Full quantum-mechanical structure of the human protein Metallothionein-2

Bioinorganic Chemistry of Zinc in Relation to the Immune System

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.

Electrostatic regulation of blue copper sites

In the last 50 years, the blue copper proteins became central targets of investigation. Extensive experiments focused on the Cu coordination to probe the effect of local perturbations on its properties. We found that local electric fields, generated by charged residues evolutionarily placed throughout the protein edifice, mainly second sphere, but also more remotely, constitute an additional significant factor regulating blue copper proteins. These fields are not random, but exhibit a highly specific directionality, negative with respect to the and vectors in the Cu first shell. The field magnitude contributes to fine-tuning of the geometric and electronic properties of Cu sites in individual blue copper proteins. Specifically, the local electric fields evidently control the Cu–S_Met bond distance, Cu(ii)–S_Cys bond covalency, and the energies of the frontier molecular orbitals, which, in turn, govern the Cu(ii/i) reduction potential and the relative absorption intensities at 450 nm and 600 nm.

Intramolecular electric fields in blue copper proteins are oriented in a fixed way to modulate properties of their copper sites: they control the first-shell copper interactions to influence geometric, spectroscopic, and redox behavior.

The Function of Transthyretin Complexes with Metallothionein in Alzheimer's Disease

Alzheimer’s disease (AD) is one of the most frequently diagnosed types of dementia in the elderly. An important pathological feature in AD is the aggregation and deposition of the β-amyloid (Aβ) in extracellular plaques. Transthyretin (TTR) can cleave Aβ, resulting in the formation of short peptides with less activity of amyloid plaques formation, as well as being able to degrade Aβ peptides that have already been aggregated. In the presence of TTR, Aβ aggregation decreases and toxicity of Aβ is abolished. This may prevent amyloidosis but the malfunction of this process leads to the development of AD. In the context of Aβplaque formation in AD, we discuss metallothionein (MT) interaction with TTR, the effects of which depend on the type of MT isoform. In the brains of patients with AD, the loss of MT-3 occurs. On the contrary, MT-1/2 level has been consistently reported to be increased. Through interaction with TTR, MT-2 reduces the ability of TTR to bind to Aβ, while MT-3 causes the opposite effect. It increases TTR-Aβ binding, providing inhibition of Aβ aggregation. The protective effect, assigned to MT-3 against the deposition of Aβ, relies also on this mechanism. Additionally, both Zn₇MT-2 and Zn₇MT-3, decrease Aβ neurotoxicity in cultured cortical neurons probably because of a metal swap between Zn₇MT and Cu(II)Aβ. Understanding the molecular mechanism of metals transfer between MT and other proteins as well as cognition of the significance of TTR interaction with different MT isoforms can help in AD treatment and prevention.

Ab initio electronic structure calculations of entire blue copper azurins

We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants.

Quantum mechanical treatment of As3+-thiol model compounds: implication for the core structure of As(III)-metallothionein

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.

Toxicity of Glutathione-Binding Metals: A Review of Targets and Mechanisms

Mercury, cadmium, arsenic and lead are among priority metals for toxicological studies due to the frequent human exposure and to the significant burden of disease following acute and chronic intoxication. Among their common characteristics is chemical affinity to proteins and non-protein thiols and their ability to generate cellular oxidative stress by the best-known Fenton mechanism. Their health effects are however diverse: kidney and liver damage, cancer at specific sites, irreversible neurological damages with metal-specific features. Mechanisms for the induction of oxidative stress by interaction with the cell thiolome will be presented, based on literature evidence and of experimental findings.

Modeling Zn²⁺ release from metallothionein

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.

Coordination of Bi3+ to metal-free metallothionein: spectroscopy and density functional calculation of structure, coordination, and electronic excitations

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.