1
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Mishra V, Pathak AK, Bandyopadhyay T. Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study. J Biomol Struct Dyn 2023; 41:7318-7328. [PMID: 36099177 DOI: 10.1080/07391102.2022.2120080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO22+). A total of six sets of initial coordinates are used for Zn2+-HSA and UO22+-HSA system at pH = 4, 7.4 and 9, respectively. Enhance sampling method, namely, well-tempered meta-dynamics (WT-MtD) is employed to study the binding and un-binding processes of UO22+ and Zn2+ ions. Potential of mean force (PMF) profiles are generated for all the six sets of complexes from the converged WT-MtD run. Various basins and barriers are observed along the (un)binding pathways. Hydrogen bond dynamics and short-range Coulomb interactions are evaluated from the equilibrium run at each basins and barriers for both the ions at all pH values. The binding of UO22+ ion with HSA is the result of the dynamical balance between UO22+-HSA and UO22+-water short range Coulomb interactions. Zn2+ ion interact more strongly than UO22+ at all pH through short range Coulomb interactions. PMF values further concludes that UO22+ cannot associate to the Zn2+ bound HSA protein but can be captured by free HSA at all pH values i.e. endosomal, alkaline and physiological pH.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijayakriti Mishra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Arup Kumar Pathak
- Homi Bhabha National Institute, Mumbai, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Tusar Bandyopadhyay
- Homi Bhabha National Institute, Mumbai, India
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
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2
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Indrakumar S, Kulakova A, Harris P, Peters GHJ. Dynamics of Human Serum Transferrin in Varying Physicochemical Conditions Explored by Using Molecular Dynamics Simulations. Mol Pharm 2022; 19:2795-2806. [PMID: 35776490 DOI: 10.1021/acs.molpharmaceut.2c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational stability of human serum transferrin (Tf) at varying pH values and salt and excipient concentrations were investigated using molecular dynamics (MD) simulations, and the results are compared with previously published small-angle X-ray scattering (SAXS) experiments. SAXS study showed that at pH 5, Tf is predominantly present in a partially open (PO) form, and the factions of PO differ based on the physicochemical condition and drift toward the closed form (HO) as the pH increases. Tf is a bilobal glycoprotein that is composed of homologous halves termed the N- and C-lobes. The current study shows that the protonation of Y188 and K206 at pH 5 is the primary conformational drive into PO, which shifts toward the closed (HO) conformer as the pH increases. Furthermore, at pH 6.5, PO is unfavorable due to negative charge-charge repulsion at the N/C-lobe interface linker region causing increased hinge distance when compared to HO, which has favorable attractive electrostatic interactions in this region. Subsequently, the effect of salt concentration was studied at 70 and 140 mM NaCl. At 70 mM NaCl and pH 5, chloride ions bind strongly in the N-lobe iron-binding site, whereas these interactions are weak at pH 6.5. With increasing salt concentration at pH 5, the regions surrounding the N-lobe iron-binding site are saturated, and as a consequence, sodium and chloride ions accumulate into the bulk. Additionally, protein-excipient interactions were investigated. At pH 5, the excipients interact in similar loop regions, E89-T93, and D416-D420, located in the N- and C-lobes of the HO conformer, respectively. It is anticipated that interactions of additives in these two loop regions cause conformational changes that lead to iron-coordinating residues in the N-lobe to drift away from iron and thus drive HO to PO conversion. Furthermore, at pH 6.5 and 140 mM histidine, these interactions are negligible leading to the stabilization of HO.
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Affiliation(s)
- Sowmya Indrakumar
- Technical University of Denmark, Department of Chemistry, 2800 Kgs. Lyngby, Denmark
| | - Alina Kulakova
- Technical University of Denmark, Department of Chemistry, 2800 Kgs. Lyngby, Denmark
| | - Pernille Harris
- Technical University of Denmark, Department of Chemistry, 2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Technical University of Denmark, Department of Chemistry, 2800 Kgs. Lyngby, Denmark
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3
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Fındık BK, Cilesiz U, Bali SK, Atilgan C, Aviyente V, Dedeoglu B. Investigation of iron release from the N- and C-lobes of human serum transferrin by quantum chemical calculations. Org Biomol Chem 2022; 20:8766-8774. [DOI: 10.1039/d2ob01518h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cluster models of iron binding sites of the N- and C-lobes highlights the inequivalence of each lobe in iron release.
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Affiliation(s)
- Basak Koca Fındık
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Umut Cilesiz
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Semiha Kevser Bali
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı-Tuzla, Istanbul, 34956, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Bogazici University, Istanbul, 34342, Bebek, Turkey
| | - Burcu Dedeoglu
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey
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4
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Silva AM, Moniz T, de Castro B, Rangel M. Human transferrin: An inorganic biochemistry perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Mishra L, Sundararajan M, Bandyopadhyay T. MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH. Proteins 2020; 89:193-206. [PMID: 32892408 DOI: 10.1002/prot.26006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/13/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023]
Abstract
The iron carrier human serum transferrin (sTf) is known to transport other metals, including some actinides (An). Radiotoxic An are routinely involved in the nuclear fuel cycle and the possibility of their accidental exposure cannot be ruled out. Understanding An interaction with sTf assumes a greater significance for the development of safe and efficacious chelators for their removal from the blood stream. Here we report several 100 ns equilibrium MD simulations of Cm(III)- and Th(IV)-loaded sTf at various protonation states of the protein to explore the possibility of the two An ions release and speciation. The results demonstrate variation in protonation state of dilysine pair (K206 and K296) and the tyrosine (Y188) residue is necessary for the opening of Cm(III)-bound protein and the release of the ion. For the tetravalent thorium, protonation of dilysine pair suffices to cause conformational changes of protein. However, in none of the protonation states, Th(IV) releases from sTf because of its strong electrostatic interaction with D63 in the first shell of the sTf binding cleft. Analysis of hydrogen bond, water bridge, and the evaluation of potential of mean forces of the An ions' release from sTf, substantiate the differential behavior of Cm(III) and Th(IV) at endosomal pH. The results provide insight in the regulation of Cm(III) and Th(IV) bioavailability that may prove useful for effective design of their decorporating agents and as well may help the future design of radiotherapy based on tetravalent ions.
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Affiliation(s)
- Lokpati Mishra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai, India.,Department of Chemical Sciences, Homi Bhabha National Institute, Mumbai, India
| | | | - Tusar Bandyopadhyay
- Department of Chemical Sciences, Homi Bhabha National Institute, Mumbai, India.,Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India
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6
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Benjamín-Rivera JA, Cardona-Rivera AE, Vázquez-Maldonado ÁL, Dones-Lassalle CY, Pabón-Colon HL, Rodríguez-Rivera HM, Rodríguez I, González-Espiet JC, Pazol J, Pérez-Ríos JD, Catala-Torres JF, Carrasquillo Rivera M, De Jesus-Soto MG, Cordero-Virella NA, Cruz-Maldonado PM, González-Pagan P, Hernández-Ríos R, Gaur K, Loza-Rosas SA, Tinoco AD. Exploring Serum Transferrin Regulation of Nonferric Metal Therapeutic Function and Toxicity. INORGANICS 2020; 8:48. [PMID: 36844373 PMCID: PMC9957567 DOI: 10.3390/inorganics8090048] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Serum transferrin (sTf) plays a pivotal role in regulating iron biodistribution and homeostasis within the body. The molecular details of sTf Fe(III) binding blood transport, and cellular delivery through transferrin receptor-mediated endocytosis are generally well-understood. Emerging interest exists in exploring sTf complexation of nonferric metals as it facilitates the therapeutic potential and toxicity of several of them. This review explores recent X-ray structural and physiologically relevant metal speciation studies to understand how sTf partakes in the bioactivity of key non-redox active hard Lewis acidic metals. It challenges preconceived notions of sTf structure function correlations that were based exclusively on the Fe(III) model by revealing distinct coordination modalities that nonferric metal ions can adopt and different modes of binding to metal-free and Fe(III)-bound sTf that can directly influence how they enter into cells and, ultimately, how they may impact human health. This knowledge informs on biomedical strategies to engineer sTf as a delivery vehicle for metal-based diagnostic and therapeutic agents in the cancer field. It is the intention of this work to open new avenues for characterizing the functionality and medical utility of nonferric-bound sTf and to expand the significance of this protein in the context of bioinorganic chemistry.
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Affiliation(s)
- Josué A. Benjamín-Rivera
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Andrés E. Cardona-Rivera
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | | | | | - Héctor L. Pabón-Colon
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | | | - Israel Rodríguez
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Jean C. González-Espiet
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Jessika Pazol
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Jobaniel D. Pérez-Ríos
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - José F. Catala-Torres
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | | | - Michael G. De Jesus-Soto
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | | | - Paola M. Cruz-Maldonado
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Patricia González-Pagan
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Raul Hernández-Ríos
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Kavita Gaur
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
| | - Sergio A. Loza-Rosas
- Departamento de Química y Bioquímica, Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja 150003, Colombia
| | - Arthur D. Tinoco
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00931, USA)
- Correspondence: ; Tel.: +1-939-319-9701
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7
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Reilley DJ, Fuller JT, Nechay MR, Victor M, Li W, Ruberry JD, Mujika JI, Lopez X, Alexandrova AN. Toxic and Physiological Metal Uptake and Release by Human Serum Transferrin. Biophys J 2020; 118:2979-2988. [PMID: 32497515 PMCID: PMC7300305 DOI: 10.1016/j.bpj.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/03/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022] Open
Abstract
An atomistic understanding of metal transport in the human body is critical to anticipate the side effects of metal-based therapeutics and holds promise for new drugs and drug delivery designs. Human serum transferrin (hTF) is a central part of the transport processes because of its ubiquitous ferrying of physiological Fe(III) and other transition metals to tightly controlled parts of the body. There is an atomistic mechanism for the uptake process with Fe(III), but not for the release process, or for other metals. This study provides initial insight into these processes for a range of transition metals-Ti(IV), Co(III), Fe(III), Ga(III), Cr(III), Fe(II), Zn(II)-through fully atomistic, extensive quantum mechanical/discrete molecular dynamics sampling and provides, to our knowledge, a new technique we developed to calculate relative binding affinities between metal cations and the protein. It identifies protonation of Tyr188 as a trigger for metal release rather than protonation of Lys206 or Lys296. The study identifies the difficulty of metal release from hTF as potentially related to cytotoxicity. Simulations identify a few critical interactions that stabilize the metal binding site in a flexible, nuanced manner.
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Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Jack T Fuller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Michael R Nechay
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Marie Victor
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; Institut Lumire Matire, Villeurbanne, France
| | - Wei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Josiah D Ruberry
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia, International Physics Center, Donostia, Euskadi, Spain
| | - Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia, International Physics Center, Donostia, Euskadi, Spain
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California.
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8
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Reilley DJ, Hennefarth MR, Alexandrova AN. The Case for Enzymatic Competitive Metal Affinity Methods. ACS Catal 2020; 10:2298-2307. [PMID: 34012720 PMCID: PMC8130888 DOI: 10.1021/acscatal.9b04831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David J Reilley
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Matthew R Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, USA
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9
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Platts JA. Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191562. [PMID: 32257321 PMCID: PMC7062105 DOI: 10.1098/rsos.191562] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/10/2019] [Indexed: 06/11/2023]
Abstract
We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal-peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict a priori possible binding modes as a precursor to longer, atomistic simulations.
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10
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Mishra L, Sundararajan M, Bandyopadhyay T. Molecular dynamics simulations of plutonium binding and its decorporation from the binding-cleft of human serum transferrin. J Biol Inorg Chem 2020; 25:213-231. [PMID: 31980924 DOI: 10.1007/s00775-020-01753-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/03/2020] [Indexed: 11/29/2022]
Abstract
The possibility of plutonium (Pu) intake by radiation workers can not be ruled out. Transportation of Pu(IV) to various organs/cells is mainly carried through iron-carrying protein, serum transferrin (sTf), by receptor-mediated endocytosis. Understanding the Pu-sTf interaction is a primary step toward future design of its decorporating agents. We report MD simulations of Pu(IV) binding with sTf and look out for its decorporation at extracellular pH using suitable ligands. MD simulations were carried out in polarizable water environment at different protonation states of the protein. Results unravel the binding motif of Pu(IV): (1) sTf binds the ion in closed conformation at extracellular serum pH with carbonate as synergistic anions, (2) change in protonation state of dilysine (K206 and K296)-trigger and that of the carbonate ion at acidic endosomal pH is found to cause conformational changes of protein, conducive for the heavy ion to be released, although; (3) strong electrostatic interaction between D63 in the binding-cleft and Pu(IV) is found not to ever set free the ion. In an endeavour to decorporate Pu(IV), fragmented molecular form of hydroxypyridinone (HOPO) and catechol (CAM)-based ligands are docked at the binding site (BS) of the protein and metadynamics simulations are conducted. Pu(IV) binding at BS is found to be so strong that it was not detached from BS with the docked HOPO. However, for the identical set of simulation parameters, CAM is found to facilitate dislodging the heavy ion from the protein's binding influence. Differential behaviour of the two chelators is further explored. Fragmented molecular form of hydroxy-pyridinone (HOPO) and catecholamide (CAM) ligands were docked at the binding-site (BS) of human serum transferrin (sTf) to explore their feasibility as plausible Pu(IV) decorporating agents by employing metadynamics method. CAM was found to dislodge Pu from the sTf BS, while HOPO could not.
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Affiliation(s)
- Lokpati Mishra
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400 085, India
| | - Tusar Bandyopadhyay
- Homi Bhabha National Institute, Mumbai, 400094, India. .,Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
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11
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Dalla Torre G, Mujika JI, Lachowicz JI, Ramos MJ, Lopez X. The interaction of aluminum with catecholamine-based neurotransmitters: can the formation of these species be considered a potential risk factor for neurodegenerative diseases? Dalton Trans 2019; 48:6003-6018. [PMID: 30688329 DOI: 10.1039/c8dt04216k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The potential neurotoxic role of Al(iii) and its proposed link with the insurgence of Alzheimer's Disease (AD) have attracted increasing interest towards the determination of the nature of bioligands that are propitious to interact with aluminum. Among them, catecholamine-based neurotransmitters have been proposed to be sensitive to the presence of this non-essential metal ion in the brain. In the present work, we characterize several aluminum-catecholamine complexes in various stoichiometries, determining their structure and thermodynamics of formation. For this purpose, we apply a recently validated computational protocol with results that show a remarkably good agreement with the available experimental data. In particular, we employ Density Functional Theory (DFT) in conjunction with continuum solvation models to calculate complexation energies of aluminum for a set of four important catecholamines: l-DOPA, dopamine, noradrenaline and adrenaline. In addition, by means of the Quantum Theory of Atoms in Molecules (QTAIM) and Energy Decomposition Analysis (EDA) we assessed the nature of the Al-ligand interactions, finding mainly ionic bonds with an important degree of covalent character. Our results point at the possibility of the formation of aluminum-catecholamine complexes with favorable formation energies, even when proton/aluminum competition is taken into account. Indeed, we found that these catecholamines are better aluminum binders than catechol at physiological pH, because of the electron withdrawing effect of the positively-charged amine that decreases their deprotonation penalty with respect to catechol. However, overall, our results show that, in an open biological environment, the formation of Al-catecholamine complexes is not thermodynamically competitive when compared with the formation of other aluminum species in solution such as Al-hydroxide, or when considering other endogenous/exogenous Al(iii) ligands such as citrate, deferiprone and EDTA. In summary, we rule out the possibility, suggested by some authors, that the formation of Al-catecholamine complexes in solution might be behind some of the toxic roles attributed to aluminum in the brain. An up-to-date view of the catecholamine biosynthesis pathway with sites of aluminum interference (according to the current literature) is presented. Alternative mechanisms that might explain the deleterious effects of this metal on the catecholamine route are thoroughly discussed, and new hypotheses that should be investigated in future are proposed.
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Affiliation(s)
- Gabriele Dalla Torre
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain.
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12
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Azarkh M, Gast P, Mason AB, Groenen EJJ, Mathies G. Analysis of the EPR spectra of transferrin: the importance of a zero-field-splitting distribution and 4 th-order terms. Phys Chem Chem Phys 2019; 21:16937-16948. [PMID: 31339131 DOI: 10.1039/c9cp02626f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Multi-frequency EPR spectroscopy can provide high-level structural information on high-spin Fe3+ sites in proteins and enzymes. Unfortunately, analysis of the EPR spectra of these spin systems is hindered by the presence of broad distributions in the zero-field-splitting (ZFS) parameters, which reflect conformational heterogeneity of the iron sites. We present the analysis of EPR spectra of high-spin Fe3+ bound to human serum transferrin. We apply a method termed the grid-of-errors to extract the distributions of the individual ZFS parameters from EPR spectra recorded in the high-field limit at a microwave frequency of 275 GHz. Study of a series of transferrin variants shows that the ZFS distributions are as characteristic of the structure of a high-spin Fe3+ site as the ZFS parameters themselves. Simulations based on the extracted ZFS distributions reproduce spectra recorded at 34 GHz (Q band) and 9.7 GHz (X band), including subtle variations that were previously difficult to quantify. The X-band spectrum of transferrin shows a characteristic double peak, which has puzzled researchers for decades. We show that the double peak is uniquely related to the term B4-3O4-3(S) in the spin Hamiltonian. Our method is generally applicable in the analysis of spectra that arise from a broad distribution of parameters.
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Affiliation(s)
- Mykhailo Azarkh
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany.
| | - Peter Gast
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Anne B Mason
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Edgar J J Groenen
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Guinevere Mathies
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany.
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Gocheva G, Ivanova A. A Look at Receptor–Ligand Pairs for Active-Targeting Drug Delivery from Crystallographic and Molecular Dynamics Perspectives. Mol Pharm 2019; 16:3293-3321. [DOI: 10.1021/acs.molpharmaceut.9b00250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gergana Gocheva
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Anela Ivanova
- Sofia University “St. Kliment Ohridski”, Faculty of Chemistry and Pharmacy, 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
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14
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D'Haese PC, Douglas G, Verhulst A, Neven E, Behets GJ, Vervaet BA, Finsterle K, Lürling M, Spears B. Human health risk associated with the management of phosphorus in freshwaters using lanthanum and aluminium. CHEMOSPHERE 2019; 220:286-299. [PMID: 30590295 DOI: 10.1016/j.chemosphere.2018.12.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/05/2018] [Accepted: 12/11/2018] [Indexed: 05/22/2023]
Abstract
The use of geo-engineering materials to manage phosphorus in lakes has increased in recent years with aluminium and lanthanum based materials being most commonly applied. Hence the potential impact of the use of these compounds on human health is receiving growing interest. This review seeks to understand, evaluate and compare potential unintended consequences on human health and ecotoxicological risks associated with the use of lanthanum- and aluminium-based materials to modify chemical and ecological conditions in water bodies. In addition to their therapeutic use for the reduction of intestinal phosphate absorption in patients with impaired renal function, the phosphate binding capacity of aluminium and lanthanum also led to the development of materials used for water treatment. Although lanthanum and aluminium share physicochemical similarities and have many common applications, their uptake and kinetics within the human body and living organisms importantly differ from each other which is reflected in a different toxicity profile. Whilst a causal role in the development of neurological pathologies, skeletal lesions, hematopoietic disorders and respiratory effects has unequivocally been demonstrated with increased exposure to aluminium, studies until now have failed to find such a clear association after exposure to lanthanum although caution is warranted. Our review indicates that lanthanum and aluminium have a distinctly different profile with respect to their potential effects on human health. Regular monitoring of both aluminium and lanthanum concentrations in lanthanum-/aluminium-treated water by the responsible authorities is recommended to avoid acute accidental or chronic low level accumulation.
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Affiliation(s)
- Patrick C D'Haese
- Laboratory of Pathophysiology, University of Antwerp, Antwerp, Belgium.
| | | | - Anja Verhulst
- Laboratory of Pathophysiology, University of Antwerp, Antwerp, Belgium
| | - Ellen Neven
- Laboratory of Pathophysiology, University of Antwerp, Antwerp, Belgium
| | - Geert J Behets
- Laboratory of Pathophysiology, University of Antwerp, Antwerp, Belgium
| | | | - Karin Finsterle
- Abteilung Limnologie, Institut Dr. Nowak, Mayenbrook 1, 28870 Ottersberg, Germany
| | - Miquel Lürling
- Department of Environmental Sciences, Wageningen University, Wageningen, the Netherlands
| | - Bryan Spears
- Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK
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15
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Mishra L, Sawant PD, Sundararajan M, Bandyopadhyay T. Binding of Cm(III) and Th(IV) with Human Transferrin at Serum pH: Combined QM and MD Investigations. J Phys Chem B 2019; 123:2729-2744. [PMID: 30864809 DOI: 10.1021/acs.jpcb.8b09473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human serum transferrin (sTf) can also function as a noniron metal transporter since only 30% of it is typically saturated with a ferric ion. While this function of sTf can be fruitfully utilized for targeted delivery of certain metal therapeutics, it also runs the risk of trafficking the lethal radionuclides into cells. A large number of actinide (An) ions are known to bind to the iron sites of sTf although molecular-level understanding of their binding is unclear. Understanding the radionuclide interaction with sTf is a primary step toward future design of their decorporating agents since irrespective of the means of contamination, the radionuclides are absorbed and transported by blood before depositing into target organs. Here, we report an extensive multiscale modeling approach of two An (curium(III) and thorium(IV)) ions' binding with sTf at serum physiological pH. We find that sTf binds both the heavy ions in a closed conformation with carbonate as synergistic anions and the An-loaded sTf maintains its closed conformation even after 100 ns of equilibrium molecular dynamics (MD) simulations. MD simulations are performed in a polarizable water environment, which also incorporates electronic continuum corrections for ions via charge rescaling. The molecular details of the An coordination and An exchange free energies with iron in the interdomain cleft of the protein are evaluated through a combination of quantum mechanical (QM) and MD studies. In line with reported experimental observations, well-tempered metadynamics results of the ions' binding energetics show that An-sTf complexes are less stable than Fe-sTf. Additionally, curium(III) is found to bind more weakly than thorium(IV). The latter result might suggest relative attenuation of thorium(IV) cytotoxicity when compared with curium(III).
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16
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Quantum chemical studies of structures and spin Hamiltonian parameters of iron transferrin using isolated and embedded clusters models. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1591-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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García Daza FA, Bonilla MR, Llordés A, Carrasco J, Akhmatskaya E. Atomistic Insight into Ion Transport and Conductivity in Ga/Al-Substituted Li 7La 3Zr 2O 12 Solid Electrolytes. ACS APPLIED MATERIALS & INTERFACES 2019; 11:753-765. [PMID: 30540169 DOI: 10.1021/acsami.8b17217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Garnet-structured Li7La3Zr2O12 is a promising solid electrolyte for next-generation solid-state Li batteries. However, sufficiently fast Li-ion mobility required for battery applications only emerges at high temperatures, upon a phase transition to cubic structure. A well-known strategy to stabilize the cubic phase at room temperature relies on aliovalent substitution; in particular, the substitution of Li+ by Al3+ and Ga3+ ions. Yet, despite having the same formal charge, Ga3+ substitution yields higher conductivities (10-3 S/cm) than Al3+ (10-4 S/cm). The reason of such difference in ionic conductivity remains a mystery. Here, we use molecular dynamic simulations and advanced sampling techniques to precisely unveil the atomistic origin of this phenomenon. Our results show that Li+ vacancies generated by Al3+ and Ga3+ substitution remain adjacent to Ga3+ and Al3+ ions, without contributing to the promotion of Li+ mobility. However, while Ga3+ ions tend to allow limited Li+ diffusion within their immediate surroundings, the less repulsive interactions associated with Al3+ ions lead to a complete blockage of neighboring Li+ diffusion paths. This effect is magnified at lower temperatures and explains the higher conductivities observed for Ga-substituted systems. Overall, this study provides a valuable insight into the fundamental ion transport mechanism in the bulk of Ga/Al-substituted Li7La3Zr2O12 and paves the way for rationalizing aliovalent substitution design strategies for enhancing ionic transport in these materials.
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Affiliation(s)
- Fabián A García Daza
- BCAM-Basque Center for Applied Mathematics , Alameda de Mazarredo 14 , E-48009 Bilbao , Spain
| | - Mauricio R Bonilla
- BCAM-Basque Center for Applied Mathematics , Alameda de Mazarredo 14 , E-48009 Bilbao , Spain
| | - Anna Llordés
- CIC EnergiGUNE , Albert Einstein 48 , E-01510 Miñano , Spain
- IKERBASQUE , Basque Foundation for Science , María Díaz de Haro 3 , E-48013 Bilbao , Spain
| | - Javier Carrasco
- CIC EnergiGUNE , Albert Einstein 48 , E-01510 Miñano , Spain
| | - Elena Akhmatskaya
- BCAM-Basque Center for Applied Mathematics , Alameda de Mazarredo 14 , E-48009 Bilbao , Spain
- IKERBASQUE , Basque Foundation for Science , María Díaz de Haro 3 , E-48013 Bilbao , Spain
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18
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Nhan C, Rix CJ, May BK, Hung A. Temperature-induced structural changes of apo-lactoferrin and their functional implications: a molecular dynamics simulation study. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1562187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Carol Nhan
- School of Science, RMIT University, Bundoora Campus, Melbourne, Australia
| | - Colin J. Rix
- School of Science, RMIT University, City Campus, Melbourne, Australia
| | - Bee K. May
- School of Science, RMIT University, Bundoora Campus, Melbourne, Australia
| | - Andrew Hung
- School of Science, RMIT University, City Campus, Melbourne, Australia
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19
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Abdizadeh H, Atilgan AR, Atilgan C, Dedeoglu B. Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics 2018; 9:1513-1533. [PMID: 28967944 DOI: 10.1039/c7mt00216e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.
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Affiliation(s)
- H Abdizadeh
- Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı 34956, Tuzla, Istanbul, Turkey.
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20
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Adam N, Trumm M, Smith VC, MacGillivray RTA, Panak PJ. Incorporation of transuranium elements: coordination of Cm(iii) to human serum transferrin. Dalton Trans 2018; 47:14612-14620. [DOI: 10.1039/c8dt02915f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure determination of Cm(iii)-transferrin by a combined spectroscopic and theoretical approach gives insight into the biochemical behaviour of incorporated actinides.
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Affiliation(s)
- Nicole Adam
- Karlsruhe Institute of Technology (KIT)
- Campus North
- Institute for Nuclear Waste Disposal (INE)
- 76021 Karlsruhe
- Germany
| | - Michael Trumm
- Karlsruhe Institute of Technology (KIT)
- Campus North
- Institute for Nuclear Waste Disposal (INE)
- 76021 Karlsruhe
- Germany
| | - Val C. Smith
- University of British Columbia
- Department of Biochemistry and Molecular Biology and Centre for Blood Research
- Vancouver
- Canada
| | - Ross T. A. MacGillivray
- University of British Columbia
- Department of Biochemistry and Molecular Biology and Centre for Blood Research
- Vancouver
- Canada
| | - Petra J. Panak
- Karlsruhe Institute of Technology (KIT)
- Campus North
- Institute for Nuclear Waste Disposal (INE)
- 76021 Karlsruhe
- Germany
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21
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Ghanbari Z, Housaindokht M, Bozorgmehr M, Izadyar M. Effects of synergistic and non-synergistic anions on the iron binding site from serum transferrin: A molecular dynamic simulation analysis. J Mol Graph Model 2017; 78:176-186. [DOI: 10.1016/j.jmgm.2017.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 11/15/2022]
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22
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Abdizadeh H, Atilgan AR, Atilgan C. Mechanisms by Which Salt Concentration Moderates the Dynamics of Human Serum Transferrin. J Phys Chem B 2017; 121:4778-4789. [DOI: 10.1021/acs.jpcb.7b02380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Haleh Abdizadeh
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
| | - Ali Rana Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
| | - Canan Atilgan
- Sabanci University, Faculty of Engineering and Natural Sciences, Tuzla, 34956 Istanbul, Turkey
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23
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Escribano B, Lozano A, Radivojević T, Fernández-Pendás M, Carrasco J, Akhmatskaya E. Enhancing sampling in atomistic simulations of solid-state materials for batteries: a focus on olivine
$$\hbox {NaFePO}_4$$
NaFePO
4. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2064-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis. J Theor Biol 2016; 404:73-81. [PMID: 27235585 DOI: 10.1016/j.jtbi.2016.05.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/10/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022]
Abstract
Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure.
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25
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Grande-Aztatzi R, Formoso E, Mujika JI, Ugalde JM, Lopez X. Phosphorylation promotes Al(iii) binding to proteins: GEGEGSGG as a case study. Phys Chem Chem Phys 2016; 18:7197-207. [DOI: 10.1039/c5cp06379e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aluminum, the third most abundant element in the Earth's crust and one of the key industrial components of our everyday life, has been associated with several neurodegenerative diseases due to its ability to promote neurofilament tangles and β-amyloid peptide aggregation.
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Affiliation(s)
- Rafael Grande-Aztatzi
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Elena Formoso
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jon I. Mujika
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jesus M. Ugalde
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Xabier Lopez
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
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26
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Yin JJ, Zhou ZW, Zhou SF. Cyclodextrin-based targeting strategies for tumor treatment. Drug Deliv Transl Res 2015; 3:364-74. [PMID: 25788282 DOI: 10.1007/s13346-013-0140-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The efficacy and applicability of anticancer drugs are greatly restricted by severe systemic toxicities and drug resistance. Targeting drug delivery strategies have been developed to prevent the shortcomings of chemotherapy. Among various approaches to specifically target drug-loaded carrier systems to the required pathological sites, ligand-attached cyclodextrin-based targeting complexes are a promising drug delivery system, which is achieved mainly through specific molecular interactions between the drugs and cell surface receptors. The principal targeting tactics include conjugation of cyclodextrin with targeting moieties or encapsulation drugs in cyclodextrins. The cyclodextrin-based supramolecules, polymers, or nanoparticles bearing bioactive substances such as folate, estrogens, carbohydrates, peptides, etc. have been reviewed.
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Affiliation(s)
- Juan-Juan Yin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
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27
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Exley C, Mold MJ. The binding, transport and fate of aluminium in biological cells. J Trace Elem Med Biol 2015; 30:90-5. [PMID: 25498314 DOI: 10.1016/j.jtemb.2014.11.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 11/13/2014] [Indexed: 11/17/2022]
Abstract
Aluminium is the most abundant metal in the Earth's crust and yet, paradoxically, it has no known biological function. Aluminium is biochemically reactive, it is simply that it is not required for any essential process in extant biota. There is evidence neither of element-specific nor evolutionarily conserved aluminium biochemistry. This means that there are no ligands or chaperones which are specific to its transport, there are no transporters or channels to selectively facilitate its passage across membranes, there are no intracellular storage proteins to aid its cellular homeostasis and there are no pathways which evolved to enable the metabolism and excretion of aluminium. Of course, aluminium is found in every compartment of every cell of every organism, from virus through to Man. Herein we have investigated each of the 'silent' pathways and metabolic events which together constitute a form of aluminium homeostasis in biota, identifying and evaluating as far as is possible what is known and, equally importantly, what is unknown about its uptake, transport, storage and excretion.
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Affiliation(s)
- Christopher Exley
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire ST5 5BG, UK.
| | - Matthew J Mold
- The Birchall Centre, Lennard-Jones Laboratories, Keele University, Staffordshire ST5 5BG, UK
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28
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Abdizadeh H, Atilgan AR, Atilgan C. Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH. J Biol Inorg Chem 2015; 20:705-18. [DOI: 10.1007/s00775-015-1256-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/10/2015] [Indexed: 11/30/2022]
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29
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Luque N, Mujika JI, Formoso E, Lopez X. Aluminum interaction with 2,3-diphosphoglyceric acid. A computational study. RSC Adv 2015. [DOI: 10.1039/c5ra06796k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Favorable formation of aluminum–2,3-DPG complexes in a variety of forms: 1 : 1, 1 : 2 and ternary complexes with citrate.
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Affiliation(s)
- Noelia Luque
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jon I. Mujika
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Elena Formoso
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Xabier Lopez
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
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30
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Exploring the Fe(III) binding sites of human serum transferrin with EPR at 275 GHz. J Biol Inorg Chem 2014; 20:487-96. [DOI: 10.1007/s00775-014-1229-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/10/2014] [Indexed: 10/24/2022]
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31
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Willhite CC, Karyakina NA, Yokel RA, Yenugadhati N, Wisniewski TM, Arnold IMF, Momoli F, Krewski D. Systematic review of potential health risks posed by pharmaceutical, occupational and consumer exposures to metallic and nanoscale aluminum, aluminum oxides, aluminum hydroxide and its soluble salts. Crit Rev Toxicol 2014; 44 Suppl 4:1-80. [PMID: 25233067 PMCID: PMC4997813 DOI: 10.3109/10408444.2014.934439] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract Aluminum (Al) is a ubiquitous substance encountered both naturally (as the third most abundant element) and intentionally (used in water, foods, pharmaceuticals, and vaccines); it is also present in ambient and occupational airborne particulates. Existing data underscore the importance of Al physical and chemical forms in relation to its uptake, accumulation, and systemic bioavailability. The present review represents a systematic examination of the peer-reviewed literature on the adverse health effects of Al materials published since a previous critical evaluation compiled by Krewski et al. (2007) . Challenges encountered in carrying out the present review reflected the experimental use of different physical and chemical Al forms, different routes of administration, and different target organs in relation to the magnitude, frequency, and duration of exposure. Wide variations in diet can result in Al intakes that are often higher than the World Health Organization provisional tolerable weekly intake (PTWI), which is based on studies with Al citrate. Comparing daily dietary Al exposures on the basis of "total Al"assumes that gastrointestinal bioavailability for all dietary Al forms is equivalent to that for Al citrate, an approach that requires validation. Current occupational exposure limits (OELs) for identical Al substances vary as much as 15-fold. The toxicity of different Al forms depends in large measure on their physical behavior and relative solubility in water. The toxicity of soluble Al forms depends upon the delivered dose of Al(+3) to target tissues. Trivalent Al reacts with water to produce bidentate superoxide coordination spheres [Al(O2)(H2O4)(+2) and Al(H2O)6 (+3)] that after complexation with O2(•-), generate Al superoxides [Al(O2(•))](H2O5)](+2). Semireduced AlO2(•) radicals deplete mitochondrial Fe and promote generation of H2O2, O2 (•-) and OH(•). Thus, it is the Al(+3)-induced formation of oxygen radicals that accounts for the oxidative damage that leads to intrinsic apoptosis. In contrast, the toxicity of the insoluble Al oxides depends primarily on their behavior as particulates. Aluminum has been held responsible for human morbidity and mortality, but there is no consistent and convincing evidence to associate the Al found in food and drinking water at the doses and chemical forms presently consumed by people living in North America and Western Europe with increased risk for Alzheimer's disease (AD). Neither is there clear evidence to show use of Al-containing underarm antiperspirants or cosmetics increases the risk of AD or breast cancer. Metallic Al, its oxides, and common Al salts have not been shown to be either genotoxic or carcinogenic. Aluminum exposures during neonatal and pediatric parenteral nutrition (PN) can impair bone mineralization and delay neurological development. Adverse effects to vaccines with Al adjuvants have occurred; however, recent controlled trials found that the immunologic response to certain vaccines with Al adjuvants was no greater, and in some cases less than, that after identical vaccination without Al adjuvants. The scientific literature on the adverse health effects of Al is extensive. Health risk assessments for Al must take into account individual co-factors (e.g., age, renal function, diet, gastric pH). Conclusions from the current review point to the need for refinement of the PTWI, reduction of Al contamination in PN solutions, justification for routine addition of Al to vaccines, and harmonization of OELs for Al substances.
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Affiliation(s)
- Calvin C. Willhite
- Risk Sciences International, Ottawa, ON, Canada
- McLaughlin Centre for Population Health Risk Assessment, Ottawa, ON, Canada
| | | | - Robert A. Yokel
- Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | | | - Thomas M. Wisniewski
- Departments of Neurology, Psychiatry and Pathology, New York University School of Medicine, New York City, New York, USA
| | - Ian M. F. Arnold
- Occupational Health Program, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Franco Momoli
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Daniel Krewski
- Risk Sciences International, Ottawa, ON, Canada
- McLaughlin Centre for Population Health Risk Assessment, Ottawa, ON, Canada
- Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Luque NB, Mujika JI, Rezabal E, Ugalde JM, Lopez X. Mapping the affinity of aluminum(iii) for biophosphates: interaction mode and binding affinity in 1 : 1 complexes. Phys Chem Chem Phys 2014; 16:20107-19. [DOI: 10.1039/c4cp02770a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions. Biochem J 2014; 461:33-42. [DOI: 10.1042/bj20140133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human serum transferrin is susceptible to modification under elevated glycaemic conditions, such as those encountered in diabetes mellitus. The study of transferrin glycation shows that key amino acid residues undergo glycation, inducing structural alterations that compromise its function as an iron-binding protein.
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Mujika JI, Ugalde JM, Lopez X. Aluminum Interaction with Glutamate and α-Ketoglutarate: A Computational Study. J Phys Chem B 2014; 118:6680-6. [DOI: 10.1021/jp502724w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. I. Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea
(UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - J. M. Ugalde
- Kimika Fakultatea, Euskal Herriko Unibertsitatea
(UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - X. Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea
(UPV/EHU) and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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Mujika JI, Rezabal E, Mercero JM, Ruipérez F, Costa D, Ugalde JM, Lopez X. Aluminium in biological environments: a computational approach. Comput Struct Biotechnol J 2014; 9:e201403002. [PMID: 24757505 PMCID: PMC3995234 DOI: 10.5936/csbj.201403002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 03/07/2014] [Accepted: 03/23/2014] [Indexed: 12/02/2022] Open
Abstract
The increased availability of aluminium in biological environments, due to human intervention in the last century, raises concerns on the effects that this so far “excluded from biology” metal might have on living organisms. Consequently, the bioinorganic chemistry of aluminium has emerged as a very active field of research. This review will focus on our contributions to this field, based on computational studies that can yield an understanding of the aluminum biochemistry at a molecular level. Aluminium can interact and be stabilized in biological environments by complexing with both low molecular mass chelants and high molecular mass peptides. The speciation of the metal is, nonetheless, dictated by the hydrolytic species dominant in each case and which vary according to the pH condition of the medium. In blood, citrate and serum transferrin are identified as the main low molecular mass and high molecular mass molecules interacting with aluminium. The complexation of aluminium to citrate and the subsequent changes exerted on the deprotonation pathways of its tritable groups will be discussed along with the mechanisms for the intake and release of aluminium in serum transferrin at two pH conditions, physiological neutral and endosomatic acidic. Aluminium can substitute other metals, in particular magnesium, in protein buried sites and trigger conformational disorder and alteration of the protonation states of the protein's sidechains. A detailed account of the interaction of aluminium with proteic sidechains will be given. Finally, it will be described how alumnium can exert oxidative stress by stabilizing superoxide radicals either as mononuclear aluminium or clustered in boehmite. The possibility of promotion of Fenton reaction, and production of hydroxyl radicals will also be discussed.
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Affiliation(s)
- Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Elixabete Rezabal
- Laboratoire de Chimie Moleculaire, Department of Chemistry, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
| | - Jose M Mercero
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Fernando Ruipérez
- POLYMAT, Euskal Herriko Unibertsitatea UPV/EHU. Joxe Mari Korta zentroa, Tolosa Etorbidea 72, 20018 Donostia-San Sebastián, Euskadi, Spain
| | - Dominique Costa
- Laboratoire de Physico-Chimie des Surfaces (UMR 7045), ENSCP Chimie-Paristech, 11 rue P. et M. Curie, 75005 Paris, France
| | - Jesus M Ugalde
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
| | - Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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Iron and bismuth bound human serum transferrin reveals a partially-opened conformation in the N-lobe. Sci Rep 2012; 2:999. [PMID: 23256035 PMCID: PMC3525939 DOI: 10.1038/srep00999] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/26/2012] [Indexed: 11/17/2022] Open
Abstract
Human serum transferrin (hTF) binds Fe(III) tightly but reversibly, and delivers it to cells via a receptor-mediated endocytosis process. The metal-binding and release result in significant conformational changes of the protein. Here, we report the crystal structures of diferric-hTF (FeNFeC-hTF) and bismuth-bound hTF (BiNFeC-hTF) at 2.8 and 2.4 Å resolutions respectively. Notably, the N-lobes of both structures exhibit unique “partially-opened” conformations between those of the apo-hTF and holo-hTF. Fe(III) and Bi(III) in the N-lobe coordinate to, besides anions, only two (Tyr95 and Tyr188) and one (Tyr188) tyrosine residues, respectively, in contrast to four residues in the holo-hTF. The C-lobe of both structures are fully closed with iron coordinating to four residues and a carbonate. The structures of hTF observed here represent key conformers captured in the dynamic nature of the transferrin family proteins and provide a structural basis for understanding the mechanism of metal uptake and release in transferrin families.
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