Tristhiolato Pseudopeptides Bind Arsenic(III) in an AsS3 Coordination Environment Imitating Metalloid Binding Sites in Proteins.

The AsIII binding of two NTA-based tripodal pseudopeptides, possessing three cysteine (ligand L1) or d-penicillamine residues (ligand L2) as potential coordinating groups for soft semimetals or metal ions, was studied by experimental (UV, CD, NMR, and ESI-MS) and theoretical (DFT) methods. All of the experimental data, obtained with the variation of the AsIII:ligand concentration ratios or pH values in some instances, evidence the exclusive formation of species with an AsS3-type coordination mode. The UV-monitored titration of the ligands with arsenous acid at pH = 7.0 provided an absorbance data set that allowed for the determination of apparent stability constants of the forming species. The obtained stabilities (logK' = 5.26 (AsL1) and logK' = 3.04 (AsL2)) reflect high affinities, especially for the sterically less restricted cysteine derivative. DFT calculated structures correlate well with the spectroscopic results and, in line with the 1H NMR data, indicate a preference for the all-endo conformers resembling the AsIII environment at the semimetal binding sites in various metalloproteins.

TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures.

AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional structure prediction methods for transmembrane proteins were both complicated and error prone, AF2 is a great help to the community. Complementing the relatively meager number of experimental structures, AF2 provides 3D predictions for thousands of new alpha-helical membrane proteins. However, the lack of reliable structural templates and the fact that AF2 was not trained to handle phase boundaries also necessitates a delicate assessment of structural correctness. In our new database, Transmembrane AlphaFold database (TmAlphaFold database), we apply TMDET, a simple geometry-based method to visualize the likeliest position of the membrane plane. In addition, we calculate several parameters to evaluate the location of the protein into the membrane. This also allows TmAlphaFold database to show whether the predicted 3D structure is realistic or not. The TmAlphaFold database is available at https://tmalphafold.ttk.hu/.

Hg2+ and Cd2+ binding of a bioinspired hexapeptide with two cysteine units constructed as a minimalistic metal ion sensing fluorescent probe.

Hg2+ and Cd2+ complexation of a short hexapeptide, Ac-DCSSCY-NH2 (DY), was studied by pH-potentiometry, UV and NMR spectroscopy and fluorimetry in aqueous solutions and the Hg2+-binding ability of the ligand was also described in an immobilized form, where the peptides were anchored to a hydrophilic resin. Hg2+ was demonstrated to form a 1 : 1 complex with the ligand even at pH = 2.0 while Cd2+ coordination by the peptide takes place only above pH ∼ 3.5. Both metal ions form bis-ligand complexes by the coordination of four Cys-thiolates at ligand excess above pH ∼ 5.5 (Cd2+) and 7.0 (Hg2+). Fluorescence studies demonstrated a Hg2+ induced concentration-dependent quenching of the Tyr fluorescence until a 1 : 1 Hg2+ : DY ratio. The fluorescence emission intensity decreases linearly with the increasing Hg2+ concentration in a range of over two orders of magnitude. The fact that this occurs even in the presence of 1.0 eq. of Cd2+ per ligand reflects a complete displacement of the latter metal ion by Hg2+ from its peptide-bound form. The immobilized peptide was also shown to bind Hg2+ very efficiently even from samples at pH = 2.0. However, the existence of lower affinity binding sites was also demonstrated by binding of more than 1.0 eq. of Hg2+ per immobilized DY molecule under Hg2+-excess conditions. Experiments performed with a mixture of four metal ions, Hg2+, Cd2+, Zn2+ and Ni2+, indicate that this molecular probe may potentially be used in Hg2+-sensing systems under acidic conditions for the measurement of µM range concentrations.

Interaction of Arsenous Acid with the Dithiol-Type Chelator British Anti-Lewisite (BAL): Structure and Stability of Species Formed in an Unexpectedly Complex System.

British anti-Lewisite (2,3-dimerkaptopropan-1-ol, dimercaprol, BAL) is one of the best-known chelator-type therapeutic agents against toxic metal ions and metalloids, especially arsenicals. Surprisingly, the mechanisms of action at the molecular level, as well as the coordination features of this traditional drug toward various arsenicals, are still poorly revealed. The present study on the interaction of arsenous acid (H3AsO3) with BAL, involving UV and NMR titrations, electrospray ionization mass spectrometry, and 2D NMR experiments combined with MP2 calculations, demonstrates that the reaction of H3AsO3 with BAL at pH = 7.0 results in a more complex speciation than was assumed before. The three reactive hydroxyl groups of H3AsO3 allow for interaction with three thiol moieties via condensation reaction, leading to the observed AsBAL2 and As2BAL3 complexes besides the AsBAL species. This indicates the strong propensity of inorganic As(III) to saturate its coordination sphere with thiolate groups. The alcoholic hydroxyl group of the ligand may also directly bind to As(III) in AsBAL. Compared to dithiothreitol or dithioeritritol, the preference of BAL to form complexes with such a tridentate binding mode is much lower owing to the more strained bridged bicyclic structure with an αAsSC < 90° bond angle and an unfavorable condensed boat-type six-membered ring. On the basis of the NMR data, the predominating, bidentately bound AsBAL species, including a five-membered chelate ring, exists in rapidly interconverting envelope forms of E and Z stereoisomers. The conditional stability constants calculated for the three macrospecies from a series of UV data [log ßpH=7.0 = 6.95 (AsBAL), 11.56 (AsBAL2), and 22.73 (As2BAL3)] reflect that BAL is still the most efficient, known, dithiol-type chelator of H3AsO3.