Destabilization of DNA through interstrand crosslinking by UO22

Towards tailoring hydrophobic interaction with uranyl(VI) oxygen for C-H activation

Bovine serum albumin (BSA) has a uranyl(VI) binding hotspot where uranium is tightly bound by three carboxylates. Uranyl oxygen is "soaked" into the hydrophobic core of BSA. Isopropyl hydrogen of Val is trapped near UO22+ and upon photoexcitation, C-H bond cleavage is initiated. A unique hydrophobic contact with "yl"-oxygen, as observed here, can be used to induce C-H activation.

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.

Polymer Ligand-Sensitized Lanthanide Metal-Organic Frameworks for an On-Site Analysis of a Radionuclide

Herein, a new strategy to increase the sensitivity of a lanthanide metal-organic framework (Ln-MOF) to UO₂²⁺ was proposed by using polymeric ligands. By utilizing [Tb(1,3,5-benzenetrisbenzoate)]n (Tb-TBT) MOF as the host, preloaded 2-vinyl terephthalic acid (VTP) was polymerized in situ, which produced a novel fluorescent composite denoted as PVTP⊂Tb-TBT. Benefiting from the coordination of PVTP to the Tb nodes, the polymeric chains performed both as molecular scaffolds that improved the water stability of the framework and as additional antennae that sensitized the photoluminescence of the Tb nodes. More importantly, the detection sensitivity and selectivity of PVTP⊂Tb-TBT to UO₂²⁺ were much improved compared to those of Tb-TBT. Detailed characterizations indicated that the incorporation of PVTP efficiently enriched UO₂²⁺ in the probe, which promoted the energy dissipation to UO₂²⁺. Besides, UO₂²⁺ was also supposed to release PVTP from PVTP⊂Tb-TBT and, thus, exposed the open metal sites to water molecules, which interrupted the sensitization effect of PVTP and induced a nonradiative energy dissipation. A limit of detection (LOD) as low as 0.75 nm was recorded by suspending the PVTP⊂Tb-TBT probe in a water sample, far below the limit in drinking water set by the United States Environmental Protection Agency (130 nm). Furthermore, a remotely controlled sampling and an on-site analysis of real water samples were realized by facilely loading PVTP⊂Tb-TBT on thin films (TFs). The LOD for UO₂²⁺ was 2.5 nm by using the TFs. This study reports a new strategy for boosting the sensitivity and selectivity of Ln-MOF to monitor UO₂²⁺ and expands the application of the strategy to an on-site analysis.

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller–Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD.

Visualized IFIE results seen from chain-B of spike protein.

Trimeric uranyl(vi)-citrate forms Na+, Ca2+, and La3+ sandwich complexes in aqueous solution

M. Basile, et al., Chem. Commun., 2015, 51, 5306-5309, showed that a sodium ion is sandwiched by uranyl(vi) oxygen atoms of two 3 : 3 uranyl(vi)-citrate complex molecules in single-crystals. By means of NMR spectroscopy supported by DFT calculations we provide unambiguous evidence for this complex to persist in aqueous solution above a critical concentration of 3 mM uranyl citrate. Unprecedented Ca²⁺ and La³⁺ coordination by a bis-(η³-uranyl(vi)-oxo) motif advances the understanding of uranium's aqueous chemistry. As determined from ¹⁷O NMR, Ca²⁺ and more distinctly La³⁺ cause strong O[double bond, length as m-dash]U[double bond, length as m-dash]O polarization, which opens up new ways for uranyl(vi)-oxygen activation and functionalization.

Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation

COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A' base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.

Amplified electrochemical determination of UO22+ based on the cleavage of the DNAzyme and DNA-modified gold nanoparticle network structure

A superior electrochemical biosensor was designed for the determination of UO₂²⁺ in aqueous solution by integration of DNAzyme and DNA-modified gold nanoparticle (DNA-AuNP) network structure. Key features of this method include UO₂²⁺ inducing the cleavage of the DNAzyme and signal amplification of DNA-AuNP network structure. In this electrochemical method, the DNA-AuNP network structure can be effectively modified on the surface of gold electrode and then employed as an ideal signal amplification unit to generate amplified electrochemical response by inserting a large amount of electrochemically active indicator methylene blue (MB). In the presence of UO₂²⁺, the specific sites on DNA-AuNP network structure can be cleaved by UO₂²⁺, releasing the DNA-AuNP network structure with detectable reduction of electrochemical response intensity. The electrochemical response intensity is related to the concentration of UO₂²⁺. The logarithm of electrochemical response intensity and UO₂²⁺ concentration showed a wide linear range of 10~100 pM, and the detection limit reached 8.1 pM (S/N = 3). This method is successfully used for determination of UO₂²⁺ in water samples. Graphical abstract Fabricated DNAzyme network structure for enhanced electrical signal. Numerical experiments show that the current signal decreases as the concentration of UO₂²⁺ increases. It can be seen that the biosensors could be used to detect UO₂²⁺ in aqueous solution effectively.

Lanthanide-induced conformational change of methanol dehydrogenase involving coordination change of cofactor pyrroloquinoline quinone

Classical molecular dynamics simulations combined with fragment molecular orbital calculations were employed to rationalize the enzymatic activities of MDH carrying different lanthanides.