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Üresin D, Schulte J, Morgner N, Soppa J. C(P)XCG Proteins of Haloferax volcanii with Predicted Zinc Finger Domains: The Majority Bind Zinc, but Several Do Not. Int J Mol Sci 2024; 25:7166. [PMID: 39000272 PMCID: PMC11241148 DOI: 10.3390/ijms25137166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
In recent years, interest in very small proteins (µ-proteins) has increased significantly, and they were found to fulfill important functions in all prokaryotic and eukaryotic species. The halophilic archaeon Haloferax volcanii encodes about 400 µ-proteins of less than 70 amino acids, 49 of which contain at least two C(P)XCG motifs and are, thus, predicted zinc finger proteins. The determination of the NMR solution structure of HVO_2753 revealed that only one of two predicted zinc fingers actually bound zinc, while a second one was metal-free. Therefore, the aim of the current study was the homologous production of additional C(P)XCG proteins and the quantification of their zinc content. Attempts to produce 31 proteins failed, underscoring the particular difficulties of working with µ-proteins. In total, 14 proteins could be produced and purified, and the zinc content was determined. Only nine proteins complexed zinc, while five proteins were zinc-free. Three of the latter could be analyzed using ESI-MS and were found to contain another metal, most likely cobalt or nickel. Therefore, at least in haloarchaea, the variability of predicted C(P)XCG zinc finger motifs is higher than anticipated, and they can be metal-free, bind zinc, or bind another metal. Notably, AlphaFold2 cannot correctly predict whether or not the four cysteines have the tetrahedral configuration that is a prerequisite for metal binding.
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Affiliation(s)
- Deniz Üresin
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; (J.S.); (N.M.)
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany;
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Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
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Dragone M, Grazioso R, D’Abrosca G, Baglivo I, Iacovino R, Esposito S, Paladino A, Pedone PV, Russo L, Fattorusso R, Malgieri G, Isernia C. Copper (I) or (II) Replacement of the Structural Zinc Ion in the Prokaryotic Zinc Finger Ros Does Not Result in a Functional Domain. Int J Mol Sci 2022; 23:ijms231911010. [PMID: 36232306 PMCID: PMC9569694 DOI: 10.3390/ijms231911010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
A strict interplay is known to involve copper and zinc in many cellular processes. For this reason, the results of copper’s interaction with zinc binding proteins are of great interest. For instance, copper interferences with the DNA-binding activity of zinc finger proteins are associated with the development of a variety of diseases. The biological impact of copper depends on the chemical properties of its two common oxidation states (Cu(I) and Cu(II)). In this framework, following the attention addressed to unveil the effect of metal ion replacement in zinc fingers and in zinc-containing proteins, we explore the effects of the Zn(II) to Cu(I) or Cu(II) replacement in the prokaryotic zinc finger domain. The prokaryotic zinc finger protein Ros, involved in the horizontal transfer of genes from A. tumefaciens to a host plant infected by it, belongs to a family of proteins, namely Ros/MucR, whose members have been recognized in different bacteria symbionts and pathogens of mammals and plants. Interestingly, the amino acids of the coordination sphere are poorly conserved in most of these proteins, although their sequence identity can be very high. In fact, some members of this family of proteins do not bind zinc or any other metal, but assume a 3D structure similar to that of Ros with the residues replacing the zinc ligands, forming a network of hydrogen bonds and hydrophobic interactions that surrogates the Zn-coordinating role. These peculiar features of the Ros ZF domain prompted us to study the metal ion replacement with ions that have different electronic configuration and ionic radius. The protein was intensely studied as a perfectly suited model of a metal-binding protein to study the effects of the metal ion replacement; it appeared to tolerate the Zn to Cd substitution, but not the replacement of the wildtype metal by Ni(II), Pb(II) and Hg(II). The structural characterization reported here gives a high-resolution description of the interaction of copper with Ros, demonstrating that copper, in both oxidation states, binds the protein, but the replacement does not give rise to a functional domain.
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Affiliation(s)
- Martina Dragone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rinaldo Grazioso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosa Iacovino
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Esposito
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Antonella Paladino
- Institute of Biostructures and Bioimaging, National Research Council (IBB-CNR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Paolo V. Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
- Correspondence:
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Zhao J, Zhou Z, Bai X, Zhang D, Zhang L, Wang J, Wu B, Zhu J, Yang Z. A novel of new class II bacteriocin from Bacillus velezensis HN-Q-8 and its antibacterial activity on Streptomyces scabies. Front Microbiol 2022; 13:943232. [PMID: 35966655 PMCID: PMC9372549 DOI: 10.3389/fmicb.2022.943232] [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: 05/13/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Potato common scab is a main soil-borne disease of potato that can significantly reduce its quality. At present, it is still a challenge to control potato common scab in the field. To address this problem, the 972 family lactococcin (Lcn972) was screened from Bacillus velezensis HN-Q-8 in this study, and an Escherichia coli overexpression system was used to obtain Lcn972, which showed a significant inhibitory effect on Streptomyces scabies, with a minimum inhibitory concentration of 10.58 μg/mL. The stability test showed that Lcn972 is stable against UV radiation and high temperature. In addition, long-term storage at room temperature and 4°C had limited effects on its activity level. The antibacterial activity of Lcn972 was enhanced by Cu2+ and Ca2+, but decreased by protease K. The protein was completely inactivated by Fe2+. Cell membrane staining showed that Lcn972 damaged the cell membrane integrity of S. scabies. Scanning electron microscope (SEM) and transmission electron microscope (TEM) observations revealed that the hyphae of S. scabies treated with Lcn972 were deformed and adhered, the cell membrane was incomplete, the cytoplasm distribution was uneven, and the cell appeared hollow inside, which led to the death of S. scabies. In conclusion, we used bacteriocin for controlling potato common scab for the first time in this study, and it provides theoretical support for the further application of bacteriocin in the control of plant diseases.
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Affiliation(s)
- Jing Zhao
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
| | - Zhijun Zhou
- Experimental Training Center of Hebei Agricultural University, Baoding, China
| | - Xuefei Bai
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
| | - Dai Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
| | - Likui Zhang
- College of Environmental Science, Yangzhou University, Yangzhou, China
| | - Jinhui Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
| | - Beibei Wu
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
| | - Jiehua Zhu
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
- *Correspondence: Jiehua Zhu,
| | - Zhihui Yang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, China
- Zhihui Yang,
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Mikhailov OV. The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years. Int J Mol Sci 2021; 23:ijms23010241. [PMID: 35008667 PMCID: PMC8745423 DOI: 10.3390/ijms23010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)—the year 2021 will only mark three years since its inception [...]
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Affiliation(s)
- Oleg V Mikhailov
- Department of Analytical Chemistry, Certification and Quality Management, Kazan National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
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6
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Diana D, Di Stasi R, García-Viñuales S, De Rosa L, Isernia C, Malgieri G, Milardi D, D'Andrea LD, Fattorusso R. Structural characterization of the thermal unfolding pathway of human VEGFR1 D2 domain. FEBS J 2021; 289:1591-1602. [PMID: 34689403 PMCID: PMC9299094 DOI: 10.1111/febs.16246] [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: 07/06/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
Folding stability is a crucial feature of protein evolution and is essential for protein functions. Thus, the comprehension of protein folding mechanisms represents an important complement to protein structure and function, crucial to determine the structural basis of protein misfolding. In this context, thermal unfolding studies represent a useful tool to get a molecular description of the conformational transitions governing the folding/unfolding equilibrium of a given protein. Here, we report the thermal folding/unfolding pathway of VEGFR1D2, a member of the immunoglobulin superfamily by means of a high-resolution thermodynamic approach that combines differential scanning calorimetry with atomic-level unfolding monitored by NMR. We show how VEGFR1D2 folding is driven by an oxidatively induced disulfide pairing: the key event in the achievement of its functional structure is the formation of a small hydrophobic core that surrounds a disulfide bridge. Such a 'folding nucleus' induces the cooperative transition to the properly folded conformation supporting the hypothesis that a disulfide bond can act as a folding nucleus that eases the folding process.
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Affiliation(s)
| | | | | | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Carla Isernia
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Gaetano Malgieri
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy
| | | | - Luca D D'Andrea
- Istituto di Scienze e Tecnologie Chimiche 'Giulio Natta', CNR, Milano, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche (DiSTABiF), Università degli Studi della Campania 'Luigi Vanvitelli', Caserta, Italy
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Ok K, Filipovic MR, Michel SLJ. Targeting Zinc Finger Proteins with Exogenous Metals and Molecules: Lessons learned from Tristetraprolin, a CCCH type Zinc Finger. Eur J Inorg Chem 2021; 2021:3795-3805. [PMID: 34867080 PMCID: PMC8635303 DOI: 10.1002/ejic.202100402] [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: 05/10/2021] [Indexed: 11/09/2022]
Abstract
ZF proteins are ubiquitous eukaryotic proteins that play important roles in gene regulation. ZFs contain small domains made up of a combination of four cysteine and histidine residues, and are classified based up on the identity of these residues and their spacing. One emerging class of ZFs are the Cys3His (or CCCH) class of ZFs. These ZFs play key roles in regulating RNA. In this minireview, an overview of the CCCH class of ZFs, with a focus on tristetraprolin (TTP) is provided. TTP regulates inflammation by controlling cytokine mRNAs, and there is an interest in modulating TTP activity to control inflammation. Two methods to control TTP activity are to target with exogenous metals (a 'metals in medicine' approach) or to target with endogenous signaling molecules. Work that has been done to target TTP with Fe, Cu, Cd and Au as well as with H2S is reviewed. This includes attention to new methods that have been developed to monitor metal exchange with the spectroscopically silent ZnII including native electro-spray ionization mass spectrometry (ESI-MS), spin-filter inductively coupled plasma mass spectrometry (ICP-MS) and cryo-electro-spray mass spectrometry (CSI-MS); along with fluorescence anisotropy (FA) to follow RNA binding.
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Affiliation(s)
- Kiwon Ok
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Milos R Filipovic
- Leibniz-Institut für Analytische, Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
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Akparov VK, Konstantinova GE, Timofeev VI, Khaliullin IG, Kuranova IP. Structure of the microbial carboxypeptidase T complexed with the transition state analog N-sulfamoyl-l-lysine. Biophys Chem 2020; 270:106535. [PMID: 33412495 DOI: 10.1016/j.bpc.2020.106535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 11/18/2022]
Abstract
Carboxypeptidase T (CPT) from Thermoactinomyces vulgaris (EC 3.4.17.18) has a broad substrate specificity, the mechanism of which remains unclear. It cleaves off arginine residues by 10, and lysine residues by 100 times worse than hydrophobic leucine residues despite the presence of negatively charged Asp260 at the bottom of the primary specificity pocket. To study the relationship between the structure and specificity the 3D structure of CPT in complex with the stable transition state analog N-sulfamoyl-l-lysine (SLys) was determined in which the S-atom imitates the sp3-hybridized carbon in the scissile-bond. Crystals grown in microgravity has the symmetry of space group P6322. The present complex structure was compared with the previously reported complex structure of CPT and N-sulfamoyl-L-arginine (SArg). The location/binding of SLys in the active site of CPT very closely resembled that of SArg, and the positively charged N-atom of SLys was at the same position as the corresponding positively charged N-atom of SArg. The SLys complex is stabilized by the hydrogen bond between the nitrogen atom and OH-group of Thr257. The contact areas of the residues Tyr255, Leu211, and Thr262 with SLys were reduced in comparison with the same of SArg. This difference in bonding of SArg and SLys side chains in the primary specificity pocket induces shifts differences within the catalytic center (especially Tyr255-O20 and S18-Arg129 N1 gap) that may influence the enzyme's catalytic reaction. Therefore, this information may be useful for the design of carboxypeptidases with improved selectivity towards Arg/Lys for biotechnological applications.
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Affiliation(s)
- Valery Kh Akparov
- National Research Center "Kurchatov institute", Ak. Kurchatova square 1, Moscow 123182, Russian Federation.
| | - Galina E Konstantinova
- National Research Center "Kurchatov institute", Ak. Kurchatova square 1, Moscow 123182, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russian Federation
| | - Ilyas G Khaliullin
- Moscow Institute of Physics and Technology (State University), 9 Institutsky per. Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russian Federation
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