Coordination properties of dithiobutylamine (DTBA), a newly introduced protein disulfide reducing agent

Role of Explicit Solvation in Computational Modeling of Chemical Reactions: Mechanism of Cu(I) Transfer Between Thiolate-Based Chelators in Water

Solvation plays important roles in controlling the thermodynamic and kinetic aspects of chemical reactions. The conventional approaches to treat solvation via electronic structure methods are likely to become inadequate, when the reacting solutes have strong electrostatic and hydrogen bonding interactions with the solvent and undergo significant structural changes during the course of the reaction. In this article, we present evidence of such solvent and structural effects in the computational study of the Cu(I) transfer reaction between thiolate-based chelators dithiobutylamine (DTBA) and dithiotheritol (DTT) in water, inspired from biological copper trafficking phenomena. We propose a general solution to the problem by combining classical molecular dynamics (MD) simulations of the bulk system and static quantum chemistry calculations. The fluctuating solvation shell was estimated from MD, and energetics was assessed by averaging QM energies of a series of molecular clusters constructed from the MD snapshots. Applying this approach, we propose a reaction pathway with estimates of relative intermediate stabilities and barriers, which suggest the overall reaction to be reversible in nature and likely to go through both two and three coordinated intermediates, confirming previous studies of similar protein analogues. An interesting fact that emerged from our study was the strong indication that the rate-determining step is the deprotonation of initial thiol bound Cu(I) complex, without involving any Cu(I)-S bonds. The proposed method will lead to a better treatment of solvations, and these mechanistic insights will aid our understanding of biological copper(I) trafficking.

Differentiated Zn(II) binding affinities in animal, plant, and bacterial metallothioneins define their zinc buffering capacity at physiological pZn

Metallothioneins (MTs) are small, Cys-rich proteins present in various but not all organisms, from bacteria to humans. They participate in zinc and copper metabolism, toxic metals detoxification, and protection against reactive species. Structurally, they contain one or multiple domains, capable of binding a variable number of metal ions. For experimental convenience, biochemical characterization of MTs is mainly performed on Cd(II)-loaded proteins, frequently omitting or limiting Zn(II) binding features and related functions. Here, by choosing 10 MTs with relatively well-characterized structures from animals, plants, and bacteria, we focused on poorly investigated Zn(II)-to-protein affinities, stability-structure relations, and the speciation of individual complexes. For that purpose, MTs were characterized in terms of stoichiometry, pH-dependent Zn(II) binding, and competition with chromogenic and fluorescent probes. To shed more light on protein folding and its relation with Zn(II) affinity, reactivity of variously Zn(II)-loaded MTs was studied by (5,5'-dithiobis(2-nitrobenzoic acid) oxidation in the presence of mild chelators. The results show that animal and plant MTs, despite their architectural differences, demonstrate the same affinities to Zn(II), varying from nano- to low picomolar range. Bacterial MTs bind Zn(II) more tightly but, importantly, with different affinities from low picomolar to low femtomolar range. The presence of weak, moderate, and tight zinc sites is related to the folding mechanisms and internal electrostatic interactions. Differentiated affinities of all MTs define their zinc buffering capacity required for Zn(II) donation and acceptance at various free Zn(II) concentrations (pZn levels). The data demonstrate critical roles of individual Zn(II)-depleted MT species in zinc buffering processes.

Multipoint Immobilization at Inert Center of Papain on Homo-Functional Diazo-Activated Silica Support: A Way of Restoring "Above Room-Temperature" Bio-Catalytic Sustainability

Although enzymes play a significant role in industrial applications, their potential usage at high-level efficiency, particularly above room temperature, has not yet been fully harnessed. It brings above room-temperature catalytic sustainability of an immobilized (imm.) bio-catalyst as a long pending issue to improve enzyme stability, activity, specificity, or selectivity, particularly the enantio-selectivity over the native-enzymes. At this juncture, in a robust methodology, a heterogeneous solid phase bio-catalyst, {Si(OSi)₄(H₂O)_1.03}_n=328{OSi(CH₃)₂-NH-C₆H₄-N═N}₄{papain}(H₂O)₂₅₁, has efficiently been prepared by immobilizing papain on homo-functionalized SG (silica-gel) via multipoint covalent attachment. The bio-catalyst is easy to be recovered and reused multiple times. The homo-functional -N═N⁺, which appears on the SG-surface, makes the multipoint diazo-links with the inert center of the tyrosine-moiety to couple the enzyme where all the amino, thiol, phenol, and so forth, groups of the protein, including those that belong to the active-site, remain intact. The immobilized enzyme (13.9 μmol g^-1) swims in pore-water within the pore-channel, remains stable up to 70 ± 5 °C, and exhibits wider temperature adaptability in performing its hydrolyzing activities. The relative activity, 78 ± 2% at 27 °C, remains quantitative for 60 days and can be reused for 60 cycles with 53% activity at room-temperature. The thermal (relative activity: 87%; incubated at 70 ± 5 °C for 24 h) and mechanical (relative activity: 92%; incubated at 2500 rpm for 2 h at 27 °C) stability was outstanding.

Phytochelatins as a Dynamic System for Cd(II) Buffering from the Micro- to Femtomolar Range

Phytochelatins (PCs) are short Cys-rich peptides with repeating γ-Glu-Cys motifs found in plants, algae, certain fungi, and worms. Their biosynthesis has been found to be induced by heavy metals-both biogenic and toxic. Among all metal inducers, Cd(II) has been the most explored from a biological and chemical point of view. Although Cd(II)-induced PC biosynthesis has been widely examined, still little is known about the structure of Cd(II) complexes and their thermodynamic stability. Here, we systematically investigated glutathione (GSH) and PC2-PC6 systems, with regard to their complex stoichiometries and spectroscopic and thermodynamic properties. We paid special attention to the determination of stability constants using several complementary techniques. All peptides form CdL complexes, but CdL2 was found for GSH, PC2, and partially for PC3. Moreover, binuclear species CdxLy were identified for the series PC3-PC6 in an excess of Cd(II). Potentiometric and competition spectroscopic studies showed that the affinity of Cd(II) complexes increases from GSH to PC4 almost linearly from micromolar (log K7.4GSH = 5.93) to the femtomolar range (log K7.4PC4 = 13.39) and additional chain elongation does not increase the stability significantly. Data show that PCs form an efficient system which buffers free Cd(II) ions in the pico- to femtomolar range under cellular conditions, avoiding significant interference with Zn(II) complexes. Our study confirms that the favorable entropy change is the factor governing the elevation of phytochelatins' stability and illuminates the importance of the chelate effect in shifting the free Gibbs energy.

Metal Exchange in the Interprotein ZnII -Binding Site of the Rad50 Hook Domain: Structural Insights into CdII -Induced DNA-Repair Inhibition

CdII is a major genotoxic agent that readily displaces ZnII in a multitude of zinc proteins, abrogates redox homeostasis, and deregulates cellular metalloproteome. To date, this displacement has been described mostly for cysteine(Cys)-rich intraprotein binding sites in certain zinc finger domains and metallothioneins. To visualize how a ZnII -to-CdII swap can affect the target protein's status and thus understand the molecular basis of CdII -induced genotoxicity an intermolecular ZnII -binding site from the crucial DNA repair protein Rad50 and its zinc hook domain were examined. By using a length-varied peptide base, ZnII -to-CdII displacement in Rad50's hook domain is demonstrated to alter it in a bimodal fashion: 1) CdII induces around a two-orders-of-magnitude stabilization effect (log  K 12 Zn II =20.8 vs. log  K 12 Cd II =22.7), which defines an extremely high affinity of a peptide towards a metal ion, and 2) the displacement disrupts the overall assembly of the domain, as shown by NMR spectroscopic and anisotropy decay data. Based on the results, a new model explaining the molecular mechanism of CdII genotoxicity that underlines CdII 's impact on Rad50's dimer stability and quaternary structure that could potentially result in abrogation of the major DNA damage response pathway is proposed.

Metal binding properties of zinc fingers with a naturally altered metal binding site

Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a K_d of 10^-9 to 10^-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.

Biodegradation tests of mercaptocarboxylic acids, their esters, related divalent sulfur compounds and mercaptans

Mercaptocarboxylic acids and their esters, a class of difunctional compounds bearing both a mercapto and a carboxylic acid or ester functional group, are industrial chemicals of potential environmental concern. Biodegradation of such compounds was systematically investigated here, both by literature search and by experiments (Closed Bottle Test OECD 301D and Manometric Respirometry Test OECD 301F). These compounds were found either readily biodegradable or at least biodegradable to a significant extent. Some related compounds of divalent sulfur were tested for comparison (mercaptans, sulfides, disulfides). For the two relevant monofunctional compound classes, carboxylic acids/esters and mercaptans, literature data were compiled, and by comparison with structurally similar compounds without these functional groups, the influence of COOH/COOR' and SH groups on biodegradability was evaluated. Thereby, an existing rule of thumb for biodegradation of carboxylic acids/esters was supported by experimental data, and a rule of thumb could be formulated for mercaptans. Concurrent to biodegradation, abiotic processes were observed in the experiments, rapid oxidative formation of disulfides (dimerisation of monomercaptans and cyclisation of dimercaptans) and hydrolysis of esters. Some problems that compromise the reproducibility of biodegradation test results were discussed.

Activation of disulfide bond cleavage triggered by hydrophobization and lipophilization of functionalized dihydroasparagusic acid

Introduction of a hydrophilic group into dihydroasparagusic acid (DHAA) indicated higher reduction ability of disulfide in protein and lower air oxidation.

Molar absorption coefficients and stability constants of Zincon metal complexes for determination of metal ions and bioinorganic applications

Zincon (ZI) is one of the most common chromophoric chelating probes for the determination of Zn²⁺ and Cu²⁺ ions. It is also known to bind other metal ions. However, literature data on its binding properties and molar absorption coefficients are rather poor, varying among publications or determined only in certain conditions. There are no systematic studies on Zn²⁺ and Cu²⁺ affinities towards ZI performed under various conditions. However, this widely commercially available and inexpensive agent is frequently the first choice probe for the measurement of metal binding and release as well as determination of affinity constants of other ligands/macromolecules of interest. Here, we establish the spectral properties and the stability of ZI and its complexes with Zn²⁺, Cu²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺ and Pb²⁺ at multiple pH values from 6 to 9.9. The obtained results show that in water solution the MZI complex is predominant, but in the case of Co²⁺ and Ni²⁺, M(ZI)₂ complexes are also formed. The molar absorption coefficient at 618 nm for ZnZI and 599nm for CuZI complexes at pH7.4 in buffered (I=0.1M) water solutions are 24,200 and 26,100M^-1cm^-1, respectively. Dissociation constants of those complexes are 2.09×10^-6 and 4.68×10^-17M. We also characterized the metal-assisted Zincon decomposition. Our results provide new and reassessed optical and stability data that are applicable to a wide range of chemical and bioinorganic applications including metal ion detection, and quantification and affinity studies of ligands of interest.

SYNOPSIS

Accurate values of molar absorption coefficients of Zincon complex with Zn²⁺, Cd²⁺, Hg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Pb²⁺ for rapid metal ion quantification are provided. Zincon stability constants with Zn²⁺ and Cu²⁺ in a wide pH range were determined.

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn²⁺-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK₁₂ = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.

A photochromic-acidochromic HCl fluorescent probe. An unexpected chloride-directed recognition

Non-classical protomerism of Schiff bases offers several advantages; for example, specific interactions in the -C[double bond, length as m-dash]N- linkage can be controlled and differentiated because the interactions are not governed by keto-enol tautomerism. Herein, the pH sensing properties of a new protomeric Schiff base probe () are reported. In particular, among several acids, the probe displays significant optical responses upon interaction with hydrochloric acid (HCl). X-ray structural analysis confirmed the existence of an intermolecular interaction with HCl through a -C[double bond, length as m-dash]NH-ClO- linkage. Moreover, an optical response via a second channel is manifested as photochromic fluorescence behavior. The properties of were investigated by UV-vis and fluorescence spectroscopy in a solution and the solid state. Its strong acidofluorochromic behavior was analyzed and its pKa and values were determined, which revealed a photobasic character. Positive solvatochromism that resulted from specific interactions taking place in was studied using four different solvent scales, namely, Lippert-Mataga, Kamlet-Taft, Catalán and the recently proposed scale of Laurence et al., which yielded consistent results. Finally, theoretical calculations were conducted to analyze the mechanism of the probe in terms of natural transition orbitals (NTOs) and the spatial extent of charge transfer excitations.

The biological inorganic chemistry of zinc ions

The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the “mobile” zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn²⁺ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn²⁺ differs from s-block cations such as Ca²⁺ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.

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Zinc ions not bound to proteins have critical roles in cell biology.

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Zinc has a unique coordination chemistry, poorly appreciated in the biosciences.

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Its coordination chemistry is significantly different from that of calcium ions.

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Specific conditions apply for buffering cellular zinc ions.

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Investigations with zinc need to consider solution chemistry and metal buffering.

Use of Protein Folding Reagents

The reagents and methods for purification and use of the most commonly used denaturants, guanidine hydrochloride (guanidine-HCl) and urea, are described. Other protein denaturants and reagents used to fold proteins are briefly mentioned. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also described.

Isothermal Titration Calorimetry Measurements of Metal Ions Binding to Proteins

ITC measurements involving metal ions are susceptible to a number of competing reactions (oxidation, precipitation, and hydrolysis) and coupled reactions involving the buffer and protons. Stabilization and delivery of the metal ion as a well-defined and well-characterized complex with the buffer, or a specific ligand, can suppress undesired solution chemistry and, depending on the stability of the metal complex, allow accurate measurements of higher affinity protein-binding sites. This requires, however, knowledge of the thermodynamics of formation of the metal complex and accounting for its contribution to the experimentally measured values (KITC and ΔHITC) through a post hoc analysis that provides the condition-independent binding thermodynamics (K, ΔG(o), ΔH, ΔS, and ΔCP). This analysis also quantifies the number of protons that are displaced when the metal ion binds to the protein.

Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol (PAR): Revisiting common chelating probe for the study of metalloproteins

4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn(2+), Cd(2+), Hg(2+), Co(2+), Ni(2+), Cu(2+), Mn(2+) and Pb(2+) at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH7.4 in buffered water solution is 71,500 M(-1) cm(-1), and the dissociation constant of the complex in these conditions is 7.08×10(-13) M(2). To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.