Axial assembly of AuNR for tumor theranostics via Zn2+-GSH chelation induced degradation of AuNR@ZIF-8 heterostructures

Tumor microenvironment responsive photothermal ablation is a noninvasive and accurately targeted approach for cancer therapy. Herein, an intracellular directional assembly strategy for enhanced photothermal therapy (PTT) was realized by using ZIF-8 encapsulated Au nanorod (AuNR) heterostructure as the precursor of photothermal convertible material. The ZIF-8 shell selectively degraded in tumor cells upon the chelation between GSH and Zn2+, while the as-formed Zn(SG) connected the released AuNR in end-to-end fashion. The coating of ZIF-8 shell significantly improves the stability and targeting of AuNR, and the released Zn2+ shielded the GSH binding site on the lateral side of AuNR, increased the plasmonic coupling efficiency of AuNR assembly geometer. This design enabled atomic-economical, efficient and low-side effect targeted photothermal therapy through the effective integration of heterostructures.

Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands

We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.

The Mechanochemistry of a Structural Zinc Finger

Zinc fingers are highly ubiquitous structural motifs that provide stability to proteins, thus contributing to their correct folding. Despite the high thermodynamic stability of the ZnCys4 centers, their kinetic properties display remarkable lability. Here, we use a combination of protein engineering with single molecule force spectroscopy atomic force microscopy (AFM) to uncover the surprising mechanical lability (∼90 pN) of the individual Zn-S bonds that form the two equivalent zinc finger motifs embedded in the structure of the multidomain DnaJ chaperone. Rational mutations within the zinc coordinating residues enable direct identification of the chemical determinants that regulate the interplay between zinc binding-requiring the presence of all four cysteines-and disulfide bond formation. Finally, our observations show that binding to hydrophobic short peptides drastically increases the mechanical stability of DnaJ. Altogether, our experimental approach offers a detailed, atomistic vista on the fine chemical mechanisms that govern the nanomechanics of individual, naturally occurring zinc finger.

Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization

DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy. By combining biochemical and structural approaches, the physical target of 2-thioxanthine (2TX), an uncompetitive inhibitor of Fpg, was identified. 2TX interacts with the zinc finger (ZnF) DNA binding domain of the enzyme. This explains why the zincless hNEIL1 enzyme is resistant to 2TX. Crystal structures of the enzyme bound to DNA in the presence of 2TX demonstrate that the inhibitor chemically reacts with cysteine thiolates of ZnF and induces the loss of zinc. The molecular mechanism by which 2TX inhibits Fpg may be generalized to all prokaryote and eukaryote ZnF-containing Fpg/Nei-DNA glycosylases. Cell experiments show that 2TX can operate in cellulo on the human Fpg/Nei DNA glycosylases. The atomic elucidation of the determinants for the interaction of 2TX to Fpg provides the foundation for the future design and synthesis of new inhibitors with high efficiency and selectivity.

Direct measurements of the mechanical stability of zinc-thiolate bonds in rubredoxin by single-molecule atomic force microscopy

Zinc (Zn) is one of the most abundant metals and is essential for life. Through ligand interactions, often with thiolate from cysteine residues in proteins, Zn can play important structural roles in organizing protein structure and augmenting protein folding and stability. However, it is difficult to separate the contributions of Zn-ligand interactions from those originating from intrinsic protein folding in experimental studies of Zn-containing metalloproteins, which makes the study of Zn-ligand interactions in proteins challenging. Here, we used single-molecule force spectroscopy to directly measure the mechanical rupture force of the Zn-thiolate bond in Zn-rubredoxin. Our results show that considerable force is needed to rupture Zn-thiolate bonds (~170 pN, which is significantly higher than the force necessary to rupture the coordination bond between Zn and histidines). To our knowledge, our study not only provides new information about Zn-thiolate bonds in rubredoxin, it also opens a new avenue for studying metal-ligand bonds in proteins using single-molecule force spectroscopy.