Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network

Crystallophores are lanthanide complexes that have demonstrated outstanding induction of crystallization for various proteins. This article explores the effect of tailored modifications of the crystallophore first generation and their impact on the nucleating properties and protein crystal structures. Through high-throughput crystallization experiments and dataset analysis, we evaluated the effectiveness of these variants, in comparison to the first crystallophore generation G1. In particular, the V1 variant, featuring a propanol pendant arm, demonstrated the ability to produce new crystallization conditions for the proteins tested (hen-egg white lysozyme, proteinase K and thaumatin). Structural analysis performed in the case of hen egg-white lysozyme along with Molecular Dynamics simulations, highlights V1's unique behavior, taking advantage of the flexibility of its propanol arm to explore different protein surfaces and form versatile supramolecular interactions.

Preparation of Polyoxometalate-Based Composite by Solidification of Highly Active Cobalt-Containing Polytungstate on Polymeric Ionic Liquid for the Efficient Isolation of Proteinase K

A novel porous polyoxometalate (POM)-based composite (Co₄PW-PDDVAC) was prepared via the solidification of water-soluble polytungstate (Co₄PW) on the polymeric ionic liquid dimethyldodecyl-4-polyethylene benzyl ammonium chloride (PDDVAC) via a cation-exchange reaction. The solidification was confirmed by EDS, SEM, FT-IR, TGA, and so on. The strong covalent coordination and hydrogen-bonding interaction between the highly active Co²⁺ of the Co₄PW and the aspartic acid residues of proteinase K endowed the obtained Co₄PW-PDDVAC composite with excellent proteinase K adsorption properties. Thermodynamic investigations indicate that the adsorption behavior of proteinase K was consistent with the linear Langmuir isothermal model, giving an adsorption capacity as high as 1428 mg g^-1. The Co₄PW-PDDVAC composite was applied in the selective isolation of highly active proteinase K from Tritirachium album Limber crude enzyme fluid.

Synthesis and characterization of the `Japanese rice-ball'-shaped Molybdenum Blue Na4[Mo2O2(OH)4(C6H4NO2)2]2[Mo120Ce6O366H12(OH)2(H2O)76]∼200H2O

The synthesis and crystal structure of a ‘Japanese rice-ball’-shaped Molybdenum Blue hybridized organically with 2-picolinic acid is presented. In addition to single-crystal X-ray analysis, the title com­pound was characterized with IR spectroscopy and elemental analyses to reinforce its framework structure, thermogravimetric analysis to qu­antify the water content, and Vis–NIR spectroscopy to determine the degree of reduction of the nanocluster.

The hybridized lanthanide-containing molybdenum blue (Ln-MB) wheel Na₄[Mo₂O₂(OH)₄(C₆H₄NO₂)₂]₂[Mo₁₂₀Ce₆O₃₆₆H₁₂(OH)₂(H₂O)₇₆]∼200H₂O ({Mo₂(C₆H₄NO₂)₂}₂{Mo₁₂₀Ce₆}) was assembled in an aqueous one-pot synthesis. The Ln-MB was hybridized with 2-picolinic acid through the generation of the organometallic counter-ion [Mo₂O₂(OH)₄(C₆H₄NO₂)₂]²⁺. Control experiments demonstrated that the position of the carb­oxy­lic acid group (2-position to the N atom) in the hybridization com­ponent is critical in yielding single crystals of Ln-MB. In addition to single-crystal X-ray diffraction (XRD) analysis, which revealed a ‘Japanese rice-ball’-shaped Ln-MB as the anion, elemental analyses, IR spectroscopy, and thermogravimetric analysis (TGA) were performed to confirm its structure and com­position. Bond-valence-sum calculations (BVS) revealed that {Mo₂(C₆H₄NO₂)₂}₂{Mo₁₂₀Ce₆} is com­posed of a 24-electron re­duced anionic ring, which was confirmed by Vis–NIR spectroscopy.

Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives

The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)₃]^3- and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(H₂O)₆)₃[Eu(DPA)₃]₂·7H₂O (1), {(Ca(H₂O)₄)₃[Eu(DPA)₃]₂}_n·10nH₂O (2), and {Cu(DPA)(H₂O)₂}_n (3), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported. On the other hand, Tb-Xo4 is perfectly soluble in the crystallization media, stable in the presence of alkaline-earth dications, and slowly decomposes (within days) by transmetalation with transition metals. The original structure of [Tb₄L₄(H₂O)₄]Cl₄·15H₂O (4) is also described, where L represents a bis(pinacolato)triazacyclononane ligand. This paper also highlights a potential synergy of interactions between Tb-Xo4 and components of the crystallization mixtures, leading to the formation of complex adducts like {AdkA/Tb-Xo4/Mg²⁺/glycerol} in the protein binding sites. The observation of such multicomponent adducts illustrated the complexity and versatility of the supramolecular chemistry occurring at the surface of the proteins.

Speciation of Transition-Metal-Substituted Keggin-Type Silicotungstates Affected by the Co-crystallization Conditions with Proteinase K

We report on the synthesis of the tetrasubstituted sandwich-type Keggin silicotungstates as the pure Na salts Na₁₄[(A-α-SiW₁₀O₃₇)₂{Co₄(OH)₂(H₂O)₂}]·37H₂O (Na{SiW₁₀Co₂}₂) and Na₁₄[(A-α-SiW₁₀O₃₇)₂{Ni₄(OH)₂(H₂O)₂}]·77.5H₂O (Na{SiW₁₀Ni₂}₂), which were prepared by applying a new synthesis protocol and characterized thoroughly in the solid state by single-crystal and powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis, and elemental analysis. Proteinase K was applied as a model protein and the polyoxotungstate (POT)–protein interactions of Na{SiW₁₀Co₂}₂ and Na{SiW₁₀Ni₂}₂ were studied side by side with the literature-known K₅Na₃[A-α-SiW₉O₃₄(OH)₃{Co₄(OAc)₃}]·28.5H₂O ({SiW₉Co₄}) featuring the same number of transition metals. Testing the solution behavior of applied POTs under the crystallization conditions (sodium acetate buffer, pH 5.5) by time-dependent UV/vis spectroscopy and electrospray ionization mass spectrometry speciation studies revealed an initial dissociation of the sandwich POTs to the disubstituted Keggin anions H_xNa_5–x[SiW₁₀Co₂O₃₈]^3– and H_xNa_5–x[SiW₁₀Ni₂O₃₈]^3– ({SiW₁₀M₂}, M = Co^II and Ni^II) followed by partial rearrangement to the monosubstituted compounds (α-{SiW₁₁Co} and α-{SiW₁₁Ni}) after 1 week of aging. The protein crystal structure analysis revealed monosubstituted α-Keggin POTs in two conserved binding positions for all three investigated compounds, with one of these positions featuring a covalent attachment of the POT anion to an aspartate carboxylate. Despite the presence of both mono- and disubstituted anions in a crystallization mixture, proteinase K selectively binds to monosubstituted anions because of their preferred charge density for POT–protein interaction.

We report on the development of a new synthesis protocol to prepare the Na salts of the tetrasubstituted sandwich-type Keggin derivatives Na₁₄[(A-α-SiW₁₀O₃₈)₂{Co₄(OH)₂(H₂O)₂}]·37H₂O (Na{SiW₁₀Co₂}₂) and Na₁₄[(A-α-SiW₁₀O₃₈)₂{Ni₄(OH)₂(H₂O)₂}]·77.5H₂O (Na{SiW₁₀Ni₂}₂). Following a thorough characterization of the polyoxotungstate (POT) dimers involving single-crystal and powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis, and elemental analysis in the solid state and UV/vis spectroscopy and electrospray ionization mass spectrometry in solution, the water-soluble compounds (>5 mM) were applied as additives for the crystallization of proteinase K along with the tetrasubstituted monomeric Keggin-type analogue K₅Na₃[A-α-SiW₉O₃₄(OH)₃{Co₄(OAc)₃}]·28.5H₂O ({SiW₉Co₄}). Crystallographic studies on the obtained protein crystals revealed monosubstituted Keggin derivatives in all three cases bound to conserved sites of the protein, which highlights a selectivity of proteinase K toward monosubstituted Keggin POTs within a narrow range of surface charge density.

Wells-Dawson phosphotungstates as mushroom tyrosinase inhibitors: a speciation study

In order to elucidate the active polyoxotungstate (POT) species that inhibit fungal polyphenol oxidase (AbPPO4) in sodium citrate buffer at pH 6.8, four Wells-Dawson phosphotungstates [α/β-P^V₂W^VI₁₈O₆₂]^6- (intact form), [α₂-P^V₂W^VI₁₇O₆₁]^10- (monolacunary), [P^V₂W^VI₁₅O₅₆]^12- (trilacunary) and [H₂P^V₂W^VI₁₂O₄₈]^12- (hexalacunary) were investigated. The speciation of the POT solutions under the dopachrome assay (50 mM Na-citrate buffer, pH 6.8; L-3,4-dihydroxyphenylalanine as a substrate) conditions were determined by ¹⁸³W-NMR, ³¹P-NMR spectroscopy and mass spectrometry. The intact Wells-Dawson POT [α/β-P^V₂W^VI₁₈O₆₂]^6- shows partial (~ 69%) disintegration into the monolacunary [α₂-P^V₂W^VI₁₇O₆₁]^10- anion with moderate activity (K_i = 9.7 mM). The monolacunary [α₂-P^V₂W^VI₁₇O₆₁]^10- retains its structural integrity and exhibits the strongest inhibition of AbPPO4 (K_i = 6.5 mM). The trilacunary POT [P^V₂W^VI₁₅O₅₆]^12- rearranges to the more stable monolacunary [α₂-P^V₂W^VI₁₇O₆₁]^10- (~ 62%) accompanied by release of free phosphates and shows the weakest inhibition (K_i = 13.6 mM). The hexalacunary anion [H₂P^V₂W^VI₁₂O₄₈]^12- undergoes time-dependent hydrolysis resulting in a mixture of [H₂P^V₂W^VI₁₂O₄₈]^12-, [P^V₈W^VI₄₈O₁₈₄]^40-, [P^V₂W^VI₁₉O₆₉(H₂O)]^14- and [α₂-P^V₂W^VI₁₇O₆₁]^10- which together leads to comparable inhibitory activity (K_i = 7.5 mM) after 48 h. For the solutions of [α/β-P^V₂W^VI₁₈O₆₂]^6-, [α₂-P^V₂W^VI₁₇O₆₁]^10- and [P^V₂W^VI₁₅O₅₆]^12- the inhibitory activity is correlated to the degree of their rearrangement to [α₂-P^V₂W^VI₁₇O₆₁]^10-. The rearrangement of hexalacunary [H₂P^V₂W^VI₁₂O₄₈]^12- into at least four POTs with a negligible amount of monolacunary anion interferes with the correlation of activity to the degree of their rearrangement to [α₂-P^V₂W^VI₁₇O₆₁]^10-. The good inhibitory effect of the Wells-Dawson [α₂-P^V₂W^VI₁₇O₆₁]^10- anion is explained by the low charge density of its protonated forms H_x[α₂-P^V₂W^VI₁₇O₆₁]^(10-x)- (x = 3 or 4) at pH 6.8.

Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C

Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies [comparison between the molecular mechanics Poisson-Boltzmann surface area analysis and the isothermal titration calorimetry measurements]. The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically driven association and notably the role of arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of a hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way toward an automated procedure to predict the supramolecular protein-cage association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.

Research progress on the inhibition of enzymes by polyoxometalates

Polyoxometalates (POMs) are a kind of inorganic cluster metal complex with various biological activities, such as anti-Alzheimer's disease, antibacterial, anti-cancer, anti-diabetes, anti-virus and so on.

Four Keggin-based compounds constructed by a series of pyridine derivatives: synthesis, and electrochemical, photocatalytic and fluorescence sensing properties

Four compounds based on Keggin anions and Ag^I ions were obtained, the photocatalytic and electrochemical properties were studied. Compound 4 can act as a Hg²⁺ fluorescence sensor.

Polyoxometalates in solution: speciation under spotlight

The review covers stability and transformations of classical polyoxometalates in aqueous solutions and provides their ion-distribution diagrams over a wide pH range.