Dalibor Milić

Cyclometalated Cluster Complex with a Butterfly-Shaped Pt2Ag2 Core

The cyclometalated platinum complex [PtMe(bhq)(dppy)] (1), in which bhq = benzo{h}quinoline and dppy = 2-(diphenylphosphino)pyridine, was prepared by the reaction of [PtMe(SMe(2))(bhq)] with 1 equiv of dppy at room temperature. Complex 1 contains one free pyridyl unit and was readily characterized by multinuclear NMR spectroscopy and elemental microanalysis. The reaction of complex 1 with 1 equiv of [Ag(CH(3)CN)(4)]BF(4) gave the cyclometalated cluster complex [Pt(2)Me(2)(bhq)(2)(mu-dppy)(2)Ag(2)(mu-acetone)](BF(4))(2) (2) in 70% yield. The crystal structure of complex 2 was determined by X-ray crystallography, indicating a rare example of a butterfly cluster with a Pt(2)Ag(2) core in which the Ag atoms occupy the edge-sharing bond. In solution, the bridging acetone dissociates from the cluster complex 2, but as shown by NMR spectroscopy, the Pt(2)Ag(2) core is retained in solution and a dynamic equilibrium is suggested to be established between the planar and butterfly skeletal geometries.

Crystallographic Snapshots of Tyrosine Phenol-lyase Show That Substrate Strain Plays a Role in C–C Bond Cleavage

The key step in the enzymatic reaction catalyzed by tyrosine phenol-lyase (TPL) is reversible cleavage of the Cβ–Cγ bond of l-tyrosine. Here, we present X-ray structures for two enzymatic states that form just before and after the cleavage of the carbon–carbon bond. As for most other pyridoxal 5′-phosphate-dependent enzymes, the first state, a quinonoid intermediate, is central for the catalysis. We captured this relatively unstable intermediate in the crystalline state by introducing substitutions Y71F or F448H in Citrobacter freundii TPL and briefly soaking crystals of the mutant enzymes with a substrate 3-fluoro-l-tyrosine followed by flash-cooling. The X-ray structures, determined at ∼2.0 Å resolution, reveal two quinonoid geometries: “relaxed” in the open and “tense” in the closed state of the active site. The “tense” state is characterized by changes in enzyme contacts made with the substrate’s phenolic moiety, which result in significantly strained conformation at Cβ and Cγ positions. We also captured, at 2.25 Å resolution, the X-ray structure for the state just after the substrate’s Cβ–Cγ bond cleavage by preparing the ternary complex between TPL, alanine quinonoid and pyridine N-oxide, which mimics the α-aminoacrylate intermediate with bound phenol. In this state, the enzyme–ligand contacts remain almost exactly the same as in the “tense” quinonoid, indicating that the strain induced by the closure of the active site facilitates elimination of phenol. Taken together, structural observations demonstrate that the enzyme serves not only to stabilize the transition state but also to destabilize the ground state.

The Formation of CuCl2‐Specific Metallogels of Pyridyloxalamide Derivatives in Alcohols

Isomeric pyridyloxalamide derivatives 1-3, which differed in the position of the nitrogen atom on the pyridyl ring, showed remarkably different gel-forming aptitudes in the presence of CuCl2 salt in alcohols. Whilst derivatives 1 and 3 formed a soluble complex and a solid precipitate, respectively, ligand 2 generated a remarkably metal- and anion-specific metallogel.

Insights Into the Catalytic Mechanism of Tyrosine Phenol-Lyase from X-Ray Structures of Quinonoid Intermediates.

Amino acid transformations catalyzed by a number of pyridoxal 5′-phosphate (PLP)-dependent enzymes involve abstraction of the Cα proton from an external aldimine formed between a substrate and the cofactor leading to the formation of a quinonoid intermediate. Despite the key role played by the quinonoid intermediates in the catalysis by PLP-dependent enzymes, limited accurate information is available about their structures. We trapped the quinonoid intermediates of Citrobacter freundii tyrosine phenol-lyase with l-alanine and l-methionine in the crystalline state and determined their structures at 1.9- and 1.95-Å resolution, respectively, by cryo-crystallography. The data reveal a network of protein-PLP-substrate interactions that stabilize the planar geometry of the quinonoid intermediate. In both structures the protein subunits are found in two conformations, open and closed, uncovering the mechanism by which binding of the substrate and restructuring of the active site during its closure protect the quinonoid intermediate from the solvent and bring catalytically important residues into positions suitable for the abstraction of phenol during the β-elimination of l-tyrosine. In addition, the structural data indicate a mechanism for alanine racemization involving two bases, Lys-257 and a water molecule. These two bases are connected by a hydrogen bonding system allowing internal transfer of the Cα proton.

Large-scale production and protein engineering of G protein-coupled receptors for structural studies

Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.

Organoplatinum(II) complexes containing chelating or bridging bis(N-heterocyclic carbene) ligands: formation of a platinum(II) carbonate complex by aerial CO2 fixation

The preparation of two new bis(N-heterocyclic carbene) platinum(II) complexes, in which NHC rings are joined by a CH(2) linker group, is described. While, the chelate complex [PtMe(2)(bis-NHC1)], 1, was formed with large tert-butyl wingtips, the iso-propyl N-substituent analogue favors formation of the cluster complex [Pt(2)Me(4)(μ-SMe(2))(μ-bis-NHC2)](2)(μ-Ag(2)Br(2)), 2, in which two binuclear platinum(II) complexes are linked together by an Ag(2)Br(2) unit. The chelating platinum complex 1 undergoes aerial CO(2) fixation and forms platinum(II) carbonate complex [Pt(CO(3))(bis-NHC1)], 3.

Vanadium-induced formation of thiadiazole and thiazoline compounds. Mononuclear and dinuclear oxovanadium(V) complexes with open-chain and cyclized thiosemicarbazone ligands

Reactions of the salicylaldehyde 4-phenylthiosemicarbazone (H(2)L) with selected vanadium(iv) and vanadium(v) precursors ([VO(acac)(2)], [VO(OAc)(2)], VOSO(4), [V(2)O(4)(acac)(2)]) were investigated under aerobic conditions in different alcohols (methanol, ethanol, propanol). In all examined cases mononuclear alkoxo vanadium(v) complexes [VOL(OR)] (1) (OR = OMe, OEt, OPr) were isolated as major products. On prolonged standing, mother liquids afforded dinuclear vanadium(v) complexes [V(2)O(3)(L(cycl))(2)(OR)(2)] (3) (OR = OMe, OEt, OPr), where L(cycl)(-) represents 1,3,4-thiadiazole ligand, formed by vanadium-induced oxidative cyclization of H(2)L. When [VO(acac)(2)] or [V(2)O(4)(acac)(2)] were used as precursors, in addition to products 1 and 3, a thiazoline derivative HL(acac)(cycl) (2) was isolated. This compound, formed by a reaction between acetylacetone and H(2)L, represented the second type of cyclic product. The products were characterized by IR and NMR spectroscopies, TG analysis, and in some cases by single-crystal X-ray diffraction. To the best of our knowledge, compounds [V(2)O(3)(L(cycl))(2)(OR)(2)] represent the first structurally characterized dinuclear vanadium(v) complexes with a thiadiazole moiety acting as a bridging ligand. Complexes 1 and 3, when dissolved in an appropriate alcohol, underwent substitution of the alkoxo ligand as confirmed by XRPD. The kinetics of reactions in methanolic solutions was qualitatively studied by UV-Vis and ESMS spectrometries. Under the experimental conditions applied, a relatively slow formation of the mononuclear complex [VOL(OMe)] and an even slower formation of the cyclic species 2 were observed, whereas the presence of dinuclear compound [V(2)O(3)(L(cycl))(2)(OMe)(2)] in the reaction mixture could not be detected.

High-throughput mutagenesis using a two-fragment PCR approach

Site-directed scanning mutagenesis is a powerful protein engineering technique which allows studies of protein functionality at single amino acid resolution and design of stabilized proteins for structural and biophysical work. However, creating libraries of hundreds of mutants remains a challenging, expensive and time-consuming process. The efficiency of the mutagenesis step is the key for fast and economical generation of such libraries. PCR artefacts such as misannealing and tandem primer repeats are often observed in mutagenesis cloning and reduce the efficiency of mutagenesis. Here we present a high-throughput mutagenesis pipeline based on established methods that significantly reduces PCR artefacts. We combined a two-fragment PCR approach, in which mutagenesis primers are used in two separate PCR reactions, with an in vitro assembly of resulting fragments. We show that this approach, despite being more laborious, is a very efficient pipeline for the creation of large libraries of mutants.

Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1

Synthetic peptides derived from ethylene-insensitive protein 2 (EIN2), a central regulator of ethylene signalling, were recently shown to delay fruit ripening by interrupting protein–protein interactions in the ethylene signalling pathway. Here, we show that the inhibitory peptide NOP-1 binds to the GAF domain of ETR1 – the prototype of the plant ethylene receptor family. Site-directed mutagenesis and computational studies reveal the peptide interaction site and a plausible molecular mechanism for the ripening inhibition.