Structural insights into the vapochromic behavior of Pt- and Pd-based compounds

Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M(bzq)(CN)2], and [Li(H2O)n][Pt(bzq)(CN)2], where ppy = 2-phenylpyridinate, bzq = 7,8-benzoquinolate, and M = Pt(II) or Pd(II). These hydrated potassium/lithium salts exhibit a change in color upon being heated to 380 K, and they transform back into the original color upon absorption of water molecules from the environment. The challenging characterization of their structure in the vapochromic transition has been carried out by combining several experimental techniques, despite the availability of partially ordered and/or impure crystalline material. Room-temperature single-crystal and powder X-ray diffraction investigation revealed that [K(H2O)][Pt(ppy)(CN)2] crystallizes in the Pbca space group and is isostructural to [K(H2O)][Pd(ppy)(CN)2]. Variable-temperature powder X-ray diffraction allowed the color transition to be related to changes in the diffraction pattern and the decrease in sample crystallinity. Water loss, monitored by thermogravimetric analysis, occurs in two stages, well separated for potassium Pt compounds and strongly overlapped for potassium Pd compounds. The local structure of potassium compounds was monitored by in situ pair distribution function (PDF) measurements, which highlighted changes in the intermolecular distances due to a rearrangement of the crystal packing upon vapochromic transition. A reaction coordinate describing the structural changes was extracted for each compound by multivariate analysis applied to PDF data. It contributed to the study of the kinetics of the structural changes related to the vapochromic transition, revealing its dependence on the transition metal ion. Instead, the ligand influences the critical temperature, higher for ppy than for bzq, and the inclination of the molecular planes with respect to the unit cell planes, higher for bzq than for ppy. The first stage of water loss triggers a unit cell contraction, determined by the increase in the b axis length and the decrease in the a (for ppy) or c (for bzq) axis lengths. Consequent interplane distance variations and in-plane roto-translations weaken the π-stacking of the room-temperature structure and modify the distances and angles of Pt(II)/Pd(II) chains. The curve describing the intermolecular Pt(II)/Pd(II) distances as a function of temperature, validated by X-ray absorption spectroscopy, was found to reproduce the coordinate reaction determined by the model-free analysis.This research has been supported by the short-term mobility program of the National Research Council (CNR) of Italy and by the Spanish Ministerio de Economía y Competitividad (Ministerio de Ciencia Innovación y Universidades)/FEDER (Project PGC2018-094749-B-I00).Peer reviewe

Effects of altered α- and β-branch carotenoid biosynthesis on photoprotection and whole-plant acclimation of Arabidopsis to photo-oxidative stress

Functions of α- and β-branch carotenoids in whole-plant acclimation to photo-oxidative stress were studied in Arabidopsis thaliana wild-type (wt) and carotenoid mutants, lutein deficient (lut2, lut5), non-photochemical quenching1 (npq1) and suppressor of zeaxanthin-less1 (szl1) npq1 double mutant. Photo-oxidative stress was applied by exposing plants to sunflecks. The sunflecks caused reduction of chlorophyll content in all plants, but more severely in those having high α- to β-branch carotenoid composition (α/β-ratio) (lut5, szl1npq1). While this did not alter carotenoid composition in wt or lut2, which accumulates only β-branch carotenoids, increased xanthophyll levels were found in the mutants with high α/β-ratios (lut5, szl1npq1) or without xanthophyll-cycle operation (npq1, szl1npq1). The PsbS protein content increased in all sunfleck plants but lut2. These changes were accompanied by no change (npq1, szl1npq1) or enhanced capacity (wt, lut5) of NPQ. Leaf mass per area increased in lut2, but decreased in wt and lut5 that showed increased NPQ. The sunflecks decelerated primary root growth in wt and npq1 having normal α/β-ratios, but suppressed lateral root formation in lut5 and szl1npq1 having high α/β-ratios. The results highlight the importance of proper regulation of the α- and β-branch carotenoid pathways for whole-plant acclimation, not only leaf photoprotection, under photo-oxidative stress.Z.L. and K.K.N. were supported by a grant from the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy (FWP number 449B).Peer Reviewe

Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes

Protein crystallization is a powerful purification tool. It is the first step for crystallographic structural investigations, and can be preparatory for biotechnological applications. However, crystallizing proteins is challenging and methods to control the crystallization process are needed. Ionic-liquid hydrogel composite membranes (IL-HCMs) have been used here as material capable of supporting protein crystallization and hosting grown crystals. We found that IL-HCMs affect the selection mechanism of glucose isomerase (GI) polymorphs and make GI crystals grow completely immersed into the hydrogel layer. X-ray diffraction studies show that IL ions do not bind to the protein, likely because IL molecules are constrained in the polymeric framework. Our GI crystal structures have been compared with many existing GI crystal structures using multivariate analysis tools, allowing a comprehensive overview of factors determining structural similarities, i.e., temperature variations and external stresses exerted during or after crystal growth, such as dehydration or presence of hydrogel of a different nature. GI crystals grown on IL-HCM fit perfectly in this framework, showing typical features induced by external forces. Overall, protein crystallization by IL-HCMs show potential for biotechnological applications, as it could constitute a natural means for containing crystallized enzymes in working conditions

Crystal structure report of the ImmR transcriptional regulator DNA-binding domain of the Bacillus subtilis ICEBs1 transposon

Bacillus subtilis is a commensal member of the human oral and gut microbiomes, which can become infectious to immunocompromised patients. It possesses a conjugative transposon, ICEBs1, which includes > 20 genes and can be passed by horizontal gene transfer to other bacteria, including pathogenic Bacillus anthracis and Listeria monocytogenes. ICEBs1 is regulated by the ImmR/ImmA tandem, which are a transcriptional repressor that constitutively blocks transcription and a metallopeptidase that acts as anti-repressor and inactivates ImmR by proteolytic cleavage. We here report the production and purification of 127-residue ImmR from ICEBs1 and the crystal structure of its DNA-binding domain. It features a five-helix bundle centred on a helix-turn-helix motif potentially binding the major grove of double-stranded target DNA. ImmR shows structural and mechanistic similarity with the B. subtilis SinR repressor, which is engaged in sporulation inhibition.This study was supported in part by Grants Spanish and Catalan public and private bodies (Grant/fellowship references PID2019-107725RB-I00, 2017SGR3 and Fundació “La Marató de TV3” 201815)

Mechanistic and structural basis for inhibition of copper trafficking by platinum anticancer drugs

Copper (Cu) is required for maturation of cuproenzymes, cell proliferation, and angiogenesis and its transport entails highly specific protein-protein interactions. In humans, the Cu chaperone Atox1 mediates Cu(I) delivery to P-type ATPases Atp7a and Atp7b (the Menkes and Wilson disease proteins, respectively), which are responsible for Cu release to the secretory pathway and excess Cu efflux. Cu(I) handover is believed to occur through the formation of three-coordinate intermediates where the metal ion is simultaneously linked to Atox1 and to a soluble domain of Cu-ATPases, both sharing a CxxC dithiol motif. The ultra-high thermodynamic stability of chelating S-donor ligands secures the redox-active and potentially toxic Cu(I) ion, while their kinetic lability allows facile metal transfer. The same CxxC motifs can interact with and mediate the biological response to antitumor platinum drugs, which are among the most used chemotherapeutics. We show that cisplatin and an oxaliplatin analogue can specifically bind to the heterodimeric complex Atox1-Cu(I)-Mnk1 (Mnk1 is the first soluble domain of Atp7a), thus leading to a kinetically stable adduct that has been structurally characterized by solution NMR and X-ray crystallography. Of the two possible binding configurations of the Cu(I) ion in the cage made by the CxxC motifs of the two proteins, one (bidentate Atox1 and monodentate Mnk1) is less stable and more reactive toward cis-Pt(II) compounds, as shown by using mutated proteins. A Cu(I) ion can be retained at the Pt(II) coordination site, but can be released to glutathione (a physiological thiol) or to other complexing agents. The Pt(II)-supported heterodimeric complex does not form if Zn(II) is used in place of Cu(I) and transplatin instead of cisplatin. The results indicate that Pt(II) drugs can specifically affect Cu(I) homeostasis by interfering with the rapid exchange of Cu(I) between Atox1 and Cu-ATPases, with consequences on cancer cell viability and migration

The structural and functional characterization of Malus domestica double bond reductase MdDBR provides insights towards the identification of its substrates

In this study we describe the crystal structures of the apoform, the binary and the ternary complexes of a double bond reductase from Malus domestica L. (MdDBR) and explore a range of potential substrates. The overall fold of MdDBR is similar to that of the medium chain reductase/dehydrogenase/zinc-dependent alcohol dehydrogenase-like family. Structural comparison of MdDBR with Arabidopsis thaliana DBR (AtDBR), Nicotiana tabacum DBR (NtDBR) and Rubus idaeus DBR (RiDBR) allowed the identification of key amino acids involved in cofactor and ligands binding and shed light on how these residues may guide the orientation of the substrates. The enzyme kinetic for the substrate trans-4-phenylbuten-2-one has been analyzed, and MdDBR activity towards a variety of substrates was tested. This enzyme has been reported to be involved in the phenylpropanoid pathway where it would catalyze the NADPH-dependent reduction of the \u3b1, \u3b2-unsaturated double bond of carbonyl metabolites. Our study provides new data towards the identification of MdDBR natural substrate and the biosynthetic pathway where it belongs. Furthermore, the originally proposed involvement in dihydrochalcone biosynthesis in apple must be questioned

Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues

Acetylcholinesterase inhibitors were introduced for the symptomatic treatment of Alzheimer’s disease (AD). Among the currently approved inhibitors, donepezil (DNP) is one of the most preferred choices in AD therapy. The X-ray crystal structures of Torpedo californica AChE in complex with two novel rigid DNP-like analogs, compounds 1 and 2, have been determined. Kinetic studies indicated that compounds 1 and 2 show a mixed-type inhibition against TcAChE, with Ki values of 11.12 ± 2.88 and 29.86 ± 1.12 nM, respectively. The DNP rigidification results in a likely entropy-enthalpy compensation with solvation effects contributing primarily to AChE binding affinity. Molecular docking evidenced the molecular basis for the binding of compounds 1 and 2 to the active site of β-secretase-1. Overall, these simplified DNP derivatives may represent new structural templates for the design of lead compounds for a more effective therapeutic strategy against AD by foreseeing a dual AChE and BACE-1 inhibitory activity