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Pallares RM, An DD, Hebert S, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Screening the complex biological behavior of late lanthanides through genome-wide interactions. Metallomics 2023; 15:mfad039. [PMID: 37336558 DOI: 10.1093/mtomcs/mfad039] [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: 01/03/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023]
Abstract
Despite their similar physicochemical properties, recent studies have demonstrated that lanthanides can display different biological behaviors. Hence, the lanthanide series can be divided into three parts, namely early, mid, and late lanthanides, based on their interactions with biological systems. In particular, the late lanthanides demonstrate distinct, but poorly understood biological activity. In the current study, we employed genome-wide functional screening to help understand biological effects of exposure to Yb(III) and Lu(III), which were selected as representatives of the late lanthanides. As a model organism, we used Saccharomyces cerevisiae, since it shares many biological functions with humans. Analysis of the functional screening results indicated toxicity of late lanthanides is consistent with disruption of vesicle-mediated transport, and further supported a role for calcium transport processes and mitophagy in mitigating toxicity. Unexpectedly, our analysis suggested that late lanthanides target proteins with SH3 domains, which may underlie the observed toxicity. This study provides fundamental insights into the unique biological chemistry of late lanthanides, which may help devise new avenues toward the development of decorporation strategies and bio-inspired separation processes.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Hospital, Forckenbeckstr. 55, Aachen 52074, Germany
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Solene Hebert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA
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2
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Alam MS, Leyva D, Michelin W, Fernandez-Lima F, Miksovska J. Distinct mechanism of Tb 3+ and Eu 3+ binding to NCS1. Phys Chem Chem Phys 2023; 25:9500-9512. [PMID: 36938969 PMCID: PMC10840756 DOI: 10.1039/d2cp05765d] [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] [Indexed: 03/02/2023]
Abstract
Lanthanides have been frequently used as biomimetic compounds for NMR and fluorescence studies of Ca2+ binding proteins due to having similar physical properties and coordination geometry to Ca2+ ions. Here we report that a member of the neuronal calcium sensor family, neuronal calcium sensor 1, complexes with two lanthanide ions Tb3+ and Eu3+. The affinity for Tb3+ is nearly 50 times higher than that for Ca2+ (Kd,Tb3+ = 0.002 ± 0.0001 μM and Kd, Ca2+ = 91 nM) whereas Eu3+ binding is notably weaker, Kd,Eu3+ = 26 ± 1 μM. Interestingly, despite having identical charge and similar ionic radii, Tb3+ and Eu3+ ions exhibit a distinct binding stoichiometry for NCS1 with one Eu3+ and two Tb3+ ions bound per NCS1 monomer, as demonstrated in fluorescence titration and mass spectrometry studies. These results suggest that the lanthanides' affinity for the individual EF hands is fine-tuned by a small variation in the ion charge density as well as EF hand binding loop amino acid sequence. As observed previously for other lanthanide:protein complexes, the emission intensity of Ln3+ is enhanced upon complexation with the protein, likely due to the displacement of water molecules by oxygen atoms from the coordinating amino acid residues. The overall shape of the Tb3+NCS1 and Eu3+NCS1 monomer shows high levels of similarity compared to the Ca2+ bound protein based on their collision cross section. However, the distinct occupation of EF hands impacts NCS1 oligomerization and affinity for the D2R peptide that mimics the NCS1 binding site on the D2R receptor. Specifically, the Tb3+NCS1 complex populates the dimer and has comparable affinity for the D2R peptide, whereas Eu3+ bound NCS1 remains in the monomeric form with a negligible affinity for the D2R peptide.
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Affiliation(s)
- Md Shofiul Alam
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Dennys Leyva
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Woodline Michelin
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Pallares R, An DD, Hébert S, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe CD, Abergel RJ. Identifying Toxicity Mechanisms Associated with Early Lanthanide Exposure through Multidimensional Genome-Wide Screening. ACS OMEGA 2022; 7:34412-34419. [PMID: 36188298 PMCID: PMC9521019 DOI: 10.1021/acsomega.2c04045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Lanthanides are a series of elements essential to a wide range of applications, from clean energy production to healthcare. Despite their presence in multiple products and technologies, their toxicological characteristics have been only partly studied. Recently, our group has employed a genomic approach to extensively characterize the toxicity mechanisms of lanthanides. Even though we identified substantially different behaviors for mid and late lanthanides, the toxicological profiles of early lanthanides remained elusive. Here, we overcome this gap by describing a multidimensional genome-wide toxicogenomic study for two early lanthanides, namely, lanthanum and praseodymium. We used Saccharomyces cerevisiae as a model system since its genome shares many biological pathways with humans. By performing functional analysis and protein-protein interaction network analysis, we identified the main genes and proteins that participate in the yeast response to counter metal harmful effects. Moreover, our analysis also highlighted key enzymes that are dysregulated by early lanthanides, inducing cytotoxicity. Several of these genes and proteins have human orthologues, indicating that they may also participate in the human response against the metals. By highlighting the key genes and proteins in lanthanide-induced toxicity, this work may contribute to the development of new prophylactic and therapeutic strategies against lanthanide harmful exposures.
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Affiliation(s)
- Roger
M. Pallares
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Dahlia D. An
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Solène Hébert
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Alex Loguinov
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Michael Proctor
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Jonathan A. Villalobos
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Kathleen A. Bjornstad
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Chris J. Rosen
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Chris D. Vulpe
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Rebecca J. Abergel
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Nuclear Engineering, University of California, Berkeley, California 94720, United States
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Mahmoodi Y, Mehrnejad F, Khanmohammadi S, Shahriari M, Rahimi F, Vakili MR, Lavasanifar A. Molecular insights into the crystalline nanocellulose and human lysozyme interactions: An experimental and theoretical research. Int J Biol Macromol 2022; 213:83-95. [PMID: 35598725 DOI: 10.1016/j.ijbiomac.2022.05.113] [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: 01/29/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
In the present research, we performed a combination of detailed computational and spectroscopic methods to determine the effect of crystalline nanocellulose (CNC) on the structure and dynamics of human lysozyme (hLyz). Fluorescence spectroscopy revealed static quenching as the major mechanism in forming a stable CNC-hLyz complex, and the binding was energetically favorable. The obtained values of the thermodynamic parameters (∆G, ∆H, and ∆S) proposed that the complex formation between the enzyme and cellulose nanocrystals is driven by electrostatic interactions, which were also confirmed by molecular dynamics (MD) simulation. Additionally, the MD simulation analysis displays that the enzyme's structural elements and tertiary structure were primarily maintained, and only loops regions were affected in the presence of cellulose nanocrystals. At the same time, circular dichroism (CD) outcomes highlighted that higher cellulose nanocrystals concentration caused a reduction in the secondary structure of hLyz. Our observations proved that low cellulose nanocrystals concentrations have no considerable effect on the human lysozyme structure. The current research results provide a valuable opportunity to elucidate the molecular interactions between protein and nanocelluloses, guiding further investigations of CNC-based material for biomedical, pharmaceutical, and food industry applications.
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Affiliation(s)
- Yasaman Mahmoodi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran.
| | - Somayeh Khanmohammadi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Masoud Shahriari
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Fereshteh Rahimi
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, 14395-1561 Tehran, Iran
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton AB T6G 2E1, Canada
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5
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Pallares RM, An DD, Hébert S, Faulkner D, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Multidimensional genome-wide screening in yeast provides mechanistic insights into europium toxicity. Metallomics 2021; 13:6409834. [PMID: 34694395 DOI: 10.1093/mtomcs/mfab061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022]
Abstract
Europium is a lanthanide metal that is highly valued in optoelectronics. Even though europium is used in many commercial products, its toxicological profile has only been partially characterized, with most studies focusing on identifying lethal doses in different systems or bioaccumulation in vivo. This paper describes a genome-wide toxicogenomic study of europium in Saccharomyces cerevisiae, which shares many biological functions with humans. By using a multidimensional approach and functional and network analyses, we have identified a group of genes and proteins associated with the yeast responses to ameliorate metal toxicity, which include metal discharge paths through vesicle-mediated transport, paths to regulate biologically relevant cations, and processes to reduce metal-induced stress. Furthermore, the analyses indicated that europium promotes yeast toxicity by disrupting the function of chaperones and cochaperones, which have metal-binding sites. Several of the genes and proteins highlighted in our study have human orthologues, suggesting they may participate in europium-induced toxicity in humans. By identifying the endogenous targets of europium as well as the already existing paths that can decrease its toxicity, we can determine specific genes and proteins that may help to develop future therapeutic strategies.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Solène Hébert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA
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6
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UÇAR B, ACAR T. Macroaggregated Albumin (MAA): Production, Size Optimization, Eu(III) and Tb(III) Complexes. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2021. [DOI: 10.18596/jotcsa.808636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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7
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Pujales-Paradela R, Carniato F, Uzal-Varela R, Brandariz I, Iglesias E, Platas-Iglesias C, Botta M, Esteban-Gómez D. A pentadentate member of the picolinate family for Mn(ii) complexation and an amphiphilic derivative. Dalton Trans 2019; 48:696-710. [PMID: 30547165 DOI: 10.1039/c8dt03856b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report a pentadentate ligand containing a 2,2'-azanediyldiacetic acid moiety functionalized with a picolinate group at the nitrogen atom (H3paada), as well as a lipophylic derivative functionalized with a dodecyloxy group at position 4 of the pyridyl ring (H3C12Opaada). The protonation constants of the paada3- ligand and the stability constant of the Mn(ii) complex were determined using a combination of potentiometric and spectrophotometric titrations (25 °C, 0.15 M NaCl). A detailed relaxometric characterisation was accomplished by recording 1H Nuclear Magnetic Relaxation Dispersion (NMRD) profiles and 17O chemical shifts and relaxation rates. These studies provide detailed information on the microscopic parameters that control their efficiency as relaxation agents in vitro. For the sake of completeness and to facilitate comparison, we also characterised the related [Mn(nta)]- complex (nta = nitrilotriacetate). Both the [Mn(paada)]- and [Mn(nta)]- complexes turned out to contain two inner-sphere water molecules in aqueous solution. The exchange rate of these coordinated water molecules was slower in [Mn(paada)]- (k298ex = 90 × 107 s-1) than in [Mn(nta)]- (k298ex = 280 × 107 s-1). The complexes were also characterised using both DFT (TPSSh/def2-TZVP) and ab initio CAS(5,5) calculations. The lipophylic [Mn(C12Opaada)]- complex forms micelles in solution characterised by a critical micellar concentration (cmc) of 0.31 ± 0.01 mM. This complex also forms a rather strong adduct with Bovine Serum Albumin (BSA) with an association constant of 5.5 × 104 M-1 at 25 °C. The enthalpy and entropy changes obtained for the formation of the adduct indicate that the binding event is driven by hydrophobic interactions.
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Affiliation(s)
- Rosa Pujales-Paradela
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Facultade de Ciencias, 15071, A Coruña, Galicia, Spain.
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8
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Mokaberi P, Reyhani V, Amiri-Tehranizadeh Z, Saberi MR, Beigoli S, Samandar F, Chamani J. New insights into the binding behavior of lomefloxacin and human hemoglobin using biophysical techniques: binary and ternary approaches. NEW J CHEM 2019. [DOI: 10.1039/c9nj01048c] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Demonstrates the overlap that had been induced between the fluorescence emission spectrum of Hb and the absorption spectrum of drugs, which has proved that there is a high probability to the occurrence of energy transfer from Hb and LMF in the absence and presence of NRF.
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Affiliation(s)
- Parisa Mokaberi
- Department of Biology
- Faculty of Sciences
- Mashhad Branch
- Islamic Azad University
- Mashhad
| | - Vida Reyhani
- Department of Biology
- Faculty of Sciences
- Mashhad Branch
- Islamic Azad University
- Mashhad
| | | | - Mohammad Reza Saberi
- Department of Medical Chemistry
- School of Pharmacy
- Mashhad University of Medical Sciences
- Mashhad
- Iran
| | - Sima Beigoli
- Endoscopic and Minimally Invasive Surgery Research Center
- Mashhad University of Medical Sciences
- Mashhad
- Iran
| | - Farzaneh Samandar
- Department of Biology
- Faculty of Sciences
- Mashhad Branch
- Islamic Azad University
- Mashhad
| | - Jamshidkhan Chamani
- Department of Biology
- Faculty of Sciences
- Mashhad Branch
- Islamic Azad University
- Mashhad
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9
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Galkina PА, Proskurnin МА. Supramolecular interaction of transition metal complexes with albumins and DNA: Spectroscopic methods of estimation of binding parameters. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Polina А. Galkina
- Moscow State M.V. Lomonosov University; Department of Chemistry; Leninskiye Gory 1, bld. 3 119991 Moscow Russia
| | - Мikhail А. Proskurnin
- Moscow State M.V. Lomonosov University; Department of Chemistry; Leninskiye Gory 1, bld. 3 119991 Moscow Russia
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10
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Plotnikova OA, Mel’nikov AG, Mel’nikov GV, Kovalenko AV. Luminescencence determination of ecotoxicants in protein-based media. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2017. [DOI: 10.1134/s1990793117040212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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The role of colloid particles in the albumin-lanthanides interaction: The study of aggregation mechanisms. Colloids Surf B Biointerfaces 2016; 146:507-13. [DOI: 10.1016/j.colsurfb.2016.06.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 11/19/2022]
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12
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Zhdanova NG, Shirshin EA, Maksimov EG, Panchishin IM, Saletsky AM, Fadeev VV. Tyrosine fluorescence probing of the surfactant-induced conformational changes of albumin. Photochem Photobiol Sci 2015; 14:897-908. [DOI: 10.1039/c4pp00432a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tyrosine fluorescence in native proteins is known to be effectively quenched, whereas its emission increases upon proteins’ unfolding.
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Affiliation(s)
- Nadezda G. Zhdanova
- Department of Physics
- M.V. Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Evgeny A. Shirshin
- Department of Physics
- M.V. Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Eugene G. Maksimov
- Department of Biology
- M.V. Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Ivan M. Panchishin
- Department of Physics
- M.V. Lomonosov Moscow State University
- Moscow 119991
- Russia
| | | | - Victor V. Fadeev
- Department of Physics
- M.V. Lomonosov Moscow State University
- Moscow 119991
- Russia
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