Modeling Zn²⁺ release from metallothionein

System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.

Physiological trade-off of marine fish under Zn deficient and excess conditions

Fish can regulate their Zn body bioaccumulation, but the mechanisms and physiological responses at the organ level are still largely unknown. In the present study, we exposed the marine seabreams under different Zn levels (deficient, optimum and excess levels) over a period of 4 weeks and examined how fish maintained its regulation of bioaccumulation with associated physiological effects at the fish intestinal organ. Our results indicated that fish intestinal organs constantly controlled the Zip family to "rob" more Zn under Zn-deficiency (with a dietary level of 7.9 mg/kg), whereas restricted the Zn efflux to preserve the intestinal function. Under Zn-excess conditions (193.3 mg/kg), the fish intestine maintained a limited Zn homeostasis (37.8-44.6 μg/mg) by initially inhibiting the influx through the Zip family receptor, but later accelerating both influx and efflux of Zn. Based on the WGCNA method, Zn deficient dietary exposure first resulted in defense response with subsequent switching to antioxidant defense. Instead, excess Zn first triggered the immunological response, but then led to physiological toxicity (abnormal in lipid metabolism). Although Zn had multiple biological functions, it was preferentially involved in lipid metabolism under different dietary Zn doses. This study provided direct evidence for Zn regulation at the organ level and detoxification mechanisms against potential environmental toxicity in fish.

The Molecular Basis for Zinc Bioavailability

Zinc is an essential micronutrient, and its deficiency is perhaps the most prevalent and least understood worldwide. Recent advances have expanded the understanding of zinc’s unique chemistry and molecular roles in a vast array of critical functions. However, beyond the concept of zinc absorption, few studies have explored the molecular basis of zinc bioavailability that determines the proportion of dietary zinc utilized in zinc-dependent processes in the body. The purpose of this review is to merge the concepts of zinc molecular biology and bioavailability with a focus on the molecular determinants of zinc luminal availability, absorption, transport, and utilization.

From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic

The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi-targeting strategy against SARS-CoV-2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+-sites in several SARS-CoV-2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+-bound, can be targeted using the same Zn-ejector drug (disulfiram/ebselen), which enables the use of broad-spectrum anti-virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn-ejector drug combined with other broad-spectrum anti-viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisStructure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Density Functional Theory.

An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species

Mammalian metallothioneins (MTs) are a group of cysteine-rich proteins that bind metal ions in two α- and β-domains and represent a major cellular Zn(II)/Cu(I) buffering system in the cell. At cellular free Zn(II) concentrations (10-11-10-9 M), MTs do not exist in fully loaded forms with seven Zn(II)-bound ions (Zn7MTs). Instead, MTs exist as partially metal-depleted species (Zn4-6MT) because their Zn(II) binding affinities are on the nano- to picomolar range comparable to the concentrations of cellular Zn(II). The mode of action of MTs remains poorly understood, and thus, the aim of this study is to characterize the mechanism of Zn(II) (un)binding to MTs, the thermodynamic properties of the Zn1-6MT2 species, and their mechanostability properties. To this end, native mass spectrometry (MS) and label-free quantitative bottom-up and top-down MS in combination with steered molecular dynamics simulations, well-tempered metadynamics (WT-MetaD), and parallel-bias WT-MetaD (amounting to 3.5 μs) were integrated to unravel the chemical coordination of Zn(II) in all Zn1-6MT2 species and to explain the differences in binding affinities of Zn(II) ions to MTs. Differences are found to be the result of the degree of water participation in MT (un)folding and the hyper-reactive character of Cys21 and Cys29 residues. The thermodynamics properties of Zn(II) (un)binding to MT2 are found to differ from those of Cd(II), justifying their distinctive roles. The potential of this integrated strategy in the investigation of numerous unexplored metalloproteins is attested by the results highlighted in the present study.

How the Local Environment of Functional Sites Regulates Protein Function

Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.

A comparison of computational methodologies for the structural modelling of biologically relevant zinc complexes

The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystallographic structures. While a previous study recommends incorporating relativistic effects into density functional theory calculations in order to improve the accuracy of obtained geometries for small Zn(II) coordination compounds, we show that, for the set in study, relativistic effects do not affect the geometries to a significant extent. The PBEh-3c composite method emerges as good alternative for the treatment of Zn(II) complexes, while the HF-3c method can be employed when computational efficiency is important. Graphical Abstract Which methods are best suited for the computation of Zn(II) bioligand complexes?

Mesoporous 3D network Ce-doped NiO nanoflakes as high performance electrodes for supercapacitor applications

In the present study, pristine NiO- and Ce (0.5, 1.0, 1.5, and 2%)-doped NiO nanoflakes were synthesised using the sol–gel method for supercapacitor applications.

The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair

The DNA base excision repair (BER) glycosylase MUTYH prevents DNA mutations by catalyzing adenine (A) excision from inappropriately formed 8-oxoguanine (8-oxoG):A mismatches. The importance of this mutation suppression activity in tumor suppressor genes is underscored by the association of inherited variants of MUTYH with colorectal polyposis in a hereditary colorectal cancer syndrome known as MUTYH-associated polyposis, or MAP. Many of the MAP variants encompass amino acid changes that occur at positions surrounding the two-metal cofactor-binding sites of MUTYH. One of these cofactors, found in nearly all MUTYH orthologs, is a [4Fe-4S]2+ cluster coordinated by four Cys residues located in the N-terminal catalytic domain. We recently uncovered a second functionally relevant metal cofactor site present only in higher eukaryotic MUTYH orthologs: a Zn2+ ion coordinated by three Cys residues located within the extended interdomain connector (IDC) region of MUTYH that connects the N-terminal adenine excision and C-terminal 8-oxoG recognition domains. In this work, we identified a candidate for the fourth Zn2+ coordinating ligand using a combination of bioinformatics and computational modeling. In addition, using in vitro enzyme activity assays, fluorescence polarization DNA binding assays, circular dichroism spectroscopy, and cell-based rifampicin resistance assays, the functional impact of reduced Zn2+ chelation was evaluated. Taken together, these results illustrate the critical role that the "Zn2+ linchpin motif" plays in MUTYH repair activity by providing for proper engagement of the functional domains on the 8-oxoG:A mismatch required for base excision catalysis. The functional importance of the Zn2+ linchpin also suggests that adjacent MAP variants or exposure to environmental chemicals may compromise Zn2+ coordination, and ability of MUTYH to prevent disease.

Crosstalk of the structural and zinc buffering properties of mammalian metallothionein-2

Structural insights into partially Zn(ii)-depleted MT2 species and their zinc buffering properties are presented and discussed.

The Application of Curve Fitting on the Voltammograms of Various Isoforms of Metallothioneins-Metal Complexes

The translation of metallothioneins (MTs) is one of the defense strategies by which organisms protect themselves from metal-induced toxicity. MTs belong to a family of proteins comprising MT-1, MT-2, MT-3, and MT-4 classes, with multiple isoforms within each class. The main aim of this study was to determine the behavior of MT in dependence on various externally modelled environments, using electrochemistry. In our study, the mass distribution of MTs was characterized using MALDI-TOF. After that, adsorptive transfer stripping technique with differential pulse voltammetry was selected for optimization of electrochemical detection of MTs with regard to accumulation time and pH effects. Our results show that utilization of 0.5 M NaCl, pH 6.4, as the supporting electrolyte provides a highly complicated fingerprint, showing a number of non-resolved voltammograms. Hence, we further resolved the voltammograms exhibiting the broad and overlapping signals using curve fitting. The separated signals were assigned to the electrochemical responses of several MT complexes with zinc(II), cadmium(II), and copper(II), respectively. Our results show that electrochemistry could serve as a great tool for metalloproteomic applications to determine the ratio of metal ion bonds within the target protein structure, however, it provides highly complicated signals, which require further resolution using a proper statistical method, such as curve fitting.

Zn(2+) at a cellular crossroads

Zinc is an essential micronutrient for cellular homeostasis. Initially proposed to only contribute to cellular viability through structural roles and non-redox catalysis, advances in quantifying changes in nM and pM quantities of Zn(2+) have elucidated increasing functions as an important signaling molecule. This includes Zn(2+)-mediated regulation of transcription factors and subsequent protein expression, storage and release of intracellular compartments of zinc quanta into the extracellular space which modulates plasma membrane protein function, as well as intracellular signaling pathways which contribute to the immune response. This review highlights some recent advances in our understanding of zinc signaling.