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Planeta Kepp K. Bioinorganic Chemistry of Zinc in Relation to the Immune System. Chembiochem 2021; 23:e202100554. [PMID: 34889510 DOI: 10.1002/cbic.202100554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/09/2021] [Indexed: 01/18/2023]
Abstract
Zinc is well-known to have a central role in human inflammation and immunity and is itself an anti-inflammatory and antiviral agent. Despite its massively documented role in such processes, the underlying chemistry of zinc in relation to specific proteins and pathways of the immune system has not received much focus. This short review provides an overview of this topic, with emphasis on the structures of key proteins, zinc coordination chemistry, and probable mechanisms involved in zinc-based immunity, with some focus points for future chemical and biological research.
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Affiliation(s)
- Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800, Kongens Lyngby, Denmark
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Kühne IA, Barker A, Zhang F, Stamenov P, O'Doherty O, Müller-Bunz H, Stein M, Rodriguez BJ, Morgan GG. Modulation of Jahn-Teller distortion and electromechanical response in a Mn 3+spin crossover complex. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:404002. [PMID: 32208375 DOI: 10.1088/1361-648x/ab82d1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
Structural, magnetic and electromechanical changes resulting from spin crossover between the spin quintet and spin triplet forms of a mononuclear Mn3+complex embedded in six lattices with different charge balancing counterions are reported. Isostructural ClO4-and BF4-salts (1) and (2) each have two unique Mn3+sites which follow different thermal evolution pathways resulting in a crossover from the spin quintet form at room temperature to a 1:1 spin triplet:quintet ratio below 150 K. The PF6-(3) and NO3-(4) salts which each have one unique Mn3+site show a complete conversion from spin quintet to spin triplet over the same temperature range. A complete two step spin crossover is observed in the CF3SO3-lattice (5) with a 1:1 ratio of spin quintet and spin triplet forms at intermediate temperature, while the BPh4-lattice (6) stabilizes the spin triplet form over most of the temperature range with gradual and incomplete spin state switching above 250 K. An electromechanical piezoresponse was detected in NO3-complex4despite crystallization in a centrosymmetric space group. The role of deformations associated with stress-induced spin triplet-spin quintet switching in breaking the local symmetry are discussed and computational analysis is used to estimate the energy gap between the two spin states.
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Affiliation(s)
- Irina A Kühne
- School of Chemistry, University College Dublin (UCD), Dublin, Ireland
| | - Andrew Barker
- School of Chemistry, University College Dublin (UCD), Dublin, Ireland
| | - Fengyuan Zhang
- School of Physics and Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Plamen Stamenov
- School of Physics, Trinity College Dublin (TCD), Dublin, Ireland
| | - Oisín O'Doherty
- School of Chemistry, University College Dublin (UCD), Dublin, Ireland
| | - Helge Müller-Bunz
- School of Chemistry, University College Dublin (UCD), Dublin, Ireland
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Brian J Rodriguez
- School of Physics and Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Dublin, Ireland
| | - Grace G Morgan
- School of Chemistry, University College Dublin (UCD), Dublin, Ireland
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Nielsen MT, Moltved KA, Kepp KP. Electron Transfer of Hydrated Transition-Metal Ions and the Electronic State of Co3+(aq). Inorg Chem 2018; 57:7914-7924. [DOI: 10.1021/acs.inorgchem.8b01011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Mathias T. Nielsen
- DTU Chemistry, Technical University of Denmark, Building 206, Kongens Lyngby 2800, Denmark
| | - Klaus A. Moltved
- DTU Chemistry, Technical University of Denmark, Building 206, Kongens Lyngby 2800, Denmark
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, Kongens Lyngby 2800, Denmark
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Garla R, Kaur N, Bansal MP, Garg ML, Mohanty BP. Quantum mechanical treatment of As 3+-thiol model compounds: implication for the core structure of As(III)-metallothionein. J Mol Model 2017; 23:78. [PMID: 28210877 DOI: 10.1007/s00894-017-3247-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 01/23/2017] [Indexed: 12/27/2022]
Abstract
Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques. Computational modeling can be a reliable approach in predicting the molecular structures of such complexes. This paper presents the results of a systematic study on different As(III)-thiol model compounds conducted by both ab initio and DFT methods with different Gaussian type basis sets. Proficiency of these theoretical methods has been evaluated in terms of bond lengths, bond angles, free energy, partial atomic charges, computational cost, and comparison with the experimental data. It has been demonstrated that the DFT-B3LYP/6-311+G(3df) functional offers better accuracy in predicting the structure and the UV absorption spectra of As(III)-thiol complexes. The results of the present study also helps in defining the boundaries for the core of arsenic bound MT so that quantum mechanical/molecular mechanical (QM/MM) methods can be employed to predict the structural and functional aspects of the protein. Graphical Abstract Optimized structural parameters of As3+-thiol model compounds.
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Affiliation(s)
- Roobee Garla
- Department of Biophysics, Panjab University, Chandigarh, India, 160014
| | - Narinder Kaur
- Department of Biophysics, Panjab University, Chandigarh, India, 160014
| | | | - Mohan Lal Garg
- Department of Biophysics, Panjab University, Chandigarh, India, 160014
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Abstract
Iron complexes are important spin crossover (SCO) systems with vital roles in oxidative metabolism and promising technological potential. The SCO tendency depends on the free energy balance of high- and low-spin states, which again depends on physical effects such as dispersion, relativistic effects, and vibrational entropy. This work studied 30 different iron SCO systems with experimentally known thermochemical data, using 12 different density functionals. Remarkably general entropy-enthalpy compensation across SCO systems was identified (R = 0.82, p = 0.002) that should be considered in rational SCO design. Iron(II) complexes displayed higher ΔH and ΔS values than iron(III) complexes and also less steep compensation effects. First-coordination sphere ΔS values computed from numerical frequencies reproduce most of the experimental entropy and should thus be included when modeling spin-state changes in inorganic chemistry (R = 0.52, p = 3.4 × 10(-3); standard error in TΔS ≈ 4.4 kJ/mol at 298 K vs 16 kJ/mol of total TΔS on average). Zero-point energies favored high-spin states by 9 kJ/mol on average. Interestingly, dispersion effects are surprisingly large for the SCO process (average: 9 kJ/mol, but up to 33 kJ/mol) and favor the more compact low-spin state. Relativistic effects favor low-spin by ∼9 kJ/mol on average, but up to 24 kJ/mol. B3LYP*, TPSSh, B2PLYP, and PW6B95 performed best for the typical calculation scheme that includes ZPE. However, if relativistic and dispersion effects are included, only B3LYP* remained accurate. On average, high-spin was favored by LYP by 11-15 kJ/mol relative to other correlation functionals, and by 4.2 kJ/mol per 1% HF exchange in hybrids. 13% HF exchange was optimal without dispersion, and 15% was optimal with all effects included for these systems.
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Affiliation(s)
- Kasper P Kepp
- DTU Chemistry, Technical University of Denmark , Building 206, Lyngby DK-2800, Denmark
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Abstract
Mammalian metallothioneins (MTs) comprise a Zn3Cys9 cluster in the β domain and a Zn4Cys11 cluster in the α domain. They play a crucial role in storing and donating Zn(2+) ions to target metalloproteins and have been implicated in several diseases, thus understanding how MTs release Zn(2+) is of widespread interest. In this work, we present a strategy to compute the free energy for releasing Zn(2+) from MTs using a combination of classical molecular dynamics (MD) simulations, quantum-mechanics/molecular-mechanics (QM/MM) minimizations, and continuum dielectric calculations. The methodology is shown to reproduce the experimental observations that (1) the Zn-binding sites do not have equal Zn(2+) affinity and (2) the isolated β domain is thermodynamically less stable and releases Zn(2+) faster with oxidizing agents than the isolated α domain. It was used to compute the free energies for Zn(2+) release from the metal cluster in the absence and presence of the protein matrix (protein architecture and coupled protein-water interactions) to yield the respective disulfide-bonded product. The results show the importance of the protein matrix as well as protein dynamics and coupled conformational changes in accounting for the differential Zn(2+)-releasing propensity of the two domains with oxidizing agents.
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Affiliation(s)
- C Satheesan Babu
- Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan , R.O.C
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Affiliation(s)
- Kasper P Kepp
- DTU Chemistry, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark.
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He Y, Chen S, Liu Y, Liang Y, Xiang J, Wu D, Zhou F. Coordination of Bi3+ to metal-free metallothionein: spectroscopy and density functional calculation of structure, coordination, and electronic excitations. J Inorg Biochem 2012; 113:9-14. [PMID: 22687489 DOI: 10.1016/j.jinorgbio.2012.02.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 02/15/2012] [Accepted: 02/15/2012] [Indexed: 11/24/2022]
Abstract
Understanding the structure of mammal Bi-containing metallothionein-2 (Bi-MT2) is of great physiological significance due to the importance of Bi-MT2 in alleviating adverse effect of anti-cancer drugs. A unique feature of rabbit liver Bi-MT2 is the metal-oxygen bond (BiO), which is absent in well-characterized Zn-MT2 and Cd-MT2. However, the ligand contributing to the BiO bonding in Bi-MT2 remains unidentified. In this study, the coordination of Bi(3+) to rabbit liver metal-free metallothionein was investigated using both experimental and theoretical methods. UV-visible and circular dichroism spectra indicate that Bi-MT2 has a different secondary structure from those of Zn-MT2 and Cd-MT2. Three possible Bi(3+) coordination structures in Bi(7)-MT2 and relative binding free energies were calculated using the density functional theory. Absorption spectra corresponding to these coordination structures were evaluated by time-dependent density functional theory. Our computation results are consistent with the UV-vis spectroscopic data and strongly suggest that the carboxyl group in the aspartic acid residues contributes to the BiO bond formation.
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Affiliation(s)
- Yonghui He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
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Greisen P, Jespersen JB, Kepp KP. Metallothionein Zn2+- and Cu2+-clusters from first-principles calculations. Dalton Trans 2011; 41:2247-56. [PMID: 22183579 DOI: 10.1039/c1dt11785h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Detailed electronic structures of Zn(II) and Cu(II) clusters from metallothioneins (MT) have been obtained using density functional theory (DFT), in order to investigate how oxidative stress-caused Cu(II) intermediates affect Zn-binding to MT and cooperatively lead to Cu(I)MT. The inferred accuracy is ∼0.02-0.03 Å for metal-thiolate bond lengths for the models that are the most realistic MT models so far studied by DFT. We find terminal Zn-S and Cu-S bond lengths of 2.35-2.38 Å and 2.30-2.34 Å, whereas bridging M-S bonds are 0.05-0.11 Å longer. This electronic effect is also reflected in changes in electron density on bridging sulfurs. Various imposed backbone constraints quantify the sensitivity of cluster electronic structure towards protein conformational changes. The large negative charge densities of the clusters are central to MT function, and the smaller β-clusters are more prone to modification. Oxidative stress-associated Cu(II) binding weakens the Zn-S bonds and is thus likely to impair the Zn(II) transfer function of MTs, providing a mechanism for cooperative Cu(II) binding leading to loss of Zn(II) and dysfunctional Cu(I)MT clusters.
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Affiliation(s)
- Per Greisen
- Technical University of Denmark, DTU Physics, 2800, Kongens Lyngby, Denmark
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Kepp KP. Full quantum-mechanical structure of the human protein Metallothionein-2. J Inorg Biochem 2011; 107:15-24. [PMID: 22178664 DOI: 10.1016/j.jinorgbio.2011.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/02/2011] [Accepted: 11/08/2011] [Indexed: 01/18/2023]
Abstract
Metallothioneins (MT) are small, metal-binding proteins with diverse functions related to metal ion homeostasis. This paper presents the full 384-388-atom structures of the two native Zn(II)- and the Cd(II)-containing domains of human MT2, optimized with density functional theory. The presented structures are accurate to ~0.03 Å for bond lengths and thus provide new physical insight into the detailed electronic structures of MTs, in particular with accurate accounts of bridging vs. terminal bonds not available from NMR or EXAFS. The MT protein enhances the asymmetry, as compared to the protein-free clusters, causing a hierarchy in binding that most likely allows MTs to transfer ions to multiple targets in vivo. The protein polarization is substantial and occurs primarily via the terminal sulfurs, a key mechanism in providing domain-specific electronic structures. The β-domain polarizes its smaller cluster less on average, due to its less polarizable, higher negative charge density, as reflected in longer MS bond lengths and smaller bond orders. This may explain why MT2β is more reactive and dynamic and why MTs have evolved two different-size, asymmetric domains with different metal binding affinities fit for different molecular targets of metal ion transfer.
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Affiliation(s)
- Kasper P Kepp
- Technical University of Denmark, DTU Chemistry, DK-2800 Kgs. Lyngby, Denmark.
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