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Zhang Y, Zhang J, Wan H, Wu Z, Xu H, Zhang Z, Wang Y, Wang J. New Insights into the Dependence of CPEB3 Ribozyme Cleavage on Mn 2+ and Mg 2. J Phys Chem Lett 2024; 15:2708-2714. [PMID: 38427973 DOI: 10.1021/acs.jpclett.3c03221] [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: 03/03/2024]
Abstract
CPEB3 ribozyme is a self-cleaving RNA that occurs naturally in mammals and requires divalent metal ions for efficient activity. Ribozymes exhibit preferences for specific metal ions, but the exact differences in the catalytic mechanisms of various metal ions on the CPEB3 ribozyme remain unclear. Our findings reveal that Mn2+ functions as a more effective cofactor for CPEB3 ribozyme catalysis compared to Mg2+, as confirmed by its stronger binding affinity to CPEB3 by EPR. Cleavage assays of CPEB3 mutants and molecular docking analyses further showed that excessive Mn2+ ions can bind to a second binding site near the catalytic site, hindering CPEB3 catalytic efficiency and contributing to the Mn2+ bell-shaped curve. These results implicate a pivotal role for the local nucleobase-Mn2+ interactions in facilitating RNA folding and modulating the directed attack of nucleophilic reagents. Our study provides new insights and experimental evidence for exploring the divalent cation dependent cleavage mechanism of the CPEB3 ribozyme.
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Affiliation(s)
- Yaoyao Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jing Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hengjia Wan
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ziwei Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huangtao Xu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Zhe Zhang
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yujuan Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- International Magnetobiology Frontier Research Center (iMFRC), Science Island, Hefei 230031, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
- International Magnetobiology Frontier Research Center (iMFRC), Science Island, Hefei 230031, China
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Amadei F, Reichenbach M, Gallo S, Sigel RKO. The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. J Inorg Biochem 2023; 242:112153. [PMID: 36774787 DOI: 10.1016/j.jinorgbio.2023.112153] [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: 10/10/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023]
Abstract
Riboswitches are structural elements of mRNA involved in the regulation of gene expression by responding to specific cellular metabolites. To fulfil their regulatory function, riboswitches prefold into an active state, the so-called binding competent form, that guarantees metabolite binding and allows a consecutive refolding of the RNA. Here, we describe the folding pathway to the binding competent form as well as the ligand free structure of the moaA riboswitch of E. coli. This RNA proposedly responds to the molybdenum cofactor (Moco), a highly oxygen-sensitive metabolite, essential in the carbon and sulfur cycles of eukaryotes. K+- and Mg2+-dependent footprinting assays and spectroscopic investigations show a high degree of structure formation of this RNA already at very low ion-concentrations. Mg2+ facilitates additionally a general compaction of the riboswitch towards its proposed active structure. We show that this fold agrees with the earlier suggested secondary structure which included also a long-range tetraloop/tetraloop-receptor like interaction. Metal ion cleavage assays revealed specific Mg2+-binding pockets within the moaA riboswitch. These Mg2+ binding pockets are good indicators for the potential Moco binding site, since in riboswitches, Mg2+ was shown to be necessary to bind phosphate-carrying metabolites. The importance of the phosphate and of other functional groups of Moco is highlighted by binding assays with tetrahydrobiopterin, the reduced and oxygen-sensitive core moiety of Moco. We demonstrate that the general molecular shape of pterin by its own is insufficient for the recognition by the riboswitch.
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Affiliation(s)
- Fabio Amadei
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - María Reichenbach
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sofia Gallo
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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3
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Hasani Zadeh P, Fermoso FG, Collins G, Serrano A, Mills S, Abram F. Impacts of metal stress on extracellular microbial products, and potential for selective metal recovery. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114604. [PMID: 36758509 DOI: 10.1016/j.ecoenv.2023.114604] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Harnessing microbial capabilities for metal recovery from secondary waste sources is an eco-friendly and sustainable approach for the management of metal-containing wastes. Soluble microbial products (SMP) and extracellular polymeric substances (EPS) are the two main groups of extracellular compounds produced by microorganisms in response to metal stress that are of great importance for remediation and recovery of metals. These include various high-, and low, molecular weight components, which serve various functional and structural roles. These compounds often contain functional groups with metal binding potential that can attenuate metal stress by sequestering metal ions, making them less bioavailable. Microorganisms can regulate the content and composition of EPS and SMP in response to metal stress in order to increase the compounds specificity and capacity for metal binding. Thus, EPS and SMP represent ideal candidates for developing technologies for selective metal recovery from complex wastes. To discover highly metal-sorptive compounds with specific metal binding affinity for metal recovery applications, it is necessary to investigate the metal binding affinity of these compounds, especially under metal stressed conditions. In this review we critically reviewed microbial EPS and SMP production as a response to metal stress with a particular emphasis on the metal binding properties of these compounds and their role in altering metal bioavailability. Furthermore, for the first time, we compiled the available data on potential application of these compounds for selective metal recovery from waste streams.
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Affiliation(s)
- Parvin Hasani Zadeh
- Bioprocesses for the Circular Economy Group, Instituto de la Grasa, Spanish National Research Council (CSIC), Seville, Spain; Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Fernando G Fermoso
- Bioprocesses for the Circular Economy Group, Instituto de la Grasa, Spanish National Research Council (CSIC), Seville, Spain
| | - Gavin Collins
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Antonio Serrano
- Institute of Water Research, University of Granada, Granada 18071, Spain; Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, Granada 18071, Spain
| | - Simon Mills
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
| | - Florence Abram
- Microbiology, School of Biological and Chemical Sciences, National University of Ireland Galway, Galway, Ireland
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4
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Yao L, Zhang T, Peng S, Xu D, Liu Z, Li H, Hu L, Mo H. Fe2+ protects postharvest pitaya (Hylocereus undulatus britt) from Aspergillus. flavus infection by directly binding its genomic DNA. FOOD CHEMISTRY: MOLECULAR SCIENCES 2022; 5:100135. [PMID: 36177106 PMCID: PMC9513725 DOI: 10.1016/j.fochms.2022.100135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/30/2022] [Accepted: 09/17/2022] [Indexed: 12/02/2022]
Abstract
Light was shield on Fe2+ application as antifungal agent on pitaya postharvest. Fe2+ prevents A. flavus infection by directly binding to A. flavus DNA. This research will promote the research on the mechanism of fungal death. A new strategy was provided to combat fungal infection in fruit postharvest industry.
Aspergillus flavus (A. flavus) is a postharvest fungus, causing pitaya fruit decay and limiting pitaya value and shelf life. However, safer and more efficient methods for preventing A. flavus contamination for pitaya fruit remain to be investigated. In this study, we successfully proved exogenous Fe2+ could inhibit A. flavus colonization in pitaya fruit and extend pitaya’s shelf life after harvest. Moreover, gel electrophoresis, CD analysis and Raman spectrum tests revealed Fe2+ could more effectively and thoroughly promote conidial death by directly binding to A. flavus DNA. Increased expression of DNA damage repair-related genes after Fe2+ treatment was observed by transcription analysis, which might eventually lead to SOS response in A. flavus. These results indicated Fe2+ could prevent A. flavus infestation on pitaya in a novel, quickly responsive mechanism. Our results shed light on the potential application of Fe2+ in the food industry and provided a more universal antifungal agent against food pathogens.
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Andrałojć W, Wieruszewska J, Pasternak K, Gdaniec Z. Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints. Chemistry 2022; 28:e202202114. [PMID: 36043489 PMCID: PMC9828363 DOI: 10.1002/chem.202202114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 01/12/2023]
Abstract
In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraints - pseudocontact shifts (PCS) induced by four different paramagnetic lanthanides - was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.
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Affiliation(s)
- Witold Andrałojć
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Julia Wieruszewska
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Karol Pasternak
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Zofia Gdaniec
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
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6
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Wuebben C, Schiemann O. Quantifying the Number and Affinity of Mn 2+-Binding Sites with EPR Spectroscopy. Methods Mol Biol 2022; 2439:91-101. [PMID: 35226317 DOI: 10.1007/978-1-0716-2047-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
During the last decades, various functional oligonucleotides have been discovered including DNAzymes, ribozymes, and riboswitches. Their function is based on their ability to form and change their three-dimensional structure. Binding of divalent ions to specific binding pockets was found to be important for the global structure and function. Here, we present a protocol that allows counting the number of Mn2+-binding sites and to determine their dissociation constants by means of continuous wave X-band Electron Paramagnetic Resonance (EPR) spectroscopy. In this method, Mn2+ is titrated into the oligonucleotide-containing sample and the intensity of the EPR spectrum is recorded. By comparison with a Mn2+-only reference sample, the binding isotherm can be constructed and fitted to binding models yielding the number and affinities of the binding sites. This method has been successfully applied to several functional oligonucleotides.
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Affiliation(s)
- Christine Wuebben
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University, Bonn, Germany.
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7
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Lai KP, Su YC, Fu BS, Lin KH, Kou HS, Wang CC. Copper nanoclusters on specific-primer PCR fragments with magnetic capture for the label-free fluorescent sensing of the T315I single nucleotide variant in the BCR– ABL1 gene. Analyst 2022; 147:5732-5738. [DOI: 10.1039/d2an01433e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A simple and facile strategy using the all or none formation of dsDNA-templated copper nanoclusters on specific-primer PCR fragments was designed to fluorescently identify the T315I single nucleotide variant on the BCR–ABL1 gene.
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Affiliation(s)
- Ke-Peng Lai
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Yu-Chen Su
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Bo-Siang Fu
- Division of Orthopedic Surgery, Department of Surgery, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan, Republic of China
| | - Kung-Hung Lin
- Department of Surgery, Division of General Surgery, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan, Republic of China
| | - Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, Republic of China
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
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8
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Hydrogel composite of lanthanum and Halorubrum ejinoor sp. cell lysate as an adsorbing material. Biotechnol Lett 2021; 43:1443-1453. [PMID: 33877517 DOI: 10.1007/s10529-021-03132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Although halophilic archaea are rich in natural environments, their biotechnological applications are not as prevalent as those of other extremophiles, such as thermophiles and alkaliphiles. This study presents an simple method to prepare a hydrogel composite using crude cell lysate of a halophilic archaea, Halorubrum ejinoor sp. (H.e.) which was isolated from a saline lake in Inner Mongolia, China. Furthermore, formation mechanism and potential applications of the hydrogel as an adsorbing material are discussed. RESULTS Halorubrum ejinoor sp. (H.e.) cell lysate was firstly prepared by adding pure water onto the H.e. cell pellet, followed by a short incubation at 60 °C. The cell lysate was injected into different metal ion (or H+) solutions to obtain the hydrogel composite. It was observed that H+, Fe3+, La3+, Cu2+, and Ca2+ induced gelation of the cell lysate, while Fe2+, Co2+, Ni2+, Mg2+, Na+, and K+ did not. DNA and extracellular polysaccharides (EPS) in the H.e. cell lysate were found to be responsible for the gelation reaction. These results suggest that DNA and EPS should be crosslinked by metal ions (or H+) and form a networked structure in which the metal ion (or H+) serves as an anchor point. Potential application of the hydrogel as an adsorbing material was explored using La3+-induced H.e. hydrogel composite. The hydrogel composite can adsorb the fluoride, phosphate and DNA-binding carcinogenic agents, such as acridine orange. CONCLUSIONS The simplicity and cost effectiveness of the preparation method might make H.e. hydrogel a promising adsorbing material. This work is expected to expand the technical applications of haloarchaea.
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Kushwaha GS, Patra A, Bhavesh NS. Structural Analysis of (p)ppGpp Reveals Its Versatile Binding Pattern for Diverse Types of Target Proteins. Front Microbiol 2020; 11:575041. [PMID: 33224117 PMCID: PMC7674647 DOI: 10.3389/fmicb.2020.575041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/06/2020] [Indexed: 11/25/2022] Open
Abstract
(p)ppGpp, highly phosphorylated guanosine, are global regulatory nucleotides that modulate several biochemical events in bacterial physiology ranging from core central dogma to various metabolic pathways. Conventionally, (p)ppGpp collectively refers to two nucleotides, ppGpp, and pppGpp in the literature. Initially, (p)ppGpp has been discovered as a transcription regulatory molecule as it binds to RNA polymerase and regulates transcriptional gene regulation. During the past decade, several other target proteins of (p)ppGpp have been discovered and as of now, more than 30 proteins have been reported to be regulated by the binding of these two signaling nucleotides. The regulation of diverse biochemical activities by (p)ppGpp requires fine-tuned molecular interactions with various classes of proteins so that it can moderate varied functions. Here we report a structural dynamics of (p)ppGpp in the unbound state using well-defined computational tools and its interactions with target proteins to understand the differential regulation by (p)ppGpp at the molecular level. We carried out replica exchange molecular dynamics simulation studies to enhance sampling of conformations during (p)ppGpp simulation. The detailed comparative analysis of torsion angle conformation of ribose sugar of unbound (p)ppGpp and bound states of (p)ppGpp was carried out. The structural dynamics shows that two linear phosphate chains provide plasticity to (p)ppGpp nucleotides for the binding to diverse proteins. Moreover, the intermolecular interactions between (p)ppGpp and target proteins were characterized through various physicochemical parameters including, hydrogen bonds, van der Waal’s interactions, aromatic stacking, and side chains of interacting residues of proteins. Surprisingly, we observed that interactions of (p)ppGpp to target protein have a consensus binding pattern for a particular functional class of enzymes. For example, the binding of (p)ppGpp to RNA polymerase is significantly different from the binding of (p)ppGpp to the proteins involved in the ribosome biogenesis pathway. Whereas, (p)ppGpp binding to enzymes involved in nucleotide metabolism facilitates the functional regulation through oligomerization. Analysis of these datasets revealed that guanine base-specific contacts are key determinants to discriminate functional class of protein. Altogether, our studies provide significant information to understand the differential interaction pattern of (p)ppGpp to its target and this information may be useful to design antibacterial compounds based on (p)ppGpp analogs.
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Affiliation(s)
- Gajraj Singh Kushwaha
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,KIIT Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) (Deemed to be University), Bhubaneswar, India
| | - Anupam Patra
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Putignano V, Rosato A, Banci L, Andreini C. MetalPDB in 2018: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2019; 46:D459-D464. [PMID: 29077942 PMCID: PMC5753354 DOI: 10.1093/nar/gkx989] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/20/2017] [Indexed: 11/14/2022] Open
Abstract
MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, ∼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure.
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Affiliation(s)
- Valeria Putignano
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Magnetic Resonance Center (CERM)—University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry—University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- To whom correspondence should be addressed. Tel: +39 55 4574267;
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Vellampatti S, Chandrasekaran G, Mitta SB, Dugasani SR, Lakshmanan VK, Park SH. Bacterial Resistance and Prostate Cancer Susceptibility Toward Metal-Ion-doped DNA Complexes. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44290-44300. [PMID: 30550272 DOI: 10.1021/acsami.8b17013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology has laid a platform to construct a variety of custom-shaped nanoscale objects for functionalization of specific target materials to achieve programmability and molecular recognition. Herein, we prepared DNA nanostructures [namely, synthetic DNA rings (RDNA) and DNA duplexes extracted from salmon (SDNA)] containing metal ions (M2+) such as Cu2+, Ni2+, and Zn2+ as payloads for delivery to exterminate highly pathologic hospital bacterial strains (e.g., Escherichia coli and Bacillus subtilis) and prostate cancer cells (i.e., PC3, LNCaP, TRAMP-C1, 22Rv1, and DU145). Morphologies of these M2+-doped RDNA were visualized using atomic force microscopy. Interactions between M2+ and DNA were studied using UV-vis and Fourier transform infrared spectroscopy. Quantitative composition and chemical changes in DNA without or with M2+ were obtained using X-ray photoelectron spectroscopy. In addition, M2+-doped DNA complexes were subjected to antibacterial activity studies. They showed no bacteriostatic or bactericidal effects on bacterial strains used. Finally, in vitro cellular toxicity study was conducted to evaluate the effect of pristine DNA and M2+-doped DNA complexes on prostate cancer cells. Cytotoxicities conferred by M2+-doped DNA complexes for most cell lines were significantly higher than those of M2+ without DNA. Cellular uptake of these complexes was confirmed by fluorescence microscopy using PhenGreen FL indicator. On the basis of our observations, DNA nanostructures can be used as safe and efficient nanocarriers for delivery of therapeutics. They have enhanced therapeutic window than bare metals.
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Affiliation(s)
- Srivithya Vellampatti
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
| | | | - Sekhar Babu Mitta
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
| | - Sreekantha Reddy Dugasani
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
| | - Vinoth-Kumar Lakshmanan
- Department of Biomedical Sciences , Chonnam National University Medical School , Gwangju 61469 , Korea
- Department of Biomedical Engineering , Sri Shakthi Institute of Engineering and Technology , Coimbatore 641062 , India
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
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12
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Geersing A, Ségaud N, van der Wijst MGP, Rots MG, Roelfes G. Importance of Metal-Ion Exchange for the Biological Activity of Coordination Complexes of the Biomimetic Ligand N4Py. Inorg Chem 2018; 57:7748-7756. [PMID: 29916702 PMCID: PMC6030684 DOI: 10.1021/acs.inorgchem.8b00714] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/24/2022]
Abstract
Metal coordination complexes can display interesting biological activity, as illustrated by the bleomycins (BLMs), a family of natural antibiotics that when coordinated to a redox-active metal ion, show antitumor activity. Yet, which metal ion is required for the activity in cells is still subject to debate. In this study, we described how different metal ions affect the intracellular behavior and activity of the synthetic BLM-mimic N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine (N4Py). Our study shows that a mixture of iron(II), copper(II), and zinc(II) complexes can be generated when N4Py is added to cell cultures but that the metal ion can also be exchanged by other metal ions present in cells. Moreover, the combination of chemical data, together with the performed biological experiments, shows that the active complex causing oxidative damage to cells is the FeII-N4Py complex and not per se the metal complex that was initially added to the cell culture medium. Finally, it is proposed that the high activity observed upon the addition of the free N4Py ligand is the result of a combination of scavenging of biologically relevant metals and oxidative damage caused by the iron(II) complex.
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Affiliation(s)
- Arjan Geersing
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nathalie Ségaud
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Monique G. P. van der Wijst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Sigel A, Operschall BP, Sigel RKO, Sigel H. Metal ion complexes of nucleoside phosphorothioates reflecting the ambivalent properties of lead(ii). NEW J CHEM 2018. [DOI: 10.1039/c7nj04989g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lead(ii)-lone pair leads to ambivalency: hemidirected (distorted, non-spherical) coordination spheres result from electronegative O-coordination and holodirected (symmetric, spherical) ones from less electronegative S-coordination.
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Affiliation(s)
- Astrid Sigel
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | - Bert P. Operschall
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
| | | | - Helmut Sigel
- Department of Chemistry
- Inorganic Chemistry
- University of Basel
- CH-4056 Basel
- Switzerland
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14
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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15
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Theophanides T, Anastassopoulou J. The effects of metal ion contaminants on the double stranded DNA helix and diseases. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2017; 52:1030-1040. [PMID: 28758877 DOI: 10.1080/10934529.2017.1328950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mineral metal ions are essential for the maintenance of the reactions that regulate homeostasis and the functions of our body. It is known that the regulation of the neurodegenerative system depends directly on life metal ions, such as Na, K, Mg, Ca, Fe, Mo, Cu, Co, Zn, Cr, Mn, while the toxic metals Cd, Pb, Hg, etc disturb homeostasis, leading to diseases. Particularly significant is the effect of toxic metals on the double stranded forms of DNA and conformations. It was found that the toxic metal ions by reacting specifically with the nucleic bases and electrostatically with the negatively phosphate groups of the DNA backbone cause changes in the structure of the DNA double helix, leading to breaks of single or double strands. Accumulation of these defects affects the protecting systems of the body and induces mutations, eventually leading to serious diseases. There are many metal ions, such as Cr, Al, Cd, Cu, Ni, which by binding directly to DNA molecule or by developing oxidative stress increase the instability of DNA, promoting epigenetic changes that lead to DNA damage. Toxic metal ions induce indirect DNA damage and influence the gene stability by inactivating encoding proteins or by changing the redox potential and the signaling of metalloenzymes.
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Affiliation(s)
- T Theophanides
- a National Technical University of Athens, Chemical Engineering Department, Radiation Chemistry & Biospectroscopy , Zografou Campus, Zografou , Athens , Greece
| | - J Anastassopoulou
- b International Anticancer Research Institute , Kapandritiou-Kalamou Road, Kapandriti , Attiki , Greece
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16
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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17
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Leonarski F, D'Ascenzo L, Auffinger P. Mg2+ ions: do they bind to nucleobase nitrogens? Nucleic Acids Res 2017; 45:987-1004. [PMID: 27923930 PMCID: PMC5314772 DOI: 10.1093/nar/gkw1175] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.
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Affiliation(s)
- Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
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18
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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19
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Leonarski F, D’Ascenzo L, Auffinger P. Binding of metals to purine N7 nitrogen atoms and implications for nucleic acids: A CSD survey. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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20
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Alberti E, Zampakou M, Donghi D. Covalent and non-covalent binding of metal complexes to RNA. J Inorg Biochem 2016; 163:278-291. [DOI: 10.1016/j.jinorgbio.2016.04.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/12/2016] [Accepted: 04/12/2016] [Indexed: 01/19/2023]
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21
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Bartova S, Alberti E, Sigel RK, Donghi D. Metal ion binding to an RNA internal loop. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations. Int J Mol Sci 2016; 17:ijms17070988. [PMID: 27355942 PMCID: PMC4964368 DOI: 10.3390/ijms17070988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/15/2022] Open
Abstract
Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca(2+), Mn(2+), Co(2+), Cu(2+), Sr(2+), and Tb(3+). The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.
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23
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Giambaşu GM, Gebala MK, Panteva MT, Luchko T, Case DA, York DM. Competitive interaction of monovalent cations with DNA from 3D-RISM. Nucleic Acids Res 2015; 43:8405-15. [PMID: 26304542 PMCID: PMC4787805 DOI: 10.1093/nar/gkv830] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 12/15/2022] Open
Abstract
The composition of the ion atmosphere surrounding nucleic acids affects their folding, condensation and binding to other molecules. It is thus of fundamental importance to gain predictive insight into the formation of the ion atmosphere and thermodynamic consequences when varying ionic conditions. An early step toward this goal is to benchmark computational models against quantitative experimental measurements. Herein, we test the ability of the three dimensional reference interaction site model (3D-RISM) to reproduce preferential interaction parameters determined from ion counting (IC) experiments for mixed alkali chlorides and dsDNA. Calculations agree well with experiment with slight deviations for salt concentrations >200 mM and capture the observed trend where the extent of cation accumulation around the DNA varies inversely with its ionic size. Ion distributions indicate that the smaller, more competitive cations accumulate to a greater extent near the phosphoryl groups, penetrating deeper into the grooves. In accord with experiment, calculated IC profiles do not vary with sequence, although the predicted ion distributions in the grooves are sequence and ion size dependent. Calculations on other nucleic acid conformations predict that the variation in linear charge density has a minor effect on the extent of cation competition.
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Affiliation(s)
- George M Giambaşu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Magdalena K Gebala
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Maria T Panteva
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Tyler Luchko
- Department of Physics & Astronomy, California State University, Northridge, CA 91330, USA
| | - David A Case
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Darrin M York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
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24
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Pérez-Toro I, Domínguez-Martín A, Choquesillo-Lazarte D, Vílchez-Rodríguez E, González-Pérez JM, Castiñeiras A, Niclós-Gutiérrez J. Lights and shadows in the challenge of binding acyclovir, a synthetic purine-like nucleoside with antiviral activity, at an apical-distal coordination site in copper(II)-polyamine chelates. J Inorg Biochem 2015; 148:84-92. [PMID: 25863571 DOI: 10.1016/j.jinorgbio.2015.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/08/2015] [Accepted: 03/09/2015] [Indexed: 11/25/2022]
Abstract
Several nucleic acid components and their metal complexes are known to be involved in crucial metabolic steps. Therefore the study of metal-nucleic acid interactions becomes essential to understand these biological processes. In this work, the synthetic purine-like nucleoside acyclovir (acv) has been used as a model of guanosine recognition with copper(II)-polyamine chelates. The chemical stability of the N9-acyclic arm in acv offers the possibility to use this antiviral drug to deepen the knowledge of metal-nucleoside interactions. Cu(II) chelates with cyclam, cyclen and trien were used as suitable receptors. All these copper(II) tetraamine chelates have in common the potential ability to yield a Cu-N7(apical) bond assisted by an appropriate (amine)N-H⋯O6(acv) intra-molecular interligand interaction. A series of synthesis afforded the following compounds: [Cu(cyclam)(ClO4)2] (1), {[Cu(cyclam)(μ2-NO3)](NO3)}n (2), {[Cu(cyclam)(μ2-SO4)]·MeOH}n (3), {[Cu(cyclam)(μ2-SO4)]·5H2O}n (4), [Cu(cyclen)(H2O)]SO4·2H2O (5), [Cu(cyclen)(H2O)]SO4·3H2O (6), [Cu(trien)(acv)](NO3)2·acv (7) and [Cu(trien)(acv)]SO4·0.71H2O (8). All these compounds have been characterized by X-ray crystallography and FT-IR spectroscopy. Our results reveal that the macrochelates Cu(cyclen)(2+) and Cu(cyclam)(2+) are unable to bind acv at an apical site. In contrast, the Cu(trien)(2+) complex has proved to be an efficient receptor for acv in compounds (7) and (8). In the ternary complex [Cu(trien)(acv)](2+), the metal binding pattern of acv consists of an apical Cu-N7 bond assisted by an intra-molecular (primary amino)N-H⋯O6(acv) interligand interaction. Structural comparisons reveal that this unprecedented apical role of acv is due to the acyclic nature of trien together with the ability of the Cu(trien)(2+) chelate to generate five-coordinated (type 4+1) copper(II) complexes.
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Affiliation(s)
- Inmaculada Pérez-Toro
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | - Alicia Domínguez-Martín
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain.
| | - Duane Choquesillo-Lazarte
- Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Av. de las Palmeras 4, E-18100 Armilla, Granada, Spain
| | - Esther Vílchez-Rodríguez
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| | | | - Alfonso Castiñeiras
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan Niclós-Gutiérrez
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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25
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Cation-induced kinetic heterogeneity of the intron-exon recognition in single group II introns. Proc Natl Acad Sci U S A 2015; 112:3403-8. [PMID: 25737541 DOI: 10.1073/pnas.1322759112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA is commonly believed to undergo a number of sequential folding steps before reaching its functional fold, i.e., the global minimum in the free energy landscape. However, there is accumulating evidence that several functional conformations are often in coexistence, corresponding to multiple (local) minima in the folding landscape. Here we use the 5'-exon-intron recognition duplex of a self-splicing ribozyme as a model system to study the influence of Mg(2+) and Ca(2+) on RNA tertiary structure formation. Bulk and single-molecule spectroscopy reveal that near-physiological M(2+) concentrations strongly promote interstrand association. Moreover, the presence of M(2+) leads to pronounced kinetic heterogeneity, suggesting the coexistence of multiple docked and undocked RNA conformations. Heterogeneity is found to decrease at saturating M(2+) concentrations. Using NMR, we locate specific Mg(2+) binding pockets and quantify their affinity toward Mg(2+). Mg(2+) pulse experiments show that M(2+) exchange occurs on the timescale of seconds. This unprecedented combination of NMR and single-molecule Förster resonance energy transfer demonstrates for the first time to our knowledge that a rugged free energy landscape coincides with incomplete occupation of specific M(2+) binding sites at near-physiological M(2+) concentrations. Unconventional kinetics in nucleic acid folding frequently encountered in single-molecule experiments are therefore likely to originate from a spectrum of conformations that differ in the occupation of M(2+) binding sites.
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26
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Skilandat M, Sigel RKO. The role of Mg(II) in DNA cleavage site recognition in group II intron ribozymes: solution structure and metal ion binding sites of the RNA-DNA complex. J Biol Chem 2015; 289:20650-63. [PMID: 24895129 DOI: 10.1074/jbc.m113.542381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Group II intron ribozymes catalyze the cleavage of (and their reinsertion into) DNA and RNA targets using a Mg2(+)-dependent reaction. The target is cleaved 3' to the last nucleotide of intron binding site 1 (IBS1), one of three regions that form base pairs with the intron's exon binding sites (EBS1 to -3).We solved the NMR solution structure of the d3' hairpin of the Sc.ai5γ intron containing EBS1 in its 11-nucleotide loop in complex with the dIBS1 DNA 7-mer and compare it with the analogous RNA-RNA contact. The EBS1-dIBS1 helix is slightly flexible and non-symmetric. NMR data reveal two major groove binding sites for divalent metal ions at the EBS1-dIBS1 helix, and surface plasmon resonance experiments show that low concentrations of Mg2(+) considerably enhance the affinity of dIBS1 for EBS1. Our results indicate that identification of both RNA and DNA IBS1 targets, presentation of the scissile bond, and stabilization of the structure by metal ions are governed by the overall structure of EBS1-dIBS1 and the surrounding loop nucleotides but are irrespective of different EBS1-(d)IBS1 geometries and interstrand affinities.
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27
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Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain. J Biol Inorg Chem 2014; 19:903-12. [PMID: 24652468 DOI: 10.1007/s00775-014-1125-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/05/2014] [Indexed: 01/18/2023]
Abstract
Three ribozymes are known to occur in humans, the CPEB3 ribozyme, the CoTC ribozyme, and the hammerhead ribozyme. Here, we present the NMR solution structure of a well-conserved motif within the CPEB3 ribozyme, the P4 domain. In addition, we discuss the binding sites and impact of Mg(2+) and [Co(NH3)6](3+), a spectroscopic probe for [Mg(H2O)6](2+), on the structure. The well-defined P4 region is a hairpin closed with a UGGU tetraloop that shows a distinct electrostatic surface potential and a characteristic, strongly curved backbone trajectory. The P4 hairpin contains two specific Mg(2+) binding sites: one outer-sphere binding site close to the proposed CPEB3 ribozyme active site with potential relevance for maintaining a compact fold of the ribozyme core, and one inner-sphere binding site, probably stabilizing the tetraloop structure. The structure of the tetraloop resembles an RNase III recognition structure, as previously described for an AGUU tetraloop. The detailed knowledge of the P4 domain and its metal ion binding preferences thus brings us closer to understanding the importance of Mg(2+) binding for the CPEB3 ribozyme's fold and function in the cell.
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28
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Kruschel D, Skilandat M, Sigel RK. NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition. RNA (NEW YORK, N.Y.) 2014; 20:295-307. [PMID: 24448450 PMCID: PMC3923125 DOI: 10.1261/rna.041137.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A crucial step of the self-splicing reaction of group II intron ribozymes is the recognition of the 5' exon by the intron. This recognition is achieved by two regions in domain 1 of the intron, the exon-binding sites EBS1 and EBS2 forming base pairs with the intron-binding sites IBS1 and IBS2 located at the end of the 5' exon. The complementarity of the EBS1•IBS1 contact is most important for ensuring site-specific cleavage of the phosphodiester bond between the 5' exon and the intron. Here, we present the NMR solution structures of the d3' hairpin including EBS1 free in solution and bound to the IBS1 7-mer. In the unbound state, EBS1 is part of a flexible 11-nucleotide (nt) loop. Binding of IBS1 restructures and freezes the entire loop region. Mg(2+) ions are bound near the termini of the EBS1•IBS1 helix, stabilizing the interaction. Formation of the 7-bp EBS1•IBS1 helix within a loop of only 11 nt forces the loop backbone to form a sharp turn opposite of the splice site, thereby presenting the scissile phosphate in a position that is structurally unique.
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29
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Choudhary PK, Gallo S, Sigel RKO. Monitoring global structural changes and specific metal-ion-binding sites in RNA by in-line probing and Tb(III) cleavage. Methods Mol Biol 2014; 1086:143-158. [PMID: 24136602 DOI: 10.1007/978-1-62703-667-2_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this chapter we describe the use of two methods, in-line probing as well as terbium(III) cleavage. Both methods can be applied to RNAs of any size, structure, and function. Aside from revealing directly metal ion-binding sites these techniques also provide structural information for longer RNA sequences that are out of range to be analyzed with other techniques such as NMR. The cleavage pattern derived from in-line probing experiments reflects local and overall conformational changes in RNA upon the addition of metal ions, metal complexes, or other ligands. On the other side, terbium(III) cleavage experiments are applied to locate specific metal ion-binding sites in RNA molecules.
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30
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Gening LV, Lakhin AV, Stelmashook EV, Isaev NK, Tarantul VZ. Inhibition of Mn2+-induced error-prone DNA synthesis with Cd2+ and Zn2+. BIOCHEMISTRY (MOSCOW) 2013; 78:1137-45. [DOI: 10.1134/s0006297913100088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Blindauer CA, Sigel A, Operschall BP, Holý A, Sigel H. Extent of Intramolecular π Stacks in Aqueous Solution in Mixed-Ligand Copper(II) Complexes Formed by Heteroaromatic Amines and 1-[2-(Phosphonomethoxy)ethyl]cytosine (PMEC), a Relative of Antivirally Active Acyclic Nucleotide Analogues (Part 72) [1, 2]. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Rowinska-Zyrek M, Skilandat M, Sigel RKO. Hexaamminecobalt(III) - Probing Metal Ion Binding Sites in Nucleic Acids by NMR Spectroscopy. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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33
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Korth MMT, Sigel RKO. Unusually high-affinity Mg(2+) binding at the AU-rich sequence within the antiterminator hairpin of a Mg(2+) riboswitch. Chem Biodivers 2013; 9:2035-49. [PMID: 22976989 DOI: 10.1002/cbdv.201200031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mg(2+)-Responsive riboswitches represent a fascinating example of bifunctional RNAs that sense Mg(2+) ions with high selectivity and autonomously regulate the expression of Mg(2+)-transporter proteins. The mechanism of the mgtA riboswitch is scarcely understood, and a detailed structural analysis is called for to study how this RNA can selectively recognize Mg(2+) and respond by switching between two alternative stem loop structures. In this work, we investigated the structure and Mg(2+)-binding properties of the lower part of the antiterminator loop C from the mgtA riboswitch of Yersinia enterocolitica by solution NMR and report a discrete Mg(2+)-binding site embedded in the AU-rich sequence. At the position of Mg(2+) binding, the helical axis exhibits a distinct kink accompanied by a widening of the major groove, which accommodates the Mg(2+)-binding pocket. An unusually large overlap between two adenine residues on the opposite strands suggests that the bending may be sequence-induced by strong stacking interactions, enabling Mg(2+) to bind at this so-far not described metal-ion binding site.
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Affiliation(s)
- Maximiliane M T Korth
- Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, (phone: +41 44 635 4652; fax: +41 44 635 6802)
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34
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Complex formation of cadmium with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids. Met Ions Life Sci 2013; 11:191-274. [PMID: 23430775 DOI: 10.1007/978-94-007-5179-8_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono- to the di- and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono- or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.
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Abstract
The review addresses issues pertinent to Mn accumulation and its mechanisms of transport, its neurotoxicity and mechanisms of neurodegeneration. The role of mitochondria and glia in this process is emphasized. We also discuss gene x environment interactions, focusing on the interplay between genes linked to Parkinson's disease (PD) and sensitivity to Mn.
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Affiliation(s)
- Jerome Roth
- Department of Pharmacology and Toxicology, University at Buffalo School of Medicine, 11 Cary Hall, Buffalo, NY, 14214, USA
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Andreini C, Cavallaro G, Lorenzini S, Rosato A. MetalPDB: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2012; 41:D312-9. [PMID: 23155064 PMCID: PMC3531106 DOI: 10.1093/nar/gks1063] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal–macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy.
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Abstract
Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (http://www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70 000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 Å radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.
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Affiliation(s)
- Joachim Schnabl
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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