The connection of α- and β-domains in mammalian metallothionein-2 differentiates Zn(II) binding affinities, affects folding, and determines zinc buffering properties

Mammalian metallothioneins (MTs) are small Cys-rich proteins involved in Zn(II) and Cu(I) homeostasis. They bind seven Zn(II) ions in two distinct β- and α-domains, forming Zn3Cys9 and Zn4Cys11 clusters, respectively. After six decades of research, their role in cellular buffering of Zn(II) ions has begun to be understood recently. This is because of different affinities of bound ions and the proteins' coexistence in variously Zn(II)-loaded Zn4-7MT species in the cell. To date, it has remained unclear how these mechanisms of action occur and how the affinities are differentiated despite the Zn(S-Cys)4 coordination environment being the same. Here, we dissect the molecular basis of these phenomena by using several MT2 mutants, hybrid protein, and isolated domains. Through a combination of spectroscopic and stability studies, thiol(ate) reactivity, and steered molecular dynamics, we demonstrate that both protein folding and thermodynamics of Zn(II) ion (un)binding significantly differ between isolated domains and the whole protein. Close proximity reduces the degrees of freedom of separated domains, making them less dynamic. It is caused by the formation of intra- and interdomain electrostatic interactions. The energetic consequence of domains connection has a critical impact on the role of MTs in the cellular environment, where they function not only as a zinc sponge but also as a zinc buffering system keeping free Zn(II) in the right concentrations. Any change of that subtle system affects the folding mechanism, zinc site stabilities, and cellular zinc buffer components.

PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety

Protein phosphorylation is a post-translational modification that is essential to cellular signaling, cellular function, and associated disease progression. Bottom-up proteomics based on enzymatic digestion is the most widely used approach for identifying and quantifying phosphoproteins in complex biological samples. Researchers have largely optimized the experimental conditions for trypsin digestion, and it is now a routine procedure. However, trypsin digestion is impaired by the presence of phosphorylated residues in the protein sequence. This impairment arises from the fact that there are commonly salt bridges between a negatively charged phosphate group and the side chain of protonated arginine or lysine. On average, 55% of all phosphopeptides have their phosphosites located less than three amino acid residues from a cleavage site. Salt bridges reduce the cleavage accessibility for trypsin by masking the basic site chain groups of arginine and lysine. Thus, there are frequent missed cleavages in the vicinity of phosphorylation sites, thereby lessening both the depth of proteome coverage and the quantification accuracy of phosphoproteomics. In this work, we propose a method termed PhosphoShield to mitigate salt bridge formation by adding a digallium complex that exhibits a high binding affinity to the phosphate group. We tested our method using quantitative mass spectrometry analysis of the phosphoproteome of human liver cancer cells (HepG2). PhosphoShield enhances the cleavage frequency of at least 17% of tryptic phosphopeptides having cleavage sites close to the phosphate group.

Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome

The presence of Zn²⁺ at protein-protein interfaces modulates complex function, stability, and introduces structural flexibility/complexity, chemical selectivity, and reversibility driven in a Zn²⁺-dependent manner. Recent studies have demonstrated that dynamically changing Zn²⁺ affects numerous cellular processes, including protein-protein communication and protein complex assembly. How Zn²⁺-involved protein-protein interactions (ZPPIs) are formed and dissociate and how their stability and reactivity are driven in a zinc interactome remain poorly understood, mostly due to experimental obstacles. Here, we review recent research advances on the role of Zn²⁺ in the formation of interprotein sites, their architecture, function, and stability. Moreover, we underline the importance of zinc networks in intersystemic communication and highlight bioinformatic and experimental challenges required for the identification and investigation of ZPPIs.

Fabrication of Yb3+-Immobilized Hydrophilic Phytic-Acid-Coated Magnetic Nanocomposites for the Selective Separation of Bovine Hemoglobin from Bovine Serum

In this work, Yb³⁺-immobilized hydrophilic phytic-acid-coated magnetic nanocomposites were prepared through a facile route and used to selectively separatrf bovine hemoglobin. Hydrophilic phytic acid (PA) was coated onto the magnetic Fe₃O₄-PEI via electrostatic interactions, followed by finally chelating with Yb³⁺ ions, which could produce specific protein binding sites at room temperature in water, and complex instrumentation was not necessary. The performance of as-prepared hybrids (Fe₃O₄-PEI-PA-Yb³⁺) was assessed by selectively isolating bovine hemoglobin (BHb). The obtained maximum binding capacity was 347.3 mg g^-1. The retained BHb could be eluted under simple elution via using 0.1 M of Na₂CO₃, giving a recovery of 83%. Moreover, the generation of nanocomposites was demonstrated. In addition, the PA and PEI could improve the hydrophilicity of nanoparticles and further reduce the nonspecific adsorption. Therefore, such nanocomposites were successfully employed to selectively bind and separate BHb from bovine serum as verified by SDS-PAGE and MALDI-TOF MS analysis, providing a new perspective for the isolation of heme proteins in proteomics.

Risks of using EDTA as an agent for trace metals dosing in anaerobic digestion of olive mill solid waste

Low concentrations of trace elements in many organic wastes recommend their supplementation in order to avoid potential limitations. Different chelating agents have been used to ensure an adequate trace metal pool in the soluble fraction, by forming dissolved complexes. Ethylenediaminetetraacetic acid (EDTA) is probably the most common, although several negative effects could be associated with its usage. Biomethane potential tests were performed using Olive Mill Solid Waste as the substrate, supplementing different combinations of Fe, Co, Ni, Ba, always under the presence of EDTA. Results show that Ni and Co slightly recovered biodegradability. However, Ba supplementation resulted in worsening the methane yield coefficient in all cases. High concentration of EDTA led to decrease in the activity of anaerobic digestion. High availability of EDTA induces the capture of trace metals like Co or Ni, key trace metals for anaerobic biomass activity. While supplementing trace metals, the addition of Ba and/or EDTA must be carefully considered.