Phosphate-Rich Biomimetic Peptides Shed Light on High-Affinity Hyperphosphorylated Uranyl Binding Sites in Phosphoproteins

A low-toxicity uranyl-selective-binding linear pentapeptide sequence as a potential uranium decorporation agent

Searching for highly selective, efficient, and low-toxicity chelating agents is central to resolving uranium contamination in vivo. Peptides composed of amino acids exhibit very low toxicity for accumulation in the human body and have been proven effective in chelating actinides within the human body. Herein, we report a rationally designed short phosphorylated peptide sequence PP-B, which exhibits high affinity and selectivity for uranyl compared to other trace elements present in the body (such as Na+, K+, Ca2+, Co2+, Fe2+, Fe3+, Mg2+, Mn2+, Zn2+). The association constant for the peptide-uranyl complex is calculated to be 7.3 ×105 M-1. The result of DFT calculation shows that the phosphate group binds strongly to the UO2 2+ center, potentially accounting for the peptide's strong affinity towards UO2 2+. The results of in vivo uranyl decorporation assays reveal that PP-B has a much lower toxicity and a much higher decorporation efficiency than that of the clinically approved DTPA. These findings render PP-B a promising candidate for utilization as a novel decorporation agent.

Insight into uranyl binding by cyclic peptides from molecular dynamics and density functional theory

It is a challenging task to develop uranyl-chelating agents based on peptide chemistry. A recently developed cationic dummy atom model of uranyl in conjunction with the classical molecular dynamics simulation presents a helpful utility to study the chelation of uranyl by peptides with a low computational cost. In the present study, it was used to describe the chelation of uranyl by the cyclic decapeptide with 4 Glu residues cyc-GluArgGluProGlyGluTrpGluProGly and its derivatives containing two phosphorylated serines in place of two Glu, termed pS16, pS18, pS38, and pS68. The obtained structures were further studied by density functional theory (DFT) and subsequent density analysis. We show that a combination of steered molecular dynamics and simulated annealing, using standard forcefields for peptide with the cationic dummy atom model of uranyl, can quickly and reliably obtain binding modes of uranyl-peptide complexes. Classical molecular dynamics simulation in explicit water produces geometry very close to the DFT-optimized structure. The presence of uranyl completely changes the conformation of these cyclic peptides from unstructured to organised. The simulation of a peptide with two uranyl units explained why only the 1:1 ratio of peptide and chelated-uranyl is observed experimentally in most cases, by the insufficiency of the anionic residues for the chelation of two UO22+ units, but that pS16 can accommodate two such units.

Hydrophilic interaction liquid chromatography: An efficient tool for assessing thorium interaction with phosphorylated biomimetic peptides

In the field of nuclear toxicology, the knowledge of the interaction of actinides (An) with biomolecules is of prime concern in order to elucidate their toxicity mechanism and to further develop selective decorporating agents. In this work, we demonstrated the great potential of hydrophilic interaction liquid chromatography (HILIC) to separate polar thorium (Th) biomimetic peptide complexes, as a key starting point to tackle these challenges. Th4+ was used as plutonium (Pu4+) analogue and pS16 and pS1368 as synthetic di- and tetra-phosphorylated peptides capable of mimicking the interaction sites of these An in osteopontin (OPN), a hyperphosphorylated protein. The objective was to determine the relative affinity of pS16 and pS1368 towards Th4+, and to evaluate the pS1368 selectivity when Th4+ was in competition complexation reaction with UO22+ at physiological pH. To meet these aims, HILIC was simultaneously coupled to electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS), which allowed to identify online the molecular structure of the separated complexes and quantify them, in a single step. Dedicated HILIC conditions were firstly set up to separate the new dimeric Th2(peptide)2 complexes with good separation resolution (peptide = pS16 or pS1368). By adding pS16 and pS1368 in different proportions relatively to Th4+, we found that lower or equal proportions of pS16 with respect to pS1368 were not sufficient to displace pS1368 from Th2pS13682 and pS16 proportion higher than pS1368 led to the formation of a predominant ternary complex Th2(pS16)(pS1368), demonstrating preferential Th4+ binding to the tetra-phosphorylated peptide. Finally, online identification and quantification of the formed complexes when Th4+ and UO22+ were mixed in equimolar ratio relatively to pS1368 showed that in spite of pS1368 has been specifically designed to coordinate UO22+, pS1368 is also Th4+-selective and exhibits stronger affinity for this latter than for UO22+. Hence, the results gathered through this approach highlight the impact of Th4+ coordination chemistry on its interaction with pS1368 and more widely to its affinity for biomolecules.

Effect of Sol-Gel Silica Matrices on the Chemical Properties of Adsorbed/Entrapped Compounds

The sol-gel process enables the preparation of silica-based matrices with tailored composition and properties that can be used in a variety of applications, including catalysis, controlled release, sensors, separation, etc. Commonly, it is assumed that silica matrices prepared via the sol-gel synthesis route are "inert" and, therefore, do not affect the properties of the substrate or the catalyst. This short review points out that porous silica affects the properties of adsorbed/entrapped species and, in some cases, takes an active part in the reactions. The charged matrix affects the diffusion of ions, thus affecting catalytic and adsorption processes. Furthermore, recent results point out that ≡Si-O. radicals are long-lived and participate in redox processes. Thus, clearly, porous silica is not an inert matrix as commonly considered.

Determining the selectivity of a tetra-phosphorylated biomimetic peptide towards uranium in the presence of competing cations through the simultaneous coupling of HILIC to ESI-MS and ICP-MS

A cyclic tetra-phosphorylated biomimetic peptide (pS1368) has been proposed as a promising starting structure to design a decorporating agent of uranyl (UO22+) due to its affinity being similar to that of osteopontin (OPN), a target UO22+ protein in vivo. The determination of this peptide's selectivity towards UO22+ in the presence of competing endogenous elements is also crucial to validate this hypothesis. In this context, the selectivity of pS1368 towards UO22+ in the presence of Ca2+, Cu2+ and Zn2+ was determined by applying the simultaneous coupling of hydrophilic interaction chromatography (HILIC) to electrospray ionization (ESI-MS) and inductively coupled plasma (ICP-MS) mass spectrometry. Sr2+ was used as Ca2+ simulant, providing less challenging ICP-MS measurements. The separation of the complexes by HILIC was first set up. The selectivity of pS1368 towards UO22+ was determined in the presence of Sr2+, by adding several proportions of the latter to UO2(pS1368). UO22+ was not displaced from UO2(pS1368) even in the presence of a ten-fold excess of Sr2+. The same approach has been undertaken to demonstrate the selectivity of pS1368 towards UO22+ in the presence of Cu2+, Zn2+ and Sr2+ as competing endogenous cations. Hence, we showed that pS1368 was selective towards UO22+ in the presence of Sr2+, but also in the presence of Cu2+ and Zn2+. This study highlights the performance of HILIC-ESI-MS/ICP-MS simultaneous coupling to assess the potential of molecules as decorporating agents of UO22+.

The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein

Uranium (U) is a naturally-occurring radionuclide that is toxic to living organisms. Given that proteins are primary targets of U(VI), their identification is an essential step towards understanding the mechanisms of radionuclide toxicity, and possibly detoxification. Here, we implemented a chromatographic strategy including immobilized metal affinity chromatography to trap protein targets of uranyl in Arabidopsis thaliana. This procedure allowed the identification of 38 uranyl-binding proteins (UraBPs) from root and shoot extracts. Among them, UraBP25, previously identified as plasma membrane-associated cation-binding protein 1 (PCaP1), was further characterized as a protein interacting in vitro with U(VI) and other metals using spectroscopic and structural approaches, and in planta through analyses of the fate of U(VI) in Arabidopsis lines with altered PCaP1 gene expression. Our results showed that recombinant PCaP1 binds U(VI) in vitro with affinity in the nM range, as well as Cu(II) and Fe(III) in high proportions, and that Ca(II) competes with U(VI) for binding. U(VI) induces PCaP1 oligomerization through binding at the monomer interface, at both the N-terminal structured domain and the C-terminal flexible region. Finally, U(VI) translocation in Arabidopsis shoots was affected in pcap1 null-mutant, suggesting a role for this protein in ion trafficking in planta.

Determination of the affinity of biomimetic peptides for uranium through the simultaneous coupling of HILIC to ESI-MS and ICP-MS

Several proteins have been identified in the past decades as targets of uranyl (UO₂²⁺) in vivo. However, the molecular interactions responsible for this affinity are still poorly known which requires the identification of the UO₂²⁺ coordination sites in these proteins. Biomimetic peptides are efficient chemical tools to characterize these sites. In this work, we developed a dedicated analytical method to determine the affinity of biomimetic, synthetic, multi-phosphorylated peptides for UO₂²⁺ and evaluate the effect of several structural parameters of these peptides on this affinity at physiological pH. The analytical strategy was based on the implementation of the simultaneous coupling of hydrophilic interaction chromatography (HILIC) with electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS). An essential step had been devoted to the definition of the best separation conditions of UO₂²⁺ complexes formed with di-phosphorylated peptide isomers and also with peptides of different structure and degrees of phosphorylation. We performed the first separations of several sets of UO₂²⁺ complexes by HILIC ever reported in the literature. A dedicated method had then been developed for identifying the separated peptide complexes online by ESI-MS and simultaneously quantifying them by ICP-MS, based on uranium quantification using external calibration. Thus, the affinity of the peptides for UO₂²⁺ was determined and made it possible to demonstrate that (i) the increasing number of phosphorylated residues (pSer) promotes the affinity of the peptides for UO₂²⁺, (ii) the position of the pSer in the peptide backbone has very low impact on this affinity (iii) and finally the cyclic structure of the peptide favors the UO₂²⁺ complexation in comparison with the linear structure. These results are in agreement with those previously obtained by spectroscopic techniques, which allowed to validate the method. Through this approach, we obtained essential information to better understand the mechanisms of toxicity of UO₂²⁺ at the molecular level and to further develop selective decorporating agents by chelation.

A Simple Fluorescence Affinity Assay to Decipher Uranyl-Binding to Native Proteins

Determining the affinity of proteins for uranyl is key to understand the toxicity of this cation and to further develop decorporation strategies. However, usual techniques to achieve that goal often require specific equipment and expertise. Here, we propose a simple, efficient, fluorescence‐based method to assess the affinity of proteins and peptides for uranyl, at equilibrium and in buffered solution. We first designed and characterized an original uranyl‐binding fluorescent probe. We then built a reference scale for uranyl affinity in solution, relying on signal quenching of our fluorescent probe in presence of high‐affinity uranyl‐binding peptides. We finally validated our approach by re‐evaluating the uranyl‐binding affinity of four native proteins. We envision that this tool will facilitate the reliable and reproducible assessment of affinities of peptides and proteins for uranyl.

Hydrophobic core formation and secondary structure elements in uranyl(VI)-binding peptides

Cyclic peptides as well as a modified EF-hand motif of calmodulin have been newly designed to achieve high affinity towards uranyl(VI). Cyclic peptides may be engineered to bind uranyl(VI) to its backbone under acidic conditions, which may enhance its selectivity. For the modified EF-hand motif of calmodulin, strong electrostatic interactions between uranyl(VI) and negatively charged side chains play an important role in achieving high affinity; however, it is also essential to have a secondary structure element and formation of hydrophobic cores in the metal-bound state of the peptide.

Separation of multiphosphorylated cyclopeptides and their positional isomers by hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS)

Peptides are efficient models used in different fields such as toxicology to study the interactions of several contaminants at the molecular scale, requiring the development of bio-analytical strategies. In this context, Hydrophilic interaction liquid chromatography (HILIC) coupled to electrospray ionization mass spectrometry (ESI-MS) was used to separate synthetic multiphosphorylated cyclopeptides and their positional isomers at physiological pH. We assessed (i) the selectivity of eleven HILIC columns, from different manufacturers and packed with diverse polar sorbents, and (ii) the effect of mobile phase composition on the separation selectivity. The best selectivity and baseline resolution were achieved with the columns grafted by neutral sorbents amide and diol. Furthermore, we investigated the HILIC retention mechanism of these peptides by examining the effect of the number of phosphorylated residues in the peptide scaffold on their retention. The peptide behavior followed the classical hydrophilic partitioning mechanism exclusively on amide and diol columns. This trend was not fully respected on bare and hybrid silica due to the attractive/repulsive interactions of the deprotonated surface silanol groups with the Arginine or Glutamate residues in the peptide scaffold according to the peptide sequence. The position of the phosphorylated amino acid in the peptide backbone also showed to have an impact on the retention, making possible the separation of positional isomers of these multiphosphorylated cyclic peptides using HILIC.

Uranyl Binding to Proteins and Structural-Functional Impacts

The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO₂²⁺). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.

Recent advances in uranyl binding in proteins thanks to biomimetic peptides

Uranium is an element belonging to the actinide series. It is ubiquitous in rock, soil, and water. Uranium is found in the ecosystem due to mining and milling industrial activities and processing to nuclear fuel, but also to the extensive use of phosphate fertilizers. Understanding uranium binding in vivo is critical, first to deepen our knowledge of molecular events leading to chemical toxicity, but also to provide new mechanistic information useful for the development of efficient decorporation treatments to be applied in case of intoxication. The most stable form in physiological conditions is the uranyl cation (UO₂²⁺), in which uranium oxidation state is +VI. This short review presents uranyl coordination properties and chelation, and what is currently known about uranium binding to proteins. Although several target proteins have been identified, the UO₂²⁺ binding sites have barely been identified. Biomimetic approaches using model peptides are good options to shed light on high affinity uranyl binding sites in proteins. A strategy based on constrained cyclodecapeptides allowed recently to propose a tetraphosphate binding site for uranyl that provides an affinity similar to the one measured with the phosphoprotein osteopontin.