High-resolution crystal structures of a “half sandwich”-type Ru(II) coordination compound bound to hen egg-white lysozyme and proteinase K

Abstract

The high-resolution X-ray crystal structures of the adducts formed between the "half sandwich"-type Ru(II) coordination compound [Ru II (1,4,7-trithiacyclononane)(ethane-1,2-diamine)Cl] + and two proteins, namely hen egg-white lysozyme and proteinase K, are presented. The structures unveil that upon reaction with both enzymes the Ru(II) compound is coordinated by solvent-exposed aspartate residues after releasing the chloride ligand (Asp101 in lysozyme, Asp200 and Asp260 in proteinase K), while retaining the two chelating ligands. The adduct with Asp101 residue at the catalytic cleft of lysozyme is accompanied by residue-specific conformational changes to accommodate the Ru(II) fragment, whereas the complexes bound at the two calcium-binding sites of proteinase K revealed minimal structural perturbation of the enzyme. To the best of our knowledge, proteinase K is used here for the first time as a model system of protein metalation and these are the first X-ray crystal structures of protein adducts of a Ru(II) coordination compound that maintains its coordination sphere almost intact upon binding. Our data demonstrate the role of ligands in stabilizing the protein adducts via hydrophobic/aromatic or hydrogen-bonding interactions, as well as their underlying role in the selection of specific sites on the electrostatic potential surface of the enzymes.

Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes

“…175 The modelling ascertained the coordination of Ru II to N(7)dG7 of CT-DNA and Glu292 of HSA; notably, the latter remembers the binding of [Ru II (1,4,7-trithiacyclononane)(ethylenediamine)Cl] + to lysozyme through the side-chain of Asp101 and to proteinase K through Asp200 or Asp260, which replace the released chloride ligand. 187 The results supported the affinity of these potential drugs either toward the CT-DNA major groove or to the IIa subdomain of HSA.…”

Anthracenyl Functionalization of Half-Sandwich Carbene Complexes: In Vitro Anticancer Activity and Reactions with Biomolecules

“…After multiple rounds of refinement without a metallo­fragment in place to develop the unbiased maps (Figure a), the Ru fragment was positioned in the center of the anomalous peak 2.08 ± 0.07 Å away from O δ2 Asp119 and refined to an occupancy of 0.8. Many Ru complexes have been found to bind to Asp residues on HEWL, most commonly with Asp101. − Previously reported Ru–Asp bond lengths were, e.g., 2.59 ± 0.09 Å for a [(η 6 - p -cymene)­Ru­(μ-Cl 2 )­Ru] fragment located at Asp101 and 1.84 ± 0.13 Å for a [Ru­(1,2-ethylenediamine)­(1,4,7-trithiacyclononane)] moiety at Asp101 . A search of the areas surrounding the Ru center for residual electron density made it apparent that the carbene ligand was still attached to the Ru center in a position trans to O δ2 Asp119 .…”

Insights into the Protein Ruthenation Mechanism by Antimetastatic Metallodrugs: High-Resolution X-ray Structures of the Adduct Formed between Hen Egg-White Lysozyme and NAMI-A at Various Time Points

“…13 This structure was obtained through cocrystallization of HEWL with a 10-fold molar excess of NAMI-A and under similar conditions to those of the present study (Table S6); however, the authors did not report the incubation time before crystallization trials or the time required for crystals to appear. Although it is well-established that Ru(II) coordination compounds can bind to the Asp residues of HEWL, 11,37 this is the only case where NAMI-A or any relevant Ru(III) compound has been shown to target acidic protein residues. For this reason, we performed a thorough investigation of the electron density map in conjunction with anomalous scattering mapping of the X-ray structure obtained after 98 h (PDB ID: 7BDM).…”

“…Tetragonal crystals appeared within 24 h and grew to full size within 2 days. Soaking of HEWL crystals with NAMI-A was performed by adding solid aliquots to the crystal drops. , Significant coloring of the colorless crystals to orange was observed within 1.5 h, which gradually turned red at 8 h and then to black within 4 days. It should be noted that the deep coloring of the crystals corresponds to that observed in solution upon prolonged hydrolysis of NAMI-A , which has been attributed to the formation and progressive growth of oligomeric/polymeric species with Ru–O–Ru bridges.…”