different structure sources (predicted structures, cryo-EM and crystallography). This facilitates residue-wise assessment and robust metal binding site design. The lightweight PMM system demands minimal computing resources and is available at https://PMM.biocloud.top. While currently trained on zinc, the PMM workflow can easily adapt to other metals through expanded training data.
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Affiliation(s)
| | | | | | | | | | | | - Lei Deng
- Hunan University College of Biology
| | | | | | - Nasui Wang
- Division of Endocrinology and Metabolism, The First Affiliated Hospital of Shantou University Medical College
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3
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Ibrahim IH. Metalloproteins and metalloproteomics in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:123-176. [PMID: 38960472 DOI: 10.1016/bs.apcsb.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Metalloproteins represents more than one third of human proteome, with huge variation in physiological functions and pathological implications, depending on the metal/metals involved and tissue context. Their functions range from catalysis, bioenergetics, redox, to DNA repair, cell proliferation, signaling, transport of vital elements, and immunity. The human metalloproteomic studies revealed that many families of metalloproteins along with individual metalloproteins are dysregulated under several clinical conditions. Also, several sorts of interaction between redox- active or redox- inert metalloproteins are observed in health and disease. Metalloproteins profiling shows distinct alterations in neurodegenerative diseases, cancer, inflammation, infection, diabetes mellitus, among other diseases. This makes metalloproteins -either individually or as families- a promising target for several therapeutic approaches. Inhibitors and activators of metalloenzymes, metal chelators, along with artificial metalloproteins could be versatile in diagnosis and treatment of several diseases, in addition to other biomedical and industrial applications.
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Affiliation(s)
- Iman Hassan Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt.
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4
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Laveglia V, Bazayeva M, Andreini C, Rosato A. Hunting down zinc(II)-binding sites in proteins with distance matrices. Bioinformatics 2023; 39:btad653. [PMID: 37878807 PMCID: PMC10630175 DOI: 10.1093/bioinformatics/btad653] [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: 08/14/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
MOTIVATION In recent years, high-throughput sequencing technologies have made available the genome sequences of a huge variety of organisms. However, the functional annotation of the encoded proteins often still relies on low-throughput and costly experimental studies. Bioinformatics approaches offer a promising alternative to accelerate this process. In this work, we focus on the binding of zinc(II) ions, which is needed for 5%-10% of any organism's proteins to achieve their physiologically relevant form. RESULTS To implement a predictor of zinc(II)-binding sites in the 3D structures of proteins, we used a neural network, followed by a filter of the network output against the local structure of all known sites. The latter was implemented as a function comparing the distance matrices of the Cα and Cβ atoms of the sites. We called the resulting tool Master of Metals (MOM). The structural models for the entire proteome of an organism generated by AlphaFold can be used as input to our tool in order to achieve annotation at the whole organism level within a few hours. To demonstrate this, we applied MOM to the yeast proteome, obtaining a precision of about 76%, based on data for homologous proteins. AVAILABILITY AND IMPLEMENTATION Master of Metals has been implemented in Python and is available at https://github.com/cerm-cirmmp/Master-of-metals.
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Affiliation(s)
- Vincenzo Laveglia
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
| | - Milana Bazayeva
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
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5
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Bazayeva M, Laveglia V, Andreini C, Rosato A. Metal-induced structural variability of mononuclear metal-binding sites from a database perspective. J Inorg Biochem 2023; 238:112025. [PMID: 36270040 DOI: 10.1016/j.jinorgbio.2022.112025] [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: 08/03/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/21/2022]
Abstract
Metalloproteins are ubiquitous in all kingdoms of life. Their role and function are tightly related to the local structure of the metal-binding site. In this regard, the MetalPDB database is an invaluable tool since it stores the 3D structure of metal-binding sites and of their corresponding apo forms. In this work, we exploited MetalPDB to compute extensive statistics over >3000 clusters of mononuclear sites about the rearrangements occurring upon change in metalation state. For each cluster, we matched the holo and apo sites so that it was possible to average the distances between all possible pairs of Cα and donor atoms and thus quantitatively assess structural variations by computing the Δ values (mean apo distance - mean holo distance). For most of the structures the backbone is rigid with little to no rearrangement, while donor atoms experience significant changes of their relative position when the metal is removed. Sodium and potassium sites are an exception to this general observation. This is most likely caused by their preference for coordination by the main-chain oxygen atoms, making the rearrangement of donor atoms superimposable to that of the backbone. Magnesium and calcium show a different behavior, despite their chemical similarity: calcium sites undergo a larger reorganization upon metalation although both metals have similar percentage of backbone oxygen as donor atoms. We ascribe this observation to the structural and energetic factors regulating the selectivity for calcium over magnesium.
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Affiliation(s)
- Milana Bazayeva
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Vincenzo Laveglia
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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6
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Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH. In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Proc Natl Acad Sci U S A 2022; 119:e2205278119. [PMID: 35951650 PMCID: PMC9388147 DOI: 10.1073/pnas.2205278119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 01/24/2023] Open
Abstract
Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
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Affiliation(s)
- Zhou Yin
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Jeremy G. Bird
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Jason T. Kaelber
- Rutgers Cryo-EM and Nanoimaging Facility, Rutgers University, Piscataway, NJ 08854
| | - Bryce E. Nickels
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Genetics, Rutgers University, Piscataway, NJ 08854
| | - Richard H. Ebright
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
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7
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Zinc in Cognitive Impairment and Aging. Biomolecules 2022; 12:biom12071000. [PMID: 35883555 PMCID: PMC9312494 DOI: 10.3390/biom12071000] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/05/2023] Open
Abstract
Zinc, an essential micronutrient for life, was first discovered in 1869 and later found to be indispensable for the normal development of plants and for the normal growth of rats and birds. Zinc plays an important role in many physiological and pathological processes in normal mammalian brain development, especially in the development of the central nervous system. Zinc deficiency can lead to neurodegenerative diseases, mental abnormalities, sleep disorders, tumors, vascular diseases, and other pathological conditions, which can cause cognitive impairment and premature aging. This study aimed to review the important effects of zinc and zinc-associated proteins in cognitive impairment and aging, to reveal its molecular mechanism, and to highlight potential interventions for zinc-associated aging and cognitive impairments.
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8
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Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022; 23:ijms23147684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.
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Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Correspondence:
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9
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A New Benzoxazole-Based Fluorescent Macrocyclic Chemosensor for Optical Detection of Zn2+ and Cd2+. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Benzoxazole-containing ligands find many applications both in medicinal chemistry, catalysis and fluorescence chemosensing. Benzoxazole-containing macrocycles could be therefore a good strategy to achieve stable and selective fluorescent complexes with suitable metal ions. In this work, the synthesis, binding, and photochemical properties of a new fluorescent ligand (L) are reported. L is a cyclophane macrocycle containing the 1,3-bis(benzo[d]oxazol-2-yl)phenyl (BBzB) fluorophore and an aliphatic tetra-amine chain to form the macrocyclic skeleton. Methods: Spectrophotometric and spectrofluorimetric measurements, 1H NMR analysis, and DFT calculations were performed. Results: L behaves as a PET-mediated chemosensor, being emissive at 390 nm at acidic pH and non-emissive at basic pH. The chemosensor is able to detect Zn2+ and Cd2+ in an aqueous medium (acetonitrile–water, 4:1 v/v) at neutral pH through a CHEF effect upon metal ion coordination. Paramagnetic metal ions (Cu2+) and heavy atoms (Pb2+, Hg2+) resulted in a quenching of fluorescence or very low emission. Conclusions: The new cyclophane macrocycle L was revealed to be a selective PET-regulated chemosensor for Zn2+ and Cd2+ in an aqueous medium, being able to bind up to two and one metal cations, respectively. The molecule showed a shifted emission towards the visible region compared to similar systems, suggesting a co-planar conformation of the aromatic fragment upon metal coordination. All these data are supported by both experimental measurements and theoretical calculations.
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10
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Varghese A, Chaturvedi SS, DiCastri B, Mehler E, Fields GB, Karabencheva-Christova TG. Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies. Chemphyschem 2021; 23:10.1002/cphc.202100680. [PMID: 35991515 PMCID: PMC9387770 DOI: 10.1002/cphc.202100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 11/06/2022]
Abstract
Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.
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Affiliation(s)
- Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Bella DiCastri
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Emerald Mehler
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458
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11
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Yoon C, Lee SJ. Selective coordination of cobalt ions by zinc fingers in
Escherichia coli
. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chungwoon Yoon
- Department of Chemistry and Institute for Molecular Biology and Genetics Jeonbuk National University Jeonju Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry and Institute for Molecular Biology and Genetics Jeonbuk National University Jeonju Republic of Korea
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12
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Panwar A, Wangchuk J, Kar M, Lodha R, Medigeshi GR. Dengue virus replication enhances labile zinc pools by modulation of ZIP8. Cell Microbiol 2021; 23:e13395. [PMID: 34619004 PMCID: PMC7612096 DOI: 10.1111/cmi.13395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/20/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Zinc‐dependent viral proteins rely on intracellular zinc homeostasis for successful completion of infectious life‐cycle. Here, we report that the intracellular labile zinc levels were elevated at early stages of dengue virus (DENV) infection in hepatic cells and this increase in free zinc was abolished in cells infected with UV‐inactivated virus or with a DENV replication inhibitor implicating a role for zinc homeostasis in viral RNA replication. This change in free zinc was mediated by zinc transporter, ZIP8, as siRNA‐mediated knockdown of ZIP8 resulted in abrogation of increase in free zinc levels leading to significant reduction in DENV titers suggesting a crucial role for ZIP8 in early stages of DENV replication. Furthermore, elevated free zinc levels correlated with high copy numbers of dengue genome in peripheral blood leukocytes obtained from dengue patients compared to healthy controls suggesting a critical role for zinc homeostasis in dengue infection.
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Affiliation(s)
- Aleksha Panwar
- Clinical and Cellular Virology lab, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Jigme Wangchuk
- Clinical and Cellular Virology lab, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Meenakshi Kar
- Clinical and Cellular Virology lab, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Guruprasad R Medigeshi
- Clinical and Cellular Virology lab, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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13
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Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach. Molecules 2021; 26:molecules26175221. [PMID: 34500655 PMCID: PMC8434281 DOI: 10.3390/molecules26175221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.
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14
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Brandis JEP, Zalesak SM, Kane MA, Michel SLJ. Cadmium Exchange with Zinc in the Non-Classical Zinc Finger Protein Tristetraprolin. Inorg Chem 2021; 60:7697-7707. [PMID: 33999622 PMCID: PMC8501473 DOI: 10.1021/acs.inorgchem.0c03808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tristetraprolin (TTP) is a nonclassical CCCH zinc finger protein that regulates inflammation. TTP targets AU-rich RNA sequences of cytokine mRNAs forming a TTP/mRNA complex. This complex is then degraded, switching off the inflammatory response. Cadmium, a known carcinogen, triggers proinflammatory effects, and there is evidence that Cd increases TTP expression in cells, suggesting that Zn-TTP may be a target for cadmium toxicity. We sought to determine whether Cd exchanges with Zn in the TTP active site and measure the effect of RNA binding on this exchange. A construct of TTP that contains the two CCCH domains (TTP-2D) was employed to investigate these interactions. A spin-filter ICP-MS experiment to quantify the metal that is bound to the ZF after metal exchange was performed, and it was determined that Cd exchanges with Zn in Zn2-TTP-2D and that Zn exchanges with Cd in Cd2-TTP-2D. A native ESI-MS experiment to identify the metal-ZF complexes formed after metal exchange was performed, and M-TTP-2D complexes with singular and double metal exchange were observed. Metal exchange was measured in both the absence and presence of TTP's partner RNA, with retention of RNA binding. These data show that Cd can exchange with Zn in TTP without affecting function.
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Affiliation(s)
- Joel E P Brandis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Stephanie M Zalesak
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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15
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Cruz-González A, Muñoz-Velasco I, Cottom-Salas W, Becerra A, Campillo-Balderas JA, Hernández-Morales R, Vázquez-Salazar A, Jácome R, Lazcano A. Structural analysis of viral ExoN domains reveals polyphyletic hijacking events. PLoS One 2021; 16:e0246981. [PMID: 33730017 PMCID: PMC7968707 DOI: 10.1371/journal.pone.0246981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Nidoviruses and arenaviruses are the only known RNA viruses encoding a 3’-5’ exonuclease domain (ExoN). The proofreading activity of the ExoN domain has played a key role in the growth of nidoviral genomes, while in arenaviruses this domain partakes in the suppression of the host innate immune signaling. Sequence and structural homology analyses suggest that these proteins have been hijacked from cellular hosts many times. Analysis of the available nidoviral ExoN sequences reveals a high conservation level comparable to that of the viral RNA-dependent RNA polymerases (RdRp), which are the most conserved viral proteins. Two highly preserved zinc fingers are present in all nidoviral exonucleases, while in the arenaviral protein only one zinc finger can be identified. This is in sharp contrast with the reported lack of zinc fingers in cellular ExoNs, and opens the possibility of therapeutic strategies in the struggle against COVID-19.
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Affiliation(s)
- Adrián Cruz-González
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
| | - Israel Muñoz-Velasco
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
| | - Wolfgang Cottom-Salas
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
- Escuela Nacional Preparatoria, Plantel 8 Miguel E. Schulz, Universidad Nacional Autónoma de México, México City, México
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
| | | | | | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, United States of America
| | - Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
- * E-mail: (AL); (RJ)
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, México
- El Colegio Nacional, México City, México
- * E-mail: (AL); (RJ)
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16
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Tran JB, Krężel A. InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. J Proteome Res 2021; 20:1889-1901. [PMID: 33502860 PMCID: PMC8023803 DOI: 10.1021/acs.jproteome.0c00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
InterMetalDB is a
free-of-charge database and browser of intermolecular
metal binding sites that are present on the interfaces of macromolecules
forming larger assemblies based on structural information deposited
in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. InterMetalDB collects the interfacial binding sites with involvement
of metal ions and clusters them on the basis of 50% sequence similarity
and the nearest metal environment (5 Å radius). The data are
available through the web interface where they can be queried, viewed,
and downloaded. Complexity of the query depends on the user, because
the questions in the query are connected with each other by a logical
AND. InterMetalDB offers several useful options for filtering records
including searching for structures by particular parameters such as
structure resolution, structure description, and date of deposition.
Records can be filtered by coordinated metal ion, number of bound
amino acid residues, coordination sphere, and other features. InterMetalDB
is regularly updated and will continue to be regularly updated with
new content in the future. InterMetalDB is a useful tool for all researchers
interested in metalloproteins, protein engineering, and metal-driven
oligomerization.
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Affiliation(s)
- Józef Ba Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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17
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Crawley-Snowdon H, Yang JC, Zaccai NR, Davis LJ, Wartosch L, Herman EK, Bright NA, Swarbrick JS, Collins BM, Jackson LP, Seaman MNJ, Luzio JP, Dacks JB, Neuhaus D, Owen DJ. Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29. Nat Commun 2020; 11:5031. [PMID: 33024112 PMCID: PMC7539009 DOI: 10.1038/s41467-020-18773-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/08/2020] [Indexed: 01/13/2023] Open
Abstract
VARP and TBC1D5 are accessory/regulatory proteins of retromer-mediated retrograde trafficking from endosomes. Using an NMR/X-ray approach, we determined the structure of the complex between retromer subunit VPS29 and a 12 residue, four-cysteine/Zn++ microdomain, which we term a Zn-fingernail, two of which are present in VARP. Mutations that abolish VPS29:VARP binding inhibit trafficking from endosomes to the cell surface. We show that VARP and TBC1D5 bind the same site on VPS29 and can compete for binding VPS29 in vivo. The relative disposition of VPS29s in hetero-hexameric, membrane-attached, retromer arches indicates that VARP will prefer binding to assembled retromer coats through simultaneous binding of two VPS29s. The TBC1D5:VPS29 interaction is over one billion years old but the Zn-fingernail appears only in VARP homologues in the lineage directly giving rise to animals at which point the retromer/VARP/TBC1D5 regulatory network became fully established.
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Affiliation(s)
- Harriet Crawley-Snowdon
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Nathan R Zaccai
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Luther J Davis
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Lena Wartosch
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3
| | | | - James S Swarbrick
- Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, QLD, 4072, Australia
| | - Lauren P Jackson
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | | | - J Paul Luzio
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3.
| | - David Neuhaus
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK.
| | - David J Owen
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
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18
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Baghalabadi V, Doucette AA. Mass spectrometry profiling of low molecular weight proteins and peptides isolated by acetone precipitation. Anal Chim Acta 2020; 1138:38-48. [PMID: 33161983 DOI: 10.1016/j.aca.2020.08.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022]
Abstract
Solvent-based protein precipitation provides exceptional recovery, particularly when the ionic strength of the solution is controlled. While precipitation is ideally suited for intact protein purification ahead of mass-spectrometry, low molecular weight (LMW) proteins and peptides are considered less susceptible to aggregation in organic solvent. As the combination of salt and organic solvent (i.e. acetone) has yet to be exploited to precipitate LMW proteins, we herein determine the low mass limit for solvent-based protein precipitation. We establish optimized conditions for high recovery precipitation of LMW proteins and peptides. Our results demonstrate a strong dependence on the type of salt to recover LMW components from complex mixtures. Inclusion of 100 mM ZnSO4 with 97% acetone provides near quantitative recovery of all peptides down to 2 kDa, and continues to exceed 90% yield for peptides at a molecular weight of 1 kDa. A detailed characterization of the precipitated peptides resulting from trypsin and pepsin digestion of complex systems is provided by bottom-up mass spectrometry.
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Affiliation(s)
- Venus Baghalabadi
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, P.O. Box 53714-161, Tabriz, Iran
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada.
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19
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Garau A, Aragoni MC, Arca M, Bencini A, Blake AJ, Caltagirone C, Giorgi C, Lippolis V, Scorciapino MA. Aza- and Mixed Thia/Aza-Macrocyclic Receptors with Quinoline-Bearing Pendant Arms for Optical Discrimination of Zinc(II) or Cadmium(II) Ions. Chempluschem 2020; 85:1789-1799. [PMID: 32808469 DOI: 10.1002/cplu.202000444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/23/2020] [Indexed: 12/21/2022]
Abstract
The synthesis and coordination properties of two fluorescent chemosensors, featuring [9]aneN3 (1,4,7-triazacyclononane; L1) and [12]aneNS3 (1-aza-4,7,10-trithiacyclododecane; L2) as receptor units, and a quinoline pendant arm with an amide group as a functional group spacer are described. The optical responses of L1 and L2 in the presence of several metal ions were analysed in MeCN/H2 O (1 : 4 v/v) solutions. A selective chelation enhancement of fluorescence (CHEF) effect was observed in the presence of Zn2+ in the case of L1, and in the presence of Cd2+ in the case of L2, following the formation of a 1 : 1 and a 1 : 2 metal/ligand complex, respectively, which was also confirmed by potentiometric measurements. 1 H and 13 C NMR measurements in CD3 CN/CDCl3 in combination with molecular mechanics calculations show that for both complexes of L1 and L2 with Zn2+ and Cd2+ , respectively, the coordination of the carbonyl group from the pendant arm could be the origin of the observed optical selectivity.
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Affiliation(s)
- Alessandra Garau
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
| | - M Carla Aragoni
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
| | - Massimiliano Arca
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
| | - Andrea Bencini
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Alexander J Blake
- School of Chemistry, University of Nottingham, University Park, NG7 2RD, Nottingham, United Kingdom
| | - Claudia Caltagirone
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
| | - Claudia Giorgi
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Vito Lippolis
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
| | - Mariano Andrea Scorciapino
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, S.S. 554 Bivio per Sestu, I-09042, Monserrato (CA), Italy
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20
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Harris JW, Bates JS, Bukowski BC, Greeley J, Gounder R. Opportunities in Catalysis over Metal-Zeotypes Enabled by Descriptions of Active Centers Beyond Their Binding Site. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02102] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- James W. Harris
- Department of Chemical and Biological Engineering, The University of Alabama, Box 870203, Tuscaloosa, Alabama 35487, United States
| | - Jason S. Bates
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brandon C. Bukowski
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Jeffrey Greeley
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Rajamani Gounder
- Charles D. Davidson School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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21
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Shafi BUD, Kumar R, Jadhav SE, Kar J. Effect of Zinc Nanoparticles on Milk Yield, Milk Composition and Somatic Cell Count in Early-Lactating Barbari Does. Biol Trace Elem Res 2020; 196:96-102. [PMID: 31595398 DOI: 10.1007/s12011-019-01900-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 09/11/2019] [Indexed: 01/21/2023]
Abstract
Nano minerals have better bioavailability, efficient utilization, smaller dose rate, and stable interactions within the biological system. Efficacy of dietary supplementation of nano zinc particles on milk yield, milk composition, and somatic cell count was studied in periparturient Barbari does. Twenty-four Barbari goats (mean body weight 35 ± 1.5 kg) of about 4 months of pregnancy were divided into four groups (Gr I, Gr II, Gr III, and Gr IV) of six animals each. All the does were fed a common basal diet (containing 38.96 mg Zn/kg DM) of concentrate pellet and Bengal gram (Cicer arietinum) straw. No zinc was supplemented in does of Gr I (control group), while Gr II, Gr III, and Gr IV does were supplemented with 20 ppm inorganic zinc oxide, 10 ppm of nano zinc, and 20 ppm of nano zinc respectively. The experimental feeding was done for 75 days (30 days before kidding to 45 days after kidding). Results showed that yield and composition of milk in different groups of lactating does were not significantly (P < 0.05) affected by zinc supplementation. The percentages of solid-nonfat, fat, protein, lactose, and total solid were comparable (P > 0.05) among different groups of lactating does. The milk mineral levels of Zn, Cu, Na, Ca, and K were statistically similar (P > 0.05) in all the groups of goats. There was significantly (P < 0.05) lower somatic cell count (SCC) in zinc-supplemented groups (Gr II, Gr III, and Gr IV) as compared with the control (Gr I) group of does. SCC was lowest in Gr IV followed by Gr III, Gr II, and Gr I. The present study concluded that supplementation of inorganic zinc @ 20 ppm and nano zinc @ 10 and 20 ppm had no significant effect on milk yield/composition but reduced milk somatic cell count. The efficacy of nano zinc was found to be better as compared with normal inorganic form.
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Affiliation(s)
- Burhan Ud Din Shafi
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Ravindra Kumar
- Division of Animal Nutrition and Product Technology, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, UP, 28112, India.
| | - S E Jadhav
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
| | - Junaid Kar
- Division of Animal Nutrition, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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22
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Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. ACS OMEGA 2020; 5:15301-15310. [PMID: 32637803 PMCID: PMC7331063 DOI: 10.1021/acsomega.0c01337] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/13/2020] [Indexed: 05/08/2023]
Abstract
We developed a novel force field in the context of AMBER parameterization for glutamate and aspartate zinc(II)-binding residues. The interaction between the zinc ion and the coordinating atoms is represented by a spherical nonbonded parameterization. The polarization effect due to the zinc ion has been taken into account by redefining the atomic charges on the residues through accurate quantum mechanical calculations. The new zinc-binding ASP and GLU residues, along with the CYS and HIS zinc-binding residues, parameterized in a recent work [Macchiagodena M.;J. Chem. Inf. Model.2019, 59, 3803-3816], allow users to reliably simulate 96% of the Zn-proteins available in the Protein Data Bank. The upgraded force field for zinc(II)-bound residues has been tested performing molecular dynamics simulations with an explicit solvent and comparing the structural information with experimental data for five different proteins binding zinc(II) with GLU, ASP, HIS, and CYS. We further validated our approach by evaluating the binding free energy of (R)-2-benzyl-3-nitropropanoic acid to carboxypeptidase A using a recently developed nonequilibrium alchemical method. We demonstrated that in this setting it is crucial to take into account polarization effects also on the metal-bound inhibitor.
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Affiliation(s)
- Marina Macchiagodena
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic
Resonance Center (CERM), Università
degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic
Resonance Center (CERM), Università
degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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23
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Strengthening the Immune System and Reducing Inflammation and Oxidative Stress through Diet and Nutrition: Considerations during the COVID-19 Crisis. Nutrients 2020; 12:nu12061562. [PMID: 32471251 PMCID: PMC7352291 DOI: 10.3390/nu12061562] [Citation(s) in RCA: 395] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 12/13/2022] Open
Abstract
The coronavirus-disease 2019 (COVID-19) was announced as a global pandemic by the World Health Organization. Challenges arise concerning how to optimally support the immune system in the general population, especially under self-confinement. An optimal immune response depends on an adequate diet and nutrition in order to keep infection at bay. For example, sufficient protein intake is crucial for optimal antibody production. Low micronutrient status, such as of vitamin A or zinc, has been associated with increased infection risk. Frequently, poor nutrient status is associated with inflammation and oxidative stress, which in turn can impact the immune system. Dietary constituents with especially high anti-inflammatory and antioxidant capacity include vitamin C, vitamin E, and phytochemicals such as carotenoids and polyphenols. Several of these can interact with transcription factors such as NF-kB and Nrf-2, related to anti-inflammatory and antioxidant effects, respectively. Vitamin D in particular may perturb viral cellular infection via interacting with cell entry receptors (angiotensin converting enzyme 2), ACE2. Dietary fiber, fermented by the gut microbiota into short-chain fatty acids, has also been shown to produce anti-inflammatory effects. In this review, we highlight the importance of an optimal status of relevant nutrients to effectively reduce inflammation and oxidative stress, thereby strengthening the immune system during the COVID-19 crisis.
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24
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Abbehausen C. Zinc finger domains as therapeutic targets for metal-based compounds - an update. Metallomics 2020; 11:15-28. [PMID: 30303505 DOI: 10.1039/c8mt00262b] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Zinc finger proteins are one of the most abundant families of proteins and present a wide range of structures and functions. The structural zinc ion provides the correct conformation to specifically recognize DNA, RNA and protein sequences. Zinc fingers have essential functions in transcription, protein degradation, DNA repair, cell migration, and others. Recently, reports on the extensive participation of zinc fingers in disease have been published. On the other hand, much information remains to be unravelled as many genomes and proteomes are being reported. A variety of zinc fingers have been identified; however, their functions are still under investigation. Because zinc fingers have identified functions in several diseases, they are being increasingly recognized as drug targets. The replacement of Zn(ii) by another metal ion in zinc fingers is one of the most prominent methods of inhibition. From one side, zinc fingers play roles in the toxicity mechanisms of Ni(ii), Hg(ii), Cd(ii) and others. From the other side, gold, platinum, cobalt, and selenium complexes are amongst the compounds being developed as zinc finger inhibitors for therapy. The main challenge in the design of therapeutic zinc finger inhibitors is to achieve selectivity. Recently, the design of novel compounds and elucidation of the mechanisms of zinc substitution have renewed the possibilities of selective zinc finger inhibition by metal complexes. This review aims to update the status of novel strategies to selectively target zinc finger domains by metal complexes.
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Affiliation(s)
- C Abbehausen
- Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, CEP 13083-970, Campinas, São Paulo, Brazil.
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25
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Ok K, Li W, Neu HM, Batelu S, Stemmler TL, Kane MA, Michel SLJ. Role of Gold in Inflammation and Tristetraprolin Activity. Chemistry 2020; 26:1535-1547. [DOI: 10.1002/chem.201904837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Kiwon Ok
- Department of Pharmaceutical Sciences University of Maryland School of Pharmacy 20 Penn St. Baltimore MD 21201 USA
| | - Wenjing Li
- Department of Pharmaceutical Sciences University of Maryland School of Pharmacy 20 Penn St. Baltimore MD 21201 USA
| | - Heather M. Neu
- Department of Pharmaceutical Sciences University of Maryland School of Pharmacy 20 Penn St. Baltimore MD 21201 USA
| | - Sharon Batelu
- Department of Pharmaceutical Sciences Wayne State University 259 Mack Avenue Detroit MI 48201 USA
| | - Timothy L. Stemmler
- Department of Pharmaceutical Sciences Wayne State University 259 Mack Avenue Detroit MI 48201 USA
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences University of Maryland School of Pharmacy 20 Penn St. Baltimore MD 21201 USA
| | - Sarah L. J. Michel
- Department of Pharmaceutical Sciences University of Maryland School of Pharmacy 20 Penn St. Baltimore MD 21201 USA
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26
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Jardin C, Chaves G, Musset B. Assessing Structural Determinants of Zn 2+ Binding to Human H V1 via Multiple MD Simulations. Biophys J 2020; 118:1221-1233. [PMID: 31972155 DOI: 10.1016/j.bpj.2019.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 01/02/2023] Open
Abstract
Voltage-gated proton channels (HV1) are essential for various physiological tasks but are strongly inhibited by Zn2+ cations. Some determinants of Zn2+ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn2+ binds to monomeric HV1 despite evidence that HV1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn2+ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human HV1. The dimer interface is more efficient for attracting and binding Zn2+ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.
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Affiliation(s)
- Christophe Jardin
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Gustavo Chaves
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Boris Musset
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany.
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27
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Garau A, Lvova L, Macedi E, Ambrosi G, Aragoni MC, Arca M, Caltagirone C, Coles SJ, Formica M, Fusi V, Giorgi L, Isaia F, Lippolis V, Orton JB, Paolesse R. N 2S 2 pyridinophane-based fluorescent chemosensors for selective optical detection of Cd 2+ in soils. NEW J CHEM 2020. [DOI: 10.1039/d0nj03858j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A fluorescent sensor array for the quantitative determination of Cd2+ in soils based on two N2S2 pyridinophane chemosensors is presented.
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28
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Abstract
Numerous zinc ectoenzymes are folded and activated in the compartments of the early secretory pathway, such as the ER and the Golgi apparatus, before reaching their final destination. During this process, zinc must be incorporated into the active site; therefore, metalation of the nascent protein is indispensable for the expression of the active enzyme. However, to date, the molecular mechanism underlying this process has been poorly investigated. This is in sharp contrast to the physiological and pathophysiological roles of zinc ectoenzymes, which have been extensively investigated over the past decades. This manuscript concisely outlines the present understanding of zinc ectoenzyme activation through metalation by zinc and compares this with copper ectoenzyme activation, in which elaborate copper metalation mechanisms are known. Moreover, based on the comparison, several hypotheses are discussed. Approximately 80 years have passed since the first zinc enzyme was identified; therefore, it is necessary to improve our understanding of zinc ectoenzymes from a biochemical perspective, which will further our understanding of their biological roles.
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Affiliation(s)
- Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies , Kyoto University , Kyoto 606-8502 , Japan
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29
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Aoki S, Kikuchi C, Kitagawa Y, Hasegawa Y, Sonoike S, Saga Y, Hatanaka M. Evaluation of Zn
2+
Coordination Structures in Chiral Zn
2+
Complexes Based on Shape Measurement Factors: Relationships between Activity and the Coordination Structure. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shin Aoki
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
- Research Institute for Science and Technology Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Chiharu Kikuchi
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Yuichi Kitagawa
- Faculty of Engineering and Graduate School of Engineering Hokkaido University Kita‐13 Jo. Nishi‐8 Chome 060‐8628 Sapporo Hokkaido Japan
| | - Yasuchika Hasegawa
- Faculty of Engineering and Graduate School of Engineering Hokkaido University Kita‐13 Jo. Nishi‐8 Chome 060‐8628 Sapporo Hokkaido Japan
| | - Shotaro Sonoike
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
- Chugai Pharmaceutical Co., Ltd. 2‐1–1‐Nihonbashi Muromachi, Cyuo‐ku 103‐8324 Tokyo Japan
| | - Yutaka Saga
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Miho Hatanaka
- Institute for Research Initiatives Division for Research Strategy Graduate School of Science and Technology, and Nara Institute of Science and Technology 8916‐5 Takayama‐cho, Ikoma‐shi 630‐0192 Nara Japan
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30
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Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. J Chem Inf Model 2019; 59:3803-3816. [PMID: 31385702 DOI: 10.1021/acs.jcim.9b00407] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.
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Affiliation(s)
- Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Claudia Andreini
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy.,Magnetic Resonance Center (CERM)-Università degli Studi di Firenze , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Antonio Rosato
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy.,Magnetic Resonance Center (CERM)-Università degli Studi di Firenze , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
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31
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Putignano V, Rosato A, Banci L, Andreini C. MetalPDB in 2018: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2019; 46:D459-D464. [PMID: 29077942 PMCID: PMC5753354 DOI: 10.1093/nar/gkx989] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 11/14/2022] Open
Abstract
MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, ∼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.
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Affiliation(s)
- Valeria Putignano
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- To whom correspondence should be addressed. Tel: +39 55 4574267;
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32
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Disruption of the Metal Ion Environment by EDTA for Silk Formation Affects the Mechanical Properties of Silkworm Silk. Int J Mol Sci 2019; 20:ijms20123026. [PMID: 31234286 PMCID: PMC6627089 DOI: 10.3390/ijms20123026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/16/2019] [Accepted: 06/16/2019] [Indexed: 11/22/2022] Open
Abstract
Silk fiber has become a research focus because of its comprehensive mechanical properties. Metal ions can influence the conformational transition of silk fibroin. Current research is mainly focused on the role of a single ion, rather than the whole metal ion environment. Here, we report the effects of the overall metal ion environment on the secondary structure and mechanical properties of silk fibers after direct injection and feeding of silkworms with EDTA. The metal composition of the hemolymph, silk gland, and silk fiber changed significantly post EDTA treatment. Synchrotron FTIR analysis indicated that the secondary structure of silk fiber after EDTA treatment changed dramatically; particularly, the β-sheets decreased and the β-turns increased. Post EDTA treatment, the silk fiber had significantly decreased strength, Young’s modulus, and toughness as compared with the control groups, while the strain exhibited no obvious change. These changes can be attributed to the change in the metal ion environment in the silk fibroin and sericin in the silk gland. Our investigation provides a new theoretical basis for the natural silk spinning process, and our findings could help develop a method to modify the mechanical properties of silk fiber using metal ions.
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33
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Abstract
Cancer is a serious health issue in the world due to a large body of cancer-related human deaths, and there is no current treatment available to efficiently treat the disease as the tumor is often diagnosed at a serious stage. Moreover, Cancer cells are often resistant to chemotherapy, radiotherapy, and molecular-targeted therapy. Upon further knowledge of mechanisms of tumorigenesis, aggressiveness, metastasis, and resistance to treatments, it is necessary to detect the disease at an earlier stage and for a better response to therapy. The hippo pathway possesses the unique capacity to lead to tumorigenesis. Mutations and altered expression of its core components (MST1/2, LATS1/2, YAP and TAZ) promote the migration, invasion, malignancy of cancer cells. The biological significance and deregulation of it have received a large body of interests in the past few years. Further understanding of hippo pathway will be responsible for cancer treatment. In this review, we try to discover the function of hippo pathway in different diversity of cancers, and discuss how Hippo pathway contributes to other cellular signaling pathways. Also, we try to describe how microRNAs, circRNAs, and ZNFs regulate hippo pathway in the process of cancer. It is necessary to find new therapy strategies for cancer.
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Affiliation(s)
- Yanyan Han
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan.
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34
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Chabert V, Lebrun V, Lebrun C, Latour JM, Sénèque O. Model peptide for anti-sigma factor domain HHCC zinc fingers: high reactivity toward 1O 2 leads to domain unfolding. Chem Sci 2019; 10:3608-3615. [PMID: 30996953 PMCID: PMC6432622 DOI: 10.1039/c9sc00341j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
All organisms have to cope with the deleterious effects of reactive oxygen species. Some of them are able to mount a transcriptional response to various oxidative stresses, which involves sensor proteins capable of assessing the redox status of the cell or to detect reactive oxygen species. In this article, we describe the design, synthesis and characterization of Zn·LASD(HHCC), a model for the Zn(Cys)2(His)2 zinc finger site of ChrR, a sensor protein involved in the bacterial defence against singlet oxygen that belongs to the family of zinc-binding anti-sigma factors possessing a characteristic H/C-X24/25-H-X3-C-X2-C motif. The 46-amino acid model peptide LASD(HHCC) was synthetized by solid phase peptide synthesis and its Zn2+-binding properties were investigated using electronic absorption, circular dichroism and NMR. LASD(HHCC) forms a 1 : 1 complex with Zn2+, namely Zn·LASD(HHCC), that adopts a well-defined conformation with the Zn2+ ion capping a 3-helix core that reproduces almost perfectly the fold of the ChrR in the vicinity of its zinc site. H2O2 reacts with Zn·LASD(HHCC) to yield a disulfide with a second order rate constant of 0.030 ± 0.002 M-1 s-1. Zn·LASD(HHCC) reacts rapidly with singlet oxygen to yield sulfinates and sulfonates. A lower limit of the chemical reaction rate constant between Zn·LASD(HHCC) and 1O2 was determined to be 3.9 × 106 M-1 s-1. Therefore, the Zn(Cys)2(His)2 site of Zn·LASD(HHCC) appears to be at least 5 times more reactive toward these two oxidants than that of a classical ββα zinc finger. Consequences for the activation mechanism of ChrR are discussed.
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Affiliation(s)
- Valentin Chabert
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Vincent Lebrun
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Colette Lebrun
- Univ. Grenoble Alpes , CEA , CNRS , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Marc Latour
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , CNRS , CEA , BIG , LCBM (UMR 5249) , F-38000 Grenoble , France .
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35
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Ireland SM, Martin ACR. ZincBind-the database of zinc binding sites. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5304468. [PMID: 30722040 PMCID: PMC6361820 DOI: 10.1093/database/baz006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/07/2019] [Indexed: 12/03/2022]
Abstract
Zinc is one of the most important biologically active metals. Ten per cent of the human genome is thought to encode a zinc binding protein and its uses encompass catalysis, structural stability, gene expression and immunity. At present, there is no specific resource devoted to identifying and presenting all currently known zinc binding sites. Here we present ZincBind, a database of zinc binding sites and its web front-end. Using the structural data in the Protein Data Bank, ZincBind identifies every instance of zinc binding to a protein, identifies its binding site and clusters sites based on 90% sequence identity. There are currently 24 992 binding sites, clustered into 7489 unique sites. The data are available over the web where they can be browsed and downloaded, and via a REST API. ZincBind is regularly updated and will continue to be updated with new data and features.
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Affiliation(s)
- Sam M Ireland
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London, UK
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36
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Abstract
Zinc ion binding is a principal event in the achievement of the correct fold in classical zinc finger domains since the motif is largely unfolded in the absence of metal. In the case of a prokaryotic zinc finger, the larger βββαα domain contributes to the folding mechanism with a larger hydrophobic core. For these reasons, following the great amount of attention devoted to unveiling the effect of xenobiotic metal ion replacement in zinc fingers and in zinc-containing proteins in general, the prokaryotic zinc finger domain appears to be an interesting model for studying metal ion interaction with metalloproteins. Here, we explore the binding of Ni(II), Hg(II), and Pb(II) to Ros87, the DNA binding domain of the prokaryotic zinc finger protein Ros. We measured Ros87-metal ion dissociation constants and monitored the effects on the structure and function of the domain. Interestingly, we found that the protein folds in the presence of Ni(II) with important structural perturbations, while in the presence of Pb(II) and Hg(II) it does not appear to be significantly folded. Accordingly, an overall strong reduction in the DNA binding capability is observed for all of the examined proteins. Our data integrate and complement the information collected in the past few years concerning the functional and structural effects of metal ion substitution in classical zinc fingers in order to contribute to a better comprehension of the toxicity of these metals in biological systems.
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37
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Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics 2018; 10:1755-1776. [PMID: 30358795 PMCID: PMC6291366 DOI: 10.1039/c8mt00269j] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is an essential cofactor for many proteins. A key mechanism of zinc homeostasis during deficiency is "zinc sparing" in which specific zinc-binding proteins are repressed to reduce the cellular requirement. In this report, we evaluated zinc sparing across the zinc proteome of Saccharomyces cerevisiae. The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. Protein abundance was determined by mass spectrometry. In zinc-replete cells, we detected over 2500 proteins among which 229 were zinc proteins. Based on copy number estimates and binding stoichiometries, a replete cell contains ∼9 million zinc-binding sites on proteins. During zinc deficiency, many zinc proteins decreased in abundance and the zinc-binding requirement decreased to ∼5 million zinc atoms per cell. Many of these effects were due at least in part to changes in mRNA levels rather than simply protein degradation. Measurements of cellular zinc content showed that the level of zinc atoms per cell dropped from over 20 million in replete cells to only 1.7 million in deficient cells. These results confirmed the ability of replete cells to store excess zinc and suggested that the majority of zinc-binding sites on proteins in deficient cells are either unmetalated or mismetalated. Our analysis of two abundant zinc proteins, Fba1 aldolase and Met6 methionine synthetase, supported that hypothesis. Thus, we have discovered widespread zinc sparing mechanisms and obtained evidence of a high accumulation of zinc proteins that lack their cofactor during deficiency.
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Affiliation(s)
- Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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38
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Zinc in Keratinocytes and Langerhans Cells: Relevance to the Epidermal Homeostasis. J Immunol Res 2018; 2018:5404093. [PMID: 30622978 PMCID: PMC6304883 DOI: 10.1155/2018/5404093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/10/2018] [Indexed: 02/07/2023] Open
Abstract
In the skin, the epidermis is continuously exposed to various kinds of external substances and stimuli. Therefore, epidermal barriers are crucial for providing protection, safeguarding health, and regulating water balance by maintaining skin homeostasis. Disruption of the epidermal barrier allows external substances and stimuli to invade or stimulate the epidermal cells, leading to the elicitation of skin inflammation. The major components of the epidermal barrier are the stratum corneum (SC) and tight junctions (TJs). The presence of zinc in the epidermis promotes epidermal homeostasis; hence, this study reviewed the role of zinc in the formation and function of the SC and TJs. Langerhans cells (LCs) are one of the antigen-presenting cells found in the epidermis. They form TJs with adjacent keratinocytes (KCs), capture external antigens, and induce antigen-specific immune reactions. Thus, the function of zinc in LCs was examined in this review. We also summarized the general knowledge of zinc and zinc transporters in the epidermis with updated findings.
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39
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Domínguez-Calva JA, Haase-Pettingell C, Serebryany E, King JA, Quintanar L. A Histidine Switch for Zn-Induced Aggregation of γ-Crystallins Reveals a Metal-Bridging Mechanism That Is Relevant to Cataract Disease. Biochemistry 2018; 57:4959-4962. [PMID: 30064223 DOI: 10.1021/acs.biochem.8b00436] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cataract disease results from non-amyloid aggregation of eye lens proteins and is the leading cause of blindness in the world. Zinc concentrations in cataractous lenses are increased significantly relative to those in healthy lenses. It was recently reported that Zn(II) ions induce the aggregation of one of the more abundant proteins in the core of the lens, human γD-crystallin. Here, the mechanism of Zn-induced aggregation has been revealed through a comparative study of three homologous human lens γ-crystallins and a combination of spectroscopic, electron microscopy, and site-directed mutagenesis studies. This work reveals that a single His residue acts as a "switch" for the Zn-induced non-amyloid aggregation of human γ-crystallins. Aggregation can be reversed by a chelating agent, revealing a metal-bridging mechanism. This study sheds light on an aberrant Zn-crystallin interaction that promotes aggregation, a process that is relevant to cataract disease.
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Affiliation(s)
- José Antonio Domínguez-Calva
- Departamento de Química , Centro de Investigación y de Estudios Avanzados (Cinvestav) , 07360 Mexico City , Mexico
| | - Cameron Haase-Pettingell
- Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02142 , United States
| | - Eugene Serebryany
- Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02142 , United States
| | - Jonathan Alan King
- Department of Biology , Massachusetts Institute of Technology , Cambridge , Massachusetts 02142 , United States
| | - Liliana Quintanar
- Departamento de Química , Centro de Investigación y de Estudios Avanzados (Cinvestav) , 07360 Mexico City , Mexico
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40
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Woodruff G, Bouwkamp CG, de Vrij FM, Lovenberg T, Bonaventure P, Kushner SA, Harrington AW. The Zinc Transporter SLC39A7 (ZIP7) Is Essential for Regulation of Cytosolic Zinc Levels. Mol Pharmacol 2018; 94:1092-1100. [PMID: 29980658 DOI: 10.1124/mol.118.112557] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/28/2018] [Indexed: 01/07/2023] Open
Abstract
Zinc homeostasis is a highly regulated process in mammalian cells that is critical for normal growth and development. Movement of zinc across cell compartments is controlled by two classes of transporters: Slc39a family members transport zinc into the cytosol from either the extracellular space or intracellular stores such as the endoplasmic reticulum (ER), whereas the SLC30A family mediates zinc efflux from the cytosol. In this study, we report that genetic ablation of SLC39A7 (ZIP7) results in decreased cytosolic zinc levels, increased ER zinc levels, impaired cell proliferation, and induction of ER stress. Confirmatory of impaired zinc transport as the causal mechanism, both the increased ER stress and impaired cell proliferation were rescued by increasing cytosolic zinc. Furthermore, using these robust cellular phenotypes, we implemented a small-molecule library screen with 2800 compounds and identified one small molecule capable of rescuing ER stress and cell proliferation in ZIP7-deficient cells in the low micromolar range.
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Affiliation(s)
- Grace Woodruff
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Christian G Bouwkamp
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Femke M de Vrij
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Timothy Lovenberg
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Pascal Bonaventure
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Steven A Kushner
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
| | - Anthony W Harrington
- Neuroscience Discovery, Janssen Research and Development, San Diego, California (G.W., T.L., P.B., A.W.H.); and Department of Psychiatry, Erasmus MC, Rotterdam, The Netherlands (C.G.B., F.M.V., S.A.K.)
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41
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Abstract
The skin is the third most zinc (Zn)-abundant tissue in the body. The skin consists of the epidermis, dermis, and subcutaneous tissue, and each fraction is composed of various types of cells. Firstly, we review the physiological functions of Zn and Zn transporters in these cells. Several human disorders accompanied with skin manifestations are caused by mutations or dysregulation in Zn transporters; acrodermatitis enteropathica (Zrt-, Irt-like protein (ZIP)4 in the intestinal epithelium and possibly epidermal basal keratinocytes), the spondylocheiro dysplastic form of Ehlers-Danlos syndrome (ZIP13 in the dermal fibroblasts), transient neonatal Zn deficiency (Zn transporter (ZnT)2 in the secretory vesicles of mammary glands), and epidermodysplasia verruciformis (ZnT1 in the epidermal keratinocytes). Additionally, acquired Zn deficiency is deeply involved in the development of some diseases related to nutritional deficiencies (acquired acrodermatitis enteropathica, necrolytic migratory erythema, pellagra, and biotin deficiency), alopecia, and delayed wound healing. Therefore, it is important to associate the existence of mutations or dysregulation in Zn transporters and Zn deficiency with skin manifestations.
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42
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Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. To what extent do structural changes in catalytic metal sites affect enzyme function? J Inorg Biochem 2018; 179:40-53. [PMID: 29161638 PMCID: PMC5760197 DOI: 10.1016/j.jinorgbio.2017.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/09/2023]
Abstract
About half of known enzymatic reactions involve metals. Enzymes belonging to the same superfamily often evolve to catalyze different reactions on the same structural scaffold. The work presented here investigates how functional differentiation, within superfamilies that contain metalloenzymes, relates to structural changes at the catalytic metal site. In general, when the catalytic metal site is unchanged across the enzymes of a superfamily, the functional differentiation within the superfamily tends to be low and the mechanism conserved. Conversely, all types of structural changes in the metal binding site are observed for superfamilies with high functional differentiation. Overall, the catalytic role of the metal ions appears to be one of the most conserved features of the enzyme mechanism within metalloenzyme superfamilies. In particular, when the catalytic role of the metal ion does not involve a redox reaction (i.e. there is no exchange of electrons with the substrate), this role is almost always maintained even when the site undergoes significant structural changes. In these enzymes, functional diversification is most often associated with modifications in the surrounding protein matrix, which has changed so much that the enzyme chemistry is significantly altered. On the other hand, in more than 50% of the examples where the metal has a redox role in catalysis, changes at the metal site modify its catalytic role. Further, we find that there are no examples in our dataset where metal sites with a redox role are lost during evolution. SYNOPSIS In this paper we investigate how functional diversity within superfamilies of metalloenzymes relates to structural changes at the catalytic metal site. Evolution tends to strictly conserve the metal site. When changes occur, they do not modify the catalytic role of non-redox metals whereas they affect the role of redox-active metals.
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Affiliation(s)
- Yana Valasatava
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Janet M Thornton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Claudia Andreini
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.
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Enrichment and Identification of the Most Abundant Zinc Binding Proteins in Developing Barley Grains by Zinc-IMAC Capture and Nano LC-MS/MS. Proteomes 2018; 6:proteomes6010003. [PMID: 29342075 PMCID: PMC5874762 DOI: 10.3390/proteomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/07/2018] [Accepted: 01/11/2018] [Indexed: 01/02/2023] Open
Abstract
Background: Zinc accumulates in the embryo, aleurone, and subaleurone layers at different amounts in cereal grains. Our hypothesis is that zinc could be stored bound, not only to low MW metabolites/proteins, but also to high MW proteins as well. Methods: In order to identify the most abundant zinc binding proteins in different grain tissues, we microdissected barley grains into (1) seed coats; (2) aleurone/subaleurone; (3) embryo; and (4) endosperm. Initial screening for putative zinc binding proteins from the different tissue types was performed by fractionating proteins according to solubility (Osborne fractionation), and resolving those via Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE) followed by polyvinylidene fluoride (PVDF) membrane blotting and dithizone staining. Selected protein fractions were subjected to Zn2+-immobilized metal ion affinity chromatography, and the captured proteins were identified using nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS). Results: In the endosperm, the most abundant zinc binding proteins were the storage protein B-hordeins, gamma-, and D-hordeins, while in the embryo, 7S globulins storage proteins exhibited zinc binding. In the aleurone/subaleurone, zinc affinity captured proteins were late abundant embryogenesis proteins, dehydrins, many isoforms of non-specific lipid transfer proteins, and alpha amylase trypsin inhibitor. Conclusions: We have shown evidence that abundant barley grain proteins have been captured by Zn-IMAC, and their zinc binding properties in relationship to the possibility of zinc storage is discussed.
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Buracco S, Peracino B, Andreini C, Bracco E, Bozzaro S. Differential Effects of Iron, Zinc, and Copper on Dictyostelium discoideum Cell Growth and Resistance to Legionella pneumophila. Front Cell Infect Microbiol 2018; 7:536. [PMID: 29379774 PMCID: PMC5770829 DOI: 10.3389/fcimb.2017.00536] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/26/2017] [Indexed: 12/29/2022] Open
Abstract
Iron, zinc, and copper play fundamental roles in eucaryotes and procaryotes, and their bioavailability regulates host-pathogen interactions. For intracellular pathogens, the source of metals is the cytoplasm of the host, which in turn manipulates intracellular metal traffic following pathogen recognition. It is established that iron is withheld from the pathogen-containing vacuole, whereas for copper and zinc the evidence is unclear. Most infection studies in mammals have concentrated on effects of metal deficiency/overloading at organismal level. Thus, zinc deficiency or supplementation correlate with high risk of respiratory tract infection or recovery from severe infection, respectively. Iron, zinc, and copper deficiency or overload affects lymphocyte proliferation/maturation, and thus the adaptive immune response. Whether they regulate innate immunity at macrophage level is open, except for iron. The early identification in a mouse mutant susceptible to mycobacterial infection of the iron transporter Nramp1 allowed dissecting Nramp1 role in phagocytes, from the social amoeba Dictyostelium to macrophages. Nramp1 regulates iron efflux from the phagosomes, thus starving pathogenic bacteria for iron. Similar studies for zinc or copper are scant, due to the large number of copper and zinc transporters. In Dictyostelium, zinc and copper transporters include 11 and 6 members, respectively. To assess the role of zinc or copper in Dictyostelium, cells were grown under conditions of metal depletion or excess and tested for resistance to Legionella pneumophila infection. Iron shortage or overload inhibited Dictyostelium cell growth within few generations. Surprisingly, zinc or copper depletion failed to affect growth. Zinc or copper overloading inhibited cell growth at, respectively, 50- or 500-fold the physiological concentration, suggesting very efficient control of their homeostasis, as confirmed by Inductively Coupled Plasma Mass Spectrometry quantification of cellular metals. Legionella infection was inhibited or enhanced in cells grown under iron shortage or overload, respectively, confirming a major role for iron in controlling resistance to pathogens. In contrast, zinc and copper depletion or excess during growth did not affect Legionella infection. Using Zinpyr-1 as fluorescent sensor, we show that zinc accumulates in endo-lysosomal vesicles, including phagosomes, and the contractile vacuole. Furthermore, we provide evidence for permeabilization of the Legionella-containing vacuole during bacterial proliferation.
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Affiliation(s)
- Simona Buracco
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Barbara Peracino
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Enrico Bracco
- Department of Oncology, University of Torino, Turin, Italy
| | - Salvatore Bozzaro
- Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
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45
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Drozd A, Wojewska D, Peris-Díaz MD, Jakimowicz P, Krężel A. Crosstalk of the structural and zinc buffering properties of mammalian metallothionein-2. Metallomics 2018; 10:595-613. [DOI: 10.1039/c7mt00332c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural insights into partially Zn(ii)-depleted MT2 species and their zinc buffering properties are presented and discussed.
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Affiliation(s)
- Agnieszka Drozd
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Dominika Wojewska
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Manuel David Peris-Díaz
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Piotr Jakimowicz
- Department of Protein Biotechnology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Artur Krężel
- Department of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław
- Poland
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46
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Zborovsky L, Smolyakova A, Baskin M, Maayan G. A Pure Polyproline Type I-like Peptoid Helix by Metal Coordination. Chemistry 2017; 24:1159-1167. [DOI: 10.1002/chem.201704497] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Lieby Zborovsky
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Alisa Smolyakova
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Maria Baskin
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
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47
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Zinc Protects Oxidative Stress-Induced RPE Death by Reducing Mitochondrial Damage and Preventing Lysosome Rupture. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:6926485. [PMID: 29348791 PMCID: PMC5733978 DOI: 10.1155/2017/6926485] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 11/30/2022]
Abstract
Zinc deficiency is known to increase the risk of the development of age-related macular degeneration (AMD), although the underlying mechanism remains poorly defined. In this study, we investigated the effect of zinc on retinal pigment epithelium (RPE) survival and function under oxidative conditions. Zinc level was 5.4 μM in normal culture conditions (DMEM/F12 with 10% FCS) and 1.5 μM in serum-free medium (DMEM/F12). Under serum-free culture conditions, the treatment of RPE cells with oxidized photoreceptor outer segment (oxPOS) significantly increased intracellular ROS production, reduced ATP production, and promoted RPE death compared to oxPOS-treated RPE under normal culture condition. Serum deprivation also reduced RPE phagocytosis of oxPOS and exacerbated oxidative insult-induced cathepsin B release from lysosome, an indicator of lysosome rupture. The addition of zinc in the serum-free culture system dose dependently reduced ROS production, recovered ATP production, and reduced oxidative stress- (oxPOS- or 4-HNE) induced cell death. Zinc supplementation also reduced oxidative stress-mediated cathepsin B release in RPE cells. Our results suggest that zinc deficiency sensitizes RPE cells to oxidative damage, and zinc supplementation protects RPE cells from oxidative stress-induced death by improving mitochondrial function and preventing lysosome rupture.
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48
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Shimberg GD, Ok K, Neu HM, Splan KE, Michel SLJ. Cu(I) Disrupts the Structure and Function of the Nonclassical Zinc Finger Protein Tristetraprolin (TTP). Inorg Chem 2017; 56:6838-6848. [PMID: 28557421 DOI: 10.1021/acs.inorgchem.7b00125] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tristetraprolin (TTP) is a nonclassical zinc finger (ZF) protein that plays a key role in regulating inflammatory response. TTP regulates cytokines at the mRNA level by binding to AU-rich sequences present at the 3'-untranslated region, forming a complex that is then degraded. TTP contains two conserved CCCH domains with the sequence CysX8CysX5CysX3His that are activated to bind RNA when zinc is coordinated. During inflammation, copper levels are elevated, which is associated with increased inflammatory response. A potential target for Cu(I) during inflammation is TTP. To determine whether Cu(I) binds to TTP and how Cu(I) can affect TTP/RNA binding, two TTP constructs were prepared. One construct contained just the first CCCH domain (TTP-1D) and serves as a peptide model for a CCCH domain; the second construct contains both CCCH domains (TTP-2D) and is functional (binds RNA) when Zn(II) is coordinated. Cu(I) binding to TTP-1D was assessed via electronic absorption spectroscopy titrations, and Cu(I) binding to TTP-2D was assessed via both absorption spectroscopy and a spin filter/inductively coupled plasma mass spectrometry (ICP-MS) assay. Cu(I) binds to TTP-1D with a 1:1 stoichiometry and to TTP-2D with a 3:1 stoichiometry. The CD spectrum of Cu(I)-TTP-2D did not exhibit any secondary structure, matching that of apo-TTP-2D, while Zn(II)-TTP-2D exhibited a secondary structure. Measurement of RNA binding via fluorescence anisotropy revealed that Cu(I)-TTP-2D does not bind to the TTP-2D RNA target sequence UUUAUUUAUUU with any measurable affinity, while Zn(II)-TTP-2D binds to this site with nanomolar affinity. Similarly, addition of Cu(I) to the Zn(II)-TTP-2D/RNA complex resulted in inhibition of RNA binding. Together, these data indicate that, while Cu(I) binds to TTP-2D, it does not result in a folded or functional protein and that Cu(I) inhibits Zn(II)-TTP-2D/RNA binding.
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Affiliation(s)
- Geoffrey D Shimberg
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Kiwon Ok
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Heather M Neu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
| | - Kathryn E Splan
- Department of Chemistry, Macalester College , 1600 Grand Avenue, Saint Paul, Minnesota 55105, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201-1180, United States
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49
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Baskin M, Fridman N, Kosa M, Maayan G. Heteroleptic complexesviasolubility control: examples of Cu(ii), Co(ii), Ni(ii) and Mn(ii) complexes based on the derivatives of terpyridine and hydroxyquinoline. Dalton Trans 2017; 46:15330-15339. [DOI: 10.1039/c7dt03387g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe the preparation of synthetically challenging heteroleptic complexes by considering the solubility properties of their corresponding favored homoleptic complexes.
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Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Natalia Fridman
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Monica Kosa
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry
- Technion-Israel Institute of Technology
- Haifa
- Israel
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50
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Boukallaba M, Kerkeni B, Lepetit C, Berthomieu D. Coordination complexes of 4-methylimidazole with ZnII and CuII in gas phase and in water: a DFT study. J Mol Model 2016; 22:301. [DOI: 10.1007/s00894-016-3167-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/09/2016] [Indexed: 10/20/2022]
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