1
|
Li H, Stoltzfus AT, Michel SLJ. Mining proteomes for zinc finger persulfidation. RSC Chem Biol 2024; 5:572-585. [PMID: 38846077 PMCID: PMC11151867 DOI: 10.1039/d3cb00106g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/03/2023] [Indexed: 06/09/2024] Open
Abstract
Hydrogen sulfide (H2S) is an endogenous gasotransmitter that signals via persulfidation. There is evidence that the cysteine residues of certain zinc finger (ZF) proteins, a common type of cysteine rich protein, are modified to persulfides by H2S. To determine how frequently ZF persulfidation occurs in cells and identify the types of ZFs that are persulfidated, persulfide specific proteomics data were evaluated. 22 datasets from 16 studies were analyzed via a meta-analysis approach. Persulfidated ZFs were identified in a range of eukaryotic species, including Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and Emiliania huxley (single-celled phytoplankton). The types of ZFs identified for each species encompassed all three common ZF ligand sets (4-cysteine, 3-cysteine-1-histidine, and 2-cysteine-2-hisitidine), indicating that persulfidation of ZFs is broad. Overlap analysis between different species identified several common ZFs. GO and KEGG analysis identified pathway enrichment for ubiquitin-dependent protein catabolic process and viral carcinogenesis. These collective findings support ZF persulfidation as a wide-ranging PTM that impacts all classes of ZFs.
Collapse
Affiliation(s)
- Haoju Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy Baltimore MD 21201 USA
| | - Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy Baltimore MD 21201 USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy Baltimore MD 21201 USA
| |
Collapse
|
2
|
Jin H, Merz KM. Modeling Zinc Complexes Using Neural Networks. J Chem Inf Model 2024; 64:3140-3148. [PMID: 38587510 DOI: 10.1021/acs.jcim.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Understanding the energetic landscapes of large molecules is necessary for the study of chemical and biological systems. Recently, deep learning has greatly accelerated the development of models based on quantum chemistry, making it possible to build potential energy surfaces and explore chemical space. However, most of this work has focused on organic molecules due to the simplicity of their electronic structures as well as the availability of data sets. In this work, we build a deep learning architecture to model the energetics of zinc organometallic complexes. To achieve this, we have compiled a configurationally and conformationally diverse data set of zinc complexes using metadynamics to overcome the limitations of traditional sampling methods. In terms of the neural network potentials, our results indicate that for zinc complexes, partial charges play an important role in modeling the long-range interactions with a neural network. Our developed model outperforms semiempirical methods in predicting the relative energy of zinc conformers, yielding a mean absolute error (MAE) of 1.32 kcal/mol with reference to the double-hybrid PWPB95 method.
Collapse
Affiliation(s)
- Hongni Jin
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
3
|
Rua AJ, Alexandrescu AT. Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588434. [PMID: 38645208 PMCID: PMC11030341 DOI: 10.1101/2024.04.06.588434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Domain Z7 of nuclear transcription factor ZNF711 has the consensus last metal-ligand H23 found in odd-numbered zinc-fingers of this protein replaced by a phenylalanine. Ever since the discovery of ZNF711 it has been thought that Z7 is probably non-functional because of the H23F substitution. The presence of H26 three positions downstream prompted us to examine if this histidine could substitute as the last metal ligand. The Z7 domain adopts a stable tertiary structure upon metal binding. The NMR structure of Zn2+-bound Z7 shows the classical ββα-fold of CCHH zinc fingers. Mutagenesis and pH titration experiments indicate that H26 is not involved in metal binding and that Z7 has a tridentate metal-binding site comprised of only residues C3, C6, and H19. By contrast, an F23H mutation that introduces a histidine in the consensus position forms a tetradentate ligand. The structure of the WT Z7 is stable causing restricted ring-flipping of phenyalanines 10 and 23. Dynamics are increased with either the H26A or F23H substitutions and aromatic ring rotation is no longer hindered in the two mutants. The mutations have only small effects on the Kd values for Zn2+ and Co2+ and retain the high thermal stability of the WT domain above 80 °C. Like two previously reported designed zinc fingers with the last ligand replaced by water, the WT Z7 domain is catalytically active, hydrolyzing 4-nitophenyl acetate. We discuss the implications of naturally occurring tridentate zinc fingers for cancer mutations and drug targeting of notoriously undruggable transcription factors. Our findings that Z7 can fold with only a subset of three metal ligands suggests the recent view that most everything about protein structure can be predicted through homology modeling might be premature for at least the resilient and versatile zinc-finger motif.
Collapse
Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
| | | |
Collapse
|
4
|
Zhong H, Barrientos A. The zinc finger motif in the mitochondrial large ribosomal subunit protein bL36m is essential for optimal yeast mitoribosome assembly and function. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119707. [PMID: 38493895 PMCID: PMC11009049 DOI: 10.1016/j.bbamcr.2024.119707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Ribosomes across species contain subsets of zinc finger proteins that play structural roles by binding to rRNA. While the majority of these zinc fingers belong to the C2-C2 type, the large subunit protein L36 in bacteria and mitochondria exhibits an atypical C2-CH motif. To comprehend the contribution of each coordinating residue in S. cerevisiae bL36m to mitoribosome assembly and function, we engineered and characterized strains carrying single and double mutations in the zinc coordinating residues. Our findings reveal that although all four residues markedly influence protein stability, C to A mutations in C66 and/or C69 have a more pronounced effect compared to those at C82 and H88. Importantly, protein stability directly correlates with the assembly and function of the mitoribosome and the growth rate of yeast in respiratory conditions. Mass spectrometry analysis of large subunit particles indicates that strains deleted for bL36m or expressing mutant variants have defective assembly of the L7/L12 stalk base, limiting their functional competence. Furthermore, we employed a synthetic bL36m protein collection, including both wild-type and mutant proteins, to elucidate their ability to bind zinc. Our data indicate that mutations in C82 and, particularly, H88 allow for some zinc binding albeit inefficient or unstable, explaining the residual accumulation and activity in mitochondria of bL36m variants carrying mutations in these residues. In conclusion, stable zinc binding by bL36m is essential for optimal mitoribosome assembly and function. MS data are available via ProteomeXchange with identifierPXD046465.
Collapse
Affiliation(s)
- Hui Zhong
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA.
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA; Department of Neurology, University of Miami Miller School of Medicine, 1600 NW 10th Ave., Miami, FL 33136, USA; The Miami Veterans Affairs (VA) Medical System, 1201 NW 16th St, Miami, FL 33125, USA.
| |
Collapse
|
5
|
Kocyła AM, Czogalla A, Wessels I, Rink L, Krężel A. A combined biochemical and cellular approach reveals Zn 2+-dependent hetero- and homodimeric CD4 and Lck assemblies in T cells. Structure 2024; 32:292-303.e7. [PMID: 38157858 DOI: 10.1016/j.str.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
The CD4 or CD8 co-receptors' interaction with the protein-tyrosine kinase Lck initiates the tyrosine phosphorylation cascade leading to T cell activation. A critical question is: to what extent are co-receptors and Lck coupled? Our contribution concerns Zn2+, indispensable for CD4- and CD8-Lck formation. We combined biochemical and cellular approaches to show that dynamic fluctuations of free Zn2+ in physiological ranges influence Zn(CD4)2 and Zn(CD4)(Lck) species formation and their ratio, although the same Zn(Cys)2(Cys)2 cores. Moreover, we demonstrated that the affinity of Zn2+ to CD4 and CD4-Lck species differs significantly. Increased intracellular free Zn2+ concentration in T cells causes higher CD4 partitioning in the plasma membrane. We additionally found that CD4 palmitoylation decreases the specificity of CD4-Lck formation in the reconstituted membrane model. Our findings help elucidate co-receptor-Lck coupling stoichiometry and demonstrate that intracellular free Zn2+ has a major role in the interplay between CD4 dimers and CD4-Lck assembly.
Collapse
Affiliation(s)
- Anna M Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Inga Wessels
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Kosmachevskaya OV, Novikova NN, Yakunin SN, Topunov AF. Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S180-S204. [PMID: 38621750 DOI: 10.1134/s0006297924140104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/21/2023] [Accepted: 10/29/2023] [Indexed: 04/17/2024]
Abstract
In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.
Collapse
Affiliation(s)
- Olga V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | | | - Sergey N Yakunin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Alexey F Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| |
Collapse
|
8
|
Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
Collapse
Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | | |
Collapse
|
9
|
Mosna K, Jurczak K, Krężel A. Differentiated Zn(II) binding affinities in animal, plant, and bacterial metallothioneins define their zinc buffering capacity at physiological pZn. Metallomics 2023; 15:mfad061. [PMID: 37804185 PMCID: PMC10612145 DOI: 10.1093/mtomcs/mfad061] [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: 05/23/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023]
Abstract
Metallothioneins (MTs) are small, Cys-rich proteins present in various but not all organisms, from bacteria to humans. They participate in zinc and copper metabolism, toxic metals detoxification, and protection against reactive species. Structurally, they contain one or multiple domains, capable of binding a variable number of metal ions. For experimental convenience, biochemical characterization of MTs is mainly performed on Cd(II)-loaded proteins, frequently omitting or limiting Zn(II) binding features and related functions. Here, by choosing 10 MTs with relatively well-characterized structures from animals, plants, and bacteria, we focused on poorly investigated Zn(II)-to-protein affinities, stability-structure relations, and the speciation of individual complexes. For that purpose, MTs were characterized in terms of stoichiometry, pH-dependent Zn(II) binding, and competition with chromogenic and fluorescent probes. To shed more light on protein folding and its relation with Zn(II) affinity, reactivity of variously Zn(II)-loaded MTs was studied by (5,5'-dithiobis(2-nitrobenzoic acid) oxidation in the presence of mild chelators. The results show that animal and plant MTs, despite their architectural differences, demonstrate the same affinities to Zn(II), varying from nano- to low picomolar range. Bacterial MTs bind Zn(II) more tightly but, importantly, with different affinities from low picomolar to low femtomolar range. The presence of weak, moderate, and tight zinc sites is related to the folding mechanisms and internal electrostatic interactions. Differentiated affinities of all MTs define their zinc buffering capacity required for Zn(II) donation and acceptance at various free Zn(II) concentrations (pZn levels). The data demonstrate critical roles of individual Zn(II)-depleted MT species in zinc buffering processes.
Collapse
Affiliation(s)
- Karolina Mosna
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Kinga Jurczak
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
10
|
Bregnard TA, Fairchild D, Erlandsen H, Semenova IV, Szczepaniak R, Ahmed A, Weller SK, Korzhnev DM, Bezsonova I. Conformational exchange at a C 2H 2 zinc-binding site facilitates redox sensing by the PML protein. Structure 2023; 31:1086-1099.e6. [PMID: 37473756 PMCID: PMC10528520 DOI: 10.1016/j.str.2023.06.014] [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: 12/20/2022] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The promyelocytic leukemia protein, PML, plays a vital role in the cellular response to oxidative stress; however, the molecular mechanism of its action remains poorly understood. Here, we identify redox-sensitive sites of PML. A molecule of PML is cysteine-rich and contains three zinc-binding domains including RING, B-box1, and B-box2. Using in vitro assays, we have compared the sensitivity of the isolated RING and B-box1 domains and shown that B-box1 is more sensitive to oxidation. NMR studies of PML dynamics showed that one of the Zn-coordination sites within the B-box1 undergoes significant conformational exchange, revealing a hotspot for exposure of reactive cysteines. In agreement with the in vitro data, enhancement of the B-box1 Zn-coordination dynamics led to more efficient recruitment of PML into PML nuclear bodies in cells. Overall, our results suggest that the increased sensitivity of B-box1 to oxidative stress makes this domain an important redox-sensing component of PML.
Collapse
Affiliation(s)
- Thomas A Bregnard
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Daniel Fairchild
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, UCONN, Storrs, CT 06269, USA
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Renata Szczepaniak
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Affrin Ahmed
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Sandra K Weller
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA.
| |
Collapse
|
11
|
Rua AJ, Whitehead Iii RD, Alexandrescu AT. WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol 2023:108003. [PMID: 37487847 DOI: 10.1016/j.jsb.2023.108003] [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: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.
Collapse
Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
| | | | | |
Collapse
|
12
|
Hall AG, King JC. The Molecular Basis for Zinc Bioavailability. Int J Mol Sci 2023; 24:ijms24076561. [PMID: 37047530 PMCID: PMC10095312 DOI: 10.3390/ijms24076561] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
Zinc is an essential micronutrient, and its deficiency is perhaps the most prevalent and least understood worldwide. Recent advances have expanded the understanding of zinc’s unique chemistry and molecular roles in a vast array of critical functions. However, beyond the concept of zinc absorption, few studies have explored the molecular basis of zinc bioavailability that determines the proportion of dietary zinc utilized in zinc-dependent processes in the body. The purpose of this review is to merge the concepts of zinc molecular biology and bioavailability with a focus on the molecular determinants of zinc luminal availability, absorption, transport, and utilization.
Collapse
|
13
|
Kerber O, Tran J, Misiaszek A, Chorążewska A, Bal W, Krężel A. Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein Complex Disruption through the Formation of Highly Stable Ag x(Cys) y Cores. Inorg Chem 2023; 62:4076-4087. [PMID: 36863010 PMCID: PMC10015552 DOI: 10.1021/acs.inorgchem.2c03767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The widespread application of silver nanoparticles in medicinal and daily life products increases the exposure to Ag(I) of thiol-rich biological environments, which help control the cellular metallome. A displacement of native metal cofactors from their cognate protein sites is a known phenomenon for carcinogenic and otherwise toxic metal ions. Here, we examined the interaction of Ag(I) with the peptide model of the interprotein zinc hook (Hk) domain of Rad50 protein from Pyrococcus furiosus, a key player in DNA double-strand break (DSB) repair. The binding of Ag(I) to 14 and 45 amino acid long peptide models of apo- and Zn(Hk)2 was experimentally investigated by UV-vis spectroscopy, circular dichroism, isothermal titration calorimetry, and mass spectrometry. The Ag(I) binding to the Hk domain was found to disrupt its structure via the replacement of the structural Zn(II) ion by multinuclear Agx(Cys)y complexes. The ITC analysis indicated that the formed Ag(I)-Hk species are at least 5 orders of magnitude stronger than the otherwise extremely stable native Zn(Hk)2 domain. These results show that Ag(I) ions may easily disrupt the interprotein zinc binding sites as an element of silver toxicity at the cellular level.
Collapse
Affiliation(s)
- Olga Kerber
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Alicja Misiaszek
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Aleksandra Chorążewska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
14
|
Guo L, Yang X, Zhang Y, Xu X, Li Y. Effect of exercise on cognitive function and synaptic plasticity in Alzheimer's disease models: A systematic review and meta-analysis. Front Aging Neurosci 2023; 14:1077732. [PMID: 36704501 PMCID: PMC9872519 DOI: 10.3389/fnagi.2022.1077732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction Cognitive decline is a central manifestation of Alzheimer's disease (AD), and its process is inseparable from changes in synaptic plasticity. The aim of this review was to summarize and evaluate the effectiveness of exercise on cognitive function and synaptic plasticity in AD animal models. Materials and methods Eligible studies were searched from PubMed, MEDLINE, EMBASE, Web of Science, and Cochrane Library from April to May 2022. The risk of bias was evaluated by Systematic Review Centre for Laboratory Animal Experimentation (SYRCLE). The Morris water maze (MWM) test and synaptic plasticity were considered outcome measures. Data were analyzed using random-effects meta-analyses using the software Stata. Heterogeneity was examined by using I2 test. Sensitivity analysis and publication bias were also assessed. Results A total of 20 randomized controlled studies were eligible for study inclusion. Compared with controls, exercise decreased escape latency (SMD = -0.86, 95% CI: -1.21 to -0.50, P < 0.001), increased platform crossover numbers (SMD = 1.34, 95% CI: 0.57-2.11, P = 0.001) and time in the target quadrant (SMD = 1.65, 95% CI: 0.95-2.36, P < 0.001) and the expression of PSD95 (SMD = 0.73, 95% CI: 0.25-1.21, P = 0.003) in AD animals. The results of the subgroup analysis showed that exercise before AD had a greater effect on escape latency (SMD = -0.88, 95% CI: -1.25 to -0.52, P < 0.001), platform crossover numbers (SMD = 1.71, 95% CI: 1.23-2.18, P < 0.001), time in the target quadrant (SMD = 2.03, 95% CI: 1.19-2.87, P < 0.001) and the expression of PSD95 (SMD = 0.94, 95% CI: 0.19-1.69, P = 0.014) than exercise after AD. The results of the subgroup analysis also showed that treadmill running might be an appropriate exercise type. Conclusion Our findings suggested that exercise had a potential effect on improving cognitive function and synaptic plasticity. It can play a better neuroprotective role before AD. Systematic review registration PROSPERO, identifier: CRD42022328438.
Collapse
Affiliation(s)
- Linlin Guo
- College of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Xinxin Yang
- College of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Yuanyuan Zhang
- College of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Xinyi Xu
- College of Nursing, Hebei Medical University, Shijiazhuang, China,Postdoctoral Research Station in Basic Medicine, Hebei Medical University, Shijiazhuang, China,*Correspondence: Xinyi Xu ✉
| | - Yan Li
- College of Nursing, Hebei Medical University, Shijiazhuang, China,Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China,Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China,*Correspondence: Yan Li ✉
| |
Collapse
|
15
|
Concentrations of Transition Metal Ions in Rat Lungs after Tobacco Smoke Exposure and Treatment with His-Leu Dipeptide. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020628. [PMID: 36677686 PMCID: PMC9862342 DOI: 10.3390/molecules28020628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Tobacco smoking is deleterious to the lungs because it exposes them to many toxic substances. These include transition metal ions, such as cadmium. However, there is a lack of information about the influence of endogenous metal-binding peptides, such as His-Leu (HL), on the lung distribution of transition metals in smokers. To address this, we administered HL subcutaneously to rats exposed to tobacco smoke for six weeks, then we measured the concentrations of transition metal ions in the lungs. We found that exposure to tobacco smoke elevates the concentrations of Cd(II) and Cu(II). Administration of the HL peptide, whose elevation is a consequence of angiotensin receptor blocker anti-hypertension therapy, increases the concentration of Fe in the lungs of rats exposed to smoke. These findings suggest that smoking is a risk factor for patients receiving angiotensin receptor blockers to treat hypertension.
Collapse
|
16
|
Łuczkowski M, Padjasek M, Ba Tran J, Hemmingsen L, Kerber O, Habjanič J, Freisinger E, Krężel A. An Extremely Stable Interprotein Tetrahedral Hg(Cys) 4 Core Forms in the Zinc Hook Domain of Rad50 Protein at Physiological pH. Chemistry 2022; 28:e202202738. [PMID: 36222310 PMCID: PMC9828754 DOI: 10.1002/chem.202202738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/09/2022]
Abstract
In nature, thiolate-based systems are the primary targets of divalent mercury (HgII ) toxicity. The formation of Hg(Cys)x cores in catalytic and structural protein centers mediates mercury's toxic effects and ultimately leads to cellular damage. Multiple studies have revealed distinct HgII -thiolate coordination preferences, among which linear HgII complexes are the most commonly observed in solution at physiological pH. Trigonal or tetrahedral geometries are formed at basic pH or in tight intraprotein Cys-rich metal sites. So far, no interprotein tetrahedral HgII complex formed at neutral pH has been reported. Rad50 protein is a part of the multiprotein MRN complex, a major player in DNA damage-repair processes. Its central region consists of a conserved CXXC motif that enables dimerization of two Rad50 molecules by coordinating ZnII . Dimerized motifs form a unique interprotein zinc hook domain (Hk) that is critical for the biological activity of the MRN. Using a series of length-differentiated peptide models of the Pyrococcus furiosus zinc hook domain, we investigated its interaction with HgII . Using UV-Vis, CD, PAC, and 199 Hg NMR spectroscopies as well as anisotropy decay, we discovered that all Rad50 fragments preferentially form homodimeric Hg(Hk)2 species with a distorted tetrahedral HgS4 coordination environment at physiological pH; this is the first example of an interprotein mercury site displaying tetrahedral geometry in solution. At higher HgII content, monomeric HgHk complexes with linear geometry are formed. The Hg(Cys)4 core of Rad50 is extremely stable and does not compete with cyanides, NAC, or DTT. Applying ITC, we found that the stability constant of the Rad50 Hg(Hk)2 complex is approximately three orders of magnitude higher than those of the strongest HgII complexes known to date.
Collapse
Affiliation(s)
- Marek Łuczkowski
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Michał Padjasek
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Józef Ba Tran
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100København ØDenmark
| | - Olga Kerber
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Jelena Habjanič
- Department of ChemistryUniversity of ZurichWinterthurerstrasse 1908057ZürichSwitzerland
| | - Eva Freisinger
- Department of ChemistryUniversity of ZurichWinterthurerstrasse 1908057ZürichSwitzerland
| | - Artur Krężel
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| |
Collapse
|
17
|
Naesens L, Muppala S, Acharya D, Nemegeer J, Bogaert D, Lee JH, Staes K, Debacker V, De Bleser P, De Bruyne M, De Baere E, van Gent M, Liu G, Lambrecht BN, Staal J, Kerre T, Beyaert R, Maelfait J, Tavernier SJ, Gack MU, Haerynck F. GTF3A mutations predispose to herpes simplex encephalitis by disrupting biogenesis of the host-derived RIG-I ligand RNA5SP141. Sci Immunol 2022; 7:eabq4531. [PMID: 36399538 PMCID: PMC10075094 DOI: 10.1126/sciimmunol.abq4531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Herpes simplex virus 1 (HSV-1) infects several billion people worldwide and can cause life-threatening herpes simplex encephalitis (HSE) in some patients. Monogenic defects in components of the type I interferon system have been identified in patients with HSE, emphasizing the role of inborn errors of immunity underlying HSE pathogenesis. Here, we identify compound heterozygous loss-of-function mutations in the gene GTF3A encoding for transcription factor IIIA (TFIIIA), a component of the RNA polymerase III complex, in a patient with common variable immunodeficiency and HSE. Patient fibroblasts and GTF3A gene-edited cells displayed impaired HSV-1-induced innate immune responses and enhanced HSV-1 replication. Chromatin immunoprecipitation sequencing analysis identified the 5S ribosomal RNA pseudogene 141 (RNA5SP141), an endogenous ligand of the RNA sensor RIG-I, as a transcriptional target of TFIIIA. GTF3A mutant cells exhibited diminished RNA5SP141 expression and abrogated RIG-I activation upon HSV-1 infection. Our work unveils a crucial role for TFIIIA in transcriptional regulation of a cellular RIG-I agonist and shows that GTF3A genetic defects lead to impaired cell-intrinsic anti-HSV-1 responses and can predispose to HSE.
Collapse
Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
| | - Santoshi Muppala
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
| | - Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Josephine Nemegeer
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signaling and Cell death, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Delfien Bogaert
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Jung-Hyun Lee
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Katrien Staes
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Veronique Debacker
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Pieter De Bleser
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Michiel van Gent
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Bart N. Lambrecht
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Laboratory of Immunoregulation and Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jens Staal
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Tessa Kerre
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Hematology, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jonathan Maelfait
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Signaling and Cell death, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Simon J. Tavernier
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Laboratory of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Michaela U. Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St Lucie, FL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
18
|
Kluska K, Chorążewska A, Peris-Díaz MD, Adamczyk J, Krężel A. Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains. Int J Mol Sci 2022; 23:ijms232314602. [PMID: 36498928 PMCID: PMC9735795 DOI: 10.3390/ijms232314602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability.
Collapse
|
19
|
Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation. Int J Mol Sci 2022; 23:ijms231911140. [PMID: 36232441 PMCID: PMC9569753 DOI: 10.3390/ijms231911140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The metal binding at protein–protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence–structure–stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein–protein interactions and illuminates their molecular basis.
Collapse
|
20
|
Abstract
Zinc is an essential element for human health. Among its many functions, zinc(II) modulates the immune response to infections and, at high concentrations or in the presence of ionophores, inhibits the replication of various RNA viruses. Structural biology studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed that zinc(II) is the most common metal ion that binds to viral proteins. However, the number of zinc(II)-binding sites identified by experimental methods is far from exhaustive, as metal ions may be lost during protein purification protocols. To better define the zinc(II)-binding proteome of coronavirus, we leveraged the wealth of deposited structural data and state-of-the-art bioinformatics methods. Through this in silico approach, 15 experimental zinc(II) sites were identified and a further 22 were predicted in Spike, open reading frame (ORF)3a/d, ORF8, and several nonstructural proteins, highlighting an essential role of zinc(II) in viral replication. Furthermore, the structural relationships between viral and eukaryotic sites (typically zinc fingers) indicate that SARS-CoV-2 can compete with human proteins for zinc(II) binding. Given the double-edged effect of zinc(II) ions, both essential and toxic to coronavirus, only the complete elucidation of the structural and regulatory zinc(II)-binding sites can guide selective antiviral strategies based on zinc supplementation.
Collapse
Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Fabio Arnesano
- Department of Chemistry, University of Bari “Aldo Moro,” Via Orabona 4, 70125 Bari, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry and Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
21
|
Ha JH, Prela O, Carpizo DR, Loh SN. p53 and Zinc: A Malleable Relationship. Front Mol Biosci 2022; 9:895887. [PMID: 35495631 PMCID: PMC9043292 DOI: 10.3389/fmolb.2022.895887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
A large percentage of transcription factors require zinc to bind DNA. In this review, we discuss what makes p53 unique among zinc-dependent transcription factors. The conformation of p53 is unusually malleable: p53 binds zinc extremely tightly when folded, but is intrinsically unstable in the absence of zinc at 37°C. Whether the wild-type protein folds in the cell is largely determined by the concentration of available zinc. Consequently, zinc dysregulation in the cell as well as a large percentage of tumorigenic p53 mutations can cause p53 to lose zinc, misfold, and forfeit its tumor suppressing activity. We highlight p53’s noteworthy biophysical properties that give rise to its malleability and how proper zinc binding can be restored by synthetic metallochaperones to reactivate mutant p53. The activity and mechanism of metallochaperones are compared to those of other mutant p53-targeted drugs with an emphasis on those that have reached the clinical trial stage.
Collapse
Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Orjola Prela
- Division of Surgical Oncology, Department of Surgery, Wilmot Cancer Center, University of Rochester, Rochester, NY, United States
| | - Darren R Carpizo
- Division of Surgical Oncology, Department of Surgery, Wilmot Cancer Center, University of Rochester, Rochester, NY, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| |
Collapse
|
22
|
Abstract
The synthesis and a detailed reactivity study of a binuclear zinc(II) bis(benzenethiolate) complex, [Zn2(BPMP)(SPh)2]+ (4), and an unprecedented binuclear zinc(II) pentasulfido complex, [Zn2(BPMP)(μ2-S5)]+ (6), are presented. While one-electron oxidation of the coordinated benzenethiolate ligands in 4 by Cp2Fe+ produces diphenyl disulfide and [Zn2(BPMP)(μ2-OH)]2+ (5), a two-electron redox reaction between coordinated benzenethiolate ligands in 4 and elemental S (S8) generated diphenyl disulfide and the binuclear zinc(II) pentasulfido complex 6. Complex 6 features a chelating, dianionic, pentasulfido (S52-) chain and can consume up to a maximum of 3 equiv of PPh3 to generate Ph3PS and 5, while the reaction of 6 with 1 equiv of diphenylphosphinoethane allowed the isolation of [Zn2(BPMP)(μ2-S4)]+ (7). A proteolysis reaction of the coordinated S52- chain in 6 with fluoroboric acid (HBF4), benzoic acid (PhCOOH), and thioacetic acid (MeCOSH) generates the complexes [Zn2(BPMP)(MeCN)2]3+ (1), [Zn2(BPMP)(μ2-PhCOO)2]+ (8), and [Zn2(BPMP)(μ2-SCOMe)2]+ (9), respectively, while the protonated S52- chain liberates S8 and hydrogen sulfide (H2S). Finally, the transfer of the coordinated benzenethiolate ligands in 4 and the S52- chain in 6 to selected organic compounds, namely, PhCH2Br and PhC(O)Cl, for the generation of various organosulfur compounds is demonstrated.
Collapse
Affiliation(s)
- Kamal Hossain
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| |
Collapse
|
23
|
Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
Collapse
|
24
|
Huang Y, Harris BS, Minami SA, Jung S, Shah PS, Nandi S, McDonald KA, Faller R. SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction. Biophys J 2021; 121:79-90. [PMID: 34883069 PMCID: PMC8648368 DOI: 10.1016/j.bpj.2021.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/08/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
Highly detailed steered molecular dynamics simulations are performed on differently glycosylated receptor binding domains of the severe acute respiratory syndrome coronavirus-2 spike protein. The binding strength and the binding range increase with glycosylation. The interaction energy rises very quickly when pulling the proteins apart and only slowly drops at larger distances. We see a catch-slip-type behavior whereby interactions during pulling break and are taken over by new interactions forming. The dominant interaction mode is hydrogen bonds, but Lennard-Jones and electrostatic interactions are relevant as well.
Collapse
Affiliation(s)
- Yihan Huang
- Department of Materials Science, UC Davis, Davis, California
| | | | - Shiaki A Minami
- Department of Chemical Engineering, UC Davis, Davis, California
| | - Seongwon Jung
- Department of Chemical Engineering, UC Davis, Davis, California
| | - Priya S Shah
- Department of Chemical Engineering, UC Davis, Davis, California; Department of Microbiology and Molecular Genetics, UC Davis, Davis, California
| | - Somen Nandi
- Department of Chemical Engineering, UC Davis, Davis, California; Global HealthShare Initiative, UC Davis, Davis, California
| | - Karen A McDonald
- Department of Chemical Engineering, UC Davis, Davis, California; Global HealthShare Initiative, UC Davis, Davis, California
| | - Roland Faller
- Department of Chemical Engineering, UC Davis, Davis, California.
| |
Collapse
|
25
|
Wang T, Zhang W, Huang W, Hua Z, Li S. LncRNA MALAT1 was regulated by HPV16 E7 independently of pRB in cervical cancer cells. J Cancer 2021; 12:6344-6355. [PMID: 34659524 PMCID: PMC8489136 DOI: 10.7150/jca.61194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/21/2021] [Indexed: 12/26/2022] Open
Abstract
High-risk human papillomavirus (HPV) infection was one of the first step in the process of carcinogenesis in cervical cancers. The expression of viral oncoprotein E7 was essential in this process by inactivating the tumor suppressor proteins RB, in addition to interacting with other host proteins. LncRNA MALAT1 was found to be altered in human cervical cancer tissues, suggesting an important role in tumorigenesis. Moreover, MALAT1 was also overexpressed in HPV16 positive cervical cancer cell lines in an HPV16 E7 dependent manner. To explore the mechanism of E7 involved in MALAT1 up-regulation, the deletion mutant E7∆N and E7∆C were constructed to test the functional domain of E7 for MALAT1 regulation. ChIP, EMSA and UV crosslink were performed to detect the interaction between E7 and MALAT1 promoter. E7 and E7∆N mutant were observed that could bind with MALAT1 promoter directly and interacted with SP1 to form triple complex. E7-SP1 interaction contributed to the transcription activation of MALAT1 promoter. E7 and E7∆N also could promote cell proliferation, invasion, and migration, and the stimulating effect could be reversed by siMALAT1. Here we showed that HPV16 E7 as well as E7∆N could associate with SP1 and bound directly to MALAT1 promoter in vitro and in vivo. This function way of E7 was independent of pRB in cervical cancer cells. To our knowledge, this was the first reported function model for E7 as transcription activator to directly bind to the target promoter.
Collapse
Affiliation(s)
- Ting Wang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Wei Zhang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| | - Wenbin Huang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Zichun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046.,Changzhou High-Tech Research Institute of Nanjing University and Jiangsu Target Pharma Laboratories Inc., Changzhou, Jiangsu 213164, P.R. China
| | - Shufeng Li
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Department of Biochemistry and Molecular Biology, Medical School of Southeast University, Nanjing, 210009, China
| |
Collapse
|
26
|
Nasuno R, Yoshioka N, Yoshikawa Y, Takagi H. Cysteine residues in the fourth zinc finger are important for activation of the nitric oxide-inducible transcription factor Fzf1 in the yeast Saccharomyces cerevisiae. Genes Cells 2021; 26:823-829. [PMID: 34245655 DOI: 10.1111/gtc.12885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022]
Abstract
Nitric oxide (NO) is a ubiquitous signaling molecule in various organisms. In the yeast Saccharomyces cerevisiae, NO functions in both cell protection and cell death, depending on its concentration. Thus, it is important for yeast cells to strictly regulate NO concentration. The transcription factor Fzf1, containing five zinc fingers, is reportedly important for NO homeostasis by regulating the expression of the YHB1 gene, which encodes NO dioxygenase. However, the mechanism by which NO activates Fzf1 is still unclear. In this study, we showed that NO activated Fzf1 specifically at the protein level by RT-qPCR and Western blotting. Our further transcriptional analyses indicated that cysteine residues in the fourth zinc finger (ZF4) are required for the NO-responsive activation of Fzf1. Additionally, the present results suggest that ZF4 is important for the protein stability of Fzf1. From these results, we proposed possible mechanisms underlying Fzf1 activation.
Collapse
Affiliation(s)
- Ryo Nasuno
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Natsuko Yoshioka
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yuki Yoshikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| |
Collapse
|
27
|
Garner TB, Hester JM, Carothers A, Diaz FJ. Role of zinc in female reproduction. Biol Reprod 2021; 104:976-994. [PMID: 33598687 PMCID: PMC8599883 DOI: 10.1093/biolre/ioab023] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/09/2021] [Accepted: 02/15/2021] [Indexed: 11/14/2022] Open
Abstract
Zinc is a critical component in a number of conserved processes that regulate female germ cell growth, fertility, and pregnancy. During follicle development, a sufficient intracellular concentration of zinc in the oocyte maintains meiotic arrest at prophase I until the germ cell is ready to undergo maturation. An adequate supply of zinc is necessary for the oocyte to form a fertilization-competent egg as dietary zinc deficiency or chelation of zinc disrupts maturation and reduces the oocyte quality. Following sperm fusion to the egg to initiate the acrosomal reaction, a quick release of zinc, known as the zinc spark, induces egg activation in addition to facilitating zona pellucida hardening and reducing sperm motility to prevent polyspermy. Symmetric division, proliferation, and differentiation of the preimplantation embryo rely on zinc availability, both during the oocyte development and post-fertilization. Further, the fetal contribution to the placenta, fetal limb growth, and neural tube development are hindered in females challenged with zinc deficiency during pregnancy. In this review, we discuss the role of zinc in germ cell development, fertilization, and pregnancy with a focus on recent studies in mammalian females. We further detail the fundamental zinc-mediated reproductive processes that have only been explored in non-mammalian species and speculate on the role of zinc in similar mechanisms of female mammals. The evidence collected over the last decade highlights the necessity of zinc for normal fertility and healthy pregnancy outcomes, which suggests zinc supplementation should be considered for reproductive age women at risk of zinc deficiency.
Collapse
Affiliation(s)
- Tyler Bruce Garner
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - James Malcolm Hester
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - Allison Carothers
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - Francisco J Diaz
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
28
|
Naskar T, Pal N, Majumdar A. Synthesis and redox reactions of binuclear zinc( ii)–thiolate complexes with elemental sulfur. NEW J CHEM 2021. [DOI: 10.1039/d1nj03012d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The synthesis, characterization and reactivity of a series of binuclear zinc(ii) complexes are described featuring the redox reaction of coordinated thiolates with elemental sulfur.
Collapse
Affiliation(s)
- Tilak Naskar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nabhendu Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India
| | - Amit Majumdar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata 700032, India
| |
Collapse
|
29
|
XANES Measurements for Studies of Adsorbed Protein Layers at Liquid Interfaces. MATERIALS 2020; 13:ma13204635. [PMID: 33080816 PMCID: PMC7603035 DOI: 10.3390/ma13204635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/31/2022]
Abstract
X-ray absorption near edge structure (XANES) spectra for protein layers adsorbed at liquid interfaces in a Langmuir trough have been recorded for the first time. We studied the parkin protein (so-called E3 ubiquitin ligase), which plays an important role in pathogenesis of Parkinson disease. Parkin contains eight Zn binding sites, consisting of cysteine and histidine residues in a tetracoordinated geometry. Zn K-edge XANES spectra were collected in the following two series: under mild radiation condition of measurements (short exposition time) and with high X-ray radiation load. XANES fingerprint analysis was applied to obtain information on ligand environments around zinc ions. Two types of zinc coordination geometry were identified depending on X-ray radiation load. We found that, under mild conditions, local zinc environment in our parkin preparations was very similar to that identified in hemoglobin, treated with a solution of ZnCl2 salt. Under high X-ray radiation load, considerable changes in the zinc site structure were observed; local zinc environment appeared to be almost identical to that defined in Zn-containing enzyme alkaline phosphatase. The formation of a similar metal site in unrelated protein molecules, observed in our experiments, highlights the significance of metal binding templates as essential structural modules in protein macromolecules.
Collapse
|
30
|
Peris-Díaz MD, Guran R, Zitka O, Adam V, Krężel A. Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software. J Proteome Res 2020; 20:776-785. [PMID: 32924499 PMCID: PMC7786378 DOI: 10.1021/acs.jproteome.0c00651] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Identification
of metal-binding sites in proteins and understanding
metal-coupled protein folding mechanisms are aspects of high importance
for the structure-to-function relationship. Mass spectrometry (MS)
has brought a powerful adjunct perspective to structural biology,
obtaining from metal-to-protein stoichiometry to quaternary structure
information. Currently, the different experimental and/or instrumental
setups usually require the use of multiple data analysis software,
and in some cases, they lack some of the main data analysis steps
(MS processing, scoring, identification). Here, we present a comprehensive
data analysis pipeline that addresses charge-state deconvolution,
statistical scoring, and mass assignment for native MS, bottom-up,
and native top-down with emphasis on metal–protein complexes.
We have evaluated all of the approaches using assemblies of increasing
complexity, including free and chemically labeled proteins, from low-
to high-resolution MS. In all cases, the results have been compared
with common software and proved how MetaOdysseus outperformed them.
Collapse
Affiliation(s)
- Manuel David Peris-Díaz
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Roman Guran
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Purkynova 123, 612 00 Brno, Czech Republic
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
31
|
Kocyła A, Tran JB, Krężel A. Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome. Trends Biochem Sci 2020; 46:64-79. [PMID: 32958327 DOI: 10.1016/j.tibs.2020.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
The presence of Zn2+ at protein-protein interfaces modulates complex function, stability, and introduces structural flexibility/complexity, chemical selectivity, and reversibility driven in a Zn2+-dependent manner. Recent studies have demonstrated that dynamically changing Zn2+ affects numerous cellular processes, including protein-protein communication and protein complex assembly. How Zn2+-involved protein-protein interactions (ZPPIs) are formed and dissociate and how their stability and reactivity are driven in a zinc interactome remain poorly understood, mostly due to experimental obstacles. Here, we review recent research advances on the role of Zn2+ in the formation of interprotein sites, their architecture, function, and stability. Moreover, we underline the importance of zinc networks in intersystemic communication and highlight bioinformatic and experimental challenges required for the identification and investigation of ZPPIs.
Collapse
Affiliation(s)
- Anna Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Ba Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| |
Collapse
|
32
|
Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family. Sci Rep 2020; 10:9283. [PMID: 32518326 PMCID: PMC7283297 DOI: 10.1038/s41598-020-66204-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56–142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-‘like’ gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1–55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic ZF family examining by means of MD and NMR the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens.
Collapse
|
33
|
Farkas E. International Symposium on Metal Complexes 2019 (ISMEC 2019) hosted by the University Debrecen, Hungary. J Inorg Biochem 2020; 206:111045. [DOI: 10.1016/j.jinorgbio.2020.111045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
34
|
Kluska K, Peris-Díaz MD, Płonka D, Moysa A, Dadlez M, Deniaud A, Bal W, Krężel A. Formation of highly stable multinuclear Ag nS n clusters in zinc fingers disrupts their structure and function. Chem Commun (Camb) 2020; 56:1329-1332. [PMID: 31912071 DOI: 10.1039/c9cc09418k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Silver (Ag(i)) binding to consensus zinc fingers (ZFs) causes Zn(ii) release inducing a gradual disruption of the hydrophobic core, followed by an overall conformational change and formation of highly stable AgnSn clusters. A compact eight-membered Ag4S4 structure formed by a CCCC ZF is the first cluster example reported for a single biological molecule. Ag(i)-induced conformational changes of ZFs can, as a consequence, affect transcriptional regulation and other cellular processes.
Collapse
Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Manuel D Peris-Díaz
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| | - Dawid Płonka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Alexander Moysa
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
| |
Collapse
|