Michaelis-Menten Quantification of Ligand Signaling Bias Applied to the Promiscuous Vasopressin V2 Receptor.

Activation of G protein-coupled receptors by agonists may result in the activation of one or more G proteins and recruitment of arrestins. The extent of the activation of each of these pathways depends on the intrinsic efficacy of the ligand. Quantification of intrinsic efficacy relative to a reference compound is essential for the development of novel compounds. In the operational model, changes in efficacy can be compensated by changes in the "functional" affinity, resulting in poorly defined values. To separate the effects of ligand affinity from the intrinsic activity of the receptor, we developed a Michaelis-Menten based quantification of G protein activation bias that uses experimentally measured ligand affinities and provides a single measure of ligand efficacy. We used it to evaluate the signaling of a promiscuous model receptor, the Vasopressin V2 receptor (V2R). Using BRET-based biosensors, we show that the V2R engages many different G proteins across all G protein subfamilies in response to its primary endogenous agonist, arginine vasopressin, including Gs and members of the Gi/o and G12/13 families. These signaling pathways are also activated by the synthetic peptide desmopressin, oxytocin, and the nonmammalian hormone vasotocin. We compared bias quantification using the operational model with Michaelis-Menten based quantification; the latter accurately quantified ligand efficacies despite large difference in ligand affinities. Together, these results showed that the V2R is promiscuous in its ability to engage several G proteins and that its' signaling profile is biased by small structural changes in the ligand. SIGNIFICANCE STATEMENT: By modelling the G protein activation as Michaelis-Menten reaction, we developed a novel way of quantifying signalling bias. V2R activates, or at least engages, G proteins from all G protein subfamilies, including Gi2, Gz, Gq, G12, and G13. Their relative activation may explain its Gs-independent signalling.

High-throughput Site-directed Scanning Mutagenesis Using a Two-fragment PCR Approach.

Site-directed scanning mutagenesis is a useful tool applied in studying protein function and designing proteins with new properties, such as increased stability or enzymatic activity. Creating a systematic library of hundreds of site-directed mutants is still a demanding and expensive task. The established protocols for making such libraries include PCR amplification of the recombinant DNA using a pair of primers carrying a target mutation in the same PCR. Unfortunately, this approach is very often coupled with PCR artifacts which compromise overall efficiency of site-directed mutagenesis. To reduce the failure rate due to the PCR artifacts, we have set up a high-throughput mutagenesis protocol based on a two-fragment PCR approach. To this end, each mutation is introduced in two separate PCRs resulting in two linear fragments of the mutated plasmid. In the next steps, the PCR template is digested and the two matching plasmid fragments are joined together using Gibson assembly. Separating the corresponding mutagenic primers into two different PCRs decreases a number of artifacts and thus increases overall cloning efficiency. Furthermore, free software that we developed facilitates both high-throughput primer design and analysis of sequencing results. Overall, this protocol enabled us to efficiently produce several alanine-scanning libraries of 400 single-point mutations with complete coverage of the protein sequence.

Molecular mechanism of leukocidin GH-integrin CD11b/CD18 recognition and species specificity.

Host-pathogen interactions are central to understanding microbial pathogenesis. The staphylococcal pore-forming cytotoxins hijack important immune molecules but little is known about the underlying molecular mechanisms of cytotoxin-receptor interaction and host specificity. Here we report the structures of a staphylococcal pore-forming cytotoxin, leukocidin GH (LukGH), in complex with its receptor (the α-I domain of complement receptor 3, CD11b-I), both for the human and murine homologs. We observe 2 binding interfaces, on the LukG and the LukH protomers, and show that human CD11b-I induces LukGH oligomerization in solution. LukGH binds murine CD11b-I weakly and is inactive toward murine neutrophils. Using a LukGH variant engineered to bind mouse CD11b-I, we demonstrate that cytolytic activity does not only require binding but also receptor-dependent oligomerization. Our studies provide an unprecedented insight into bicomponent leukocidin-host receptor interaction, enabling the development of antitoxin approaches and improved animal models to explore these approaches.

Soluble and membrane-bound protein carrier mediate direct copper transport to the ethylene receptor family.

The plant hormone ethylene is a key regulator of plant growth, development and stress adaption. Ethylene perception and response are mediated by a family of integral membrane receptors (ETRs) localized at the ER-Golgi network. The biological function of these receptors relies on a protein-bound copper cofactor. Nonetheless, molecular processes and structures controlling assembly and integration of the metal into the functional plant hormone receptor are still unknown. Here, we have explored the molecular pathways of copper transfer from the plant cytosol to the ethylene receptor family by analyzing protein-protein interactions of receptors with soluble and membrane-bound plant copper carriers. Our results suggest that receptors primarily acquire their metal cofactor from copper transporter RESPONSIVE-TO-ANTAGONIST-1 (RAN1) which has been loaded with the transition metal beforehand by soluble copper carriers of the ATX1-family. In addition, we found evidence for a direct interaction of ETRs with soluble chaperones ANTIOXIDANT-1 (ATX1) and COPPER TRANSPORT PROTEIN (CCH) raising the possibility of a direct copper exchange between soluble chaperones and receptors.

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.

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.

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.

Crystal structures and magnetic properties of a set of dihalo-bridged oxalamidato copper(II) dimers.

A set of four copper(ii) complexes, and (X = Cl, Br; = N-(l-leucine methyl ester)-N'-((2-pyridin-2-yl)methyl)oxalamide and = N-benzyl-N'-((2-pyridin-2-yl)methyl)oxalamide), have been synthesized and characterized by X-ray structural analysis, electron paramagnetic resonance (EPR) spectroscopy on single crystals and by SQUID magnetization measurements. X-ray diffraction studies show one-dimensional hydrogen bonded networks of dimeric copper(ii)-complexes bridged by two halide ions and with the two metal centers 3.44-3.69 Šapart. The geometry at each copper(ii) atom is ideal or near ideal square pyramidal. EPR and SQUID studies indicate that all complexes exhibit weak antiferromagnetic interactions between the Cu(ii) paramagnetic centers, with exchange parameter |J| ∼ 1 cm(-1). Magneto-structural comparisons among similar dihalo-bridged Cu(ii) dinuclear complexes are also provided, and a possible correlation has been established.

Cyclometalated heteronuclear Pt/Ag and Pt/Tl complexes: a structural and photophysical study.

To investigate the factors influencing the luminescent properties of polymetallic cycloplatinated complexes a detailed study of the photophysical and structural properties of the heteronuclear complexes [Pt2Me2(bhq)2(µ-dppy)2Ag2(µ-acetone)](BF4)2, 2, [PtMe(bhq)(dppy)Tl]PF6, 3, and [Pt2Me2(bhq)2(dppy)2Tl]PF6, 4, [bhq = benzo[h]quinoline, dppy = 2-(diphenylphosphino)pyridine] was conducted. Complexes 3 and 4 synthesized by the reaction of [PtMe(bhq)(dppy)], 1, with TlPF6 (1 or 1/2 equiv.) and stabilized by unsupported Pt-Tl bonds as revealed by multinuclear NMR spectroscopy and confirmed by X-ray crystallography for 3. DFT calculations for the previously reported butterfly Pt2Ag2 cluster 2 reveal that in the optimized geometry the bridging acetone molecule is removed and the metal core displays a planar-shaped geometry in which according to a QTAIM calculation and natural bond orbital (NBO) analysis the Ag···Ag metallophilic interaction is strengthened. In contrast to the precursor 1, which is only emissive in glassy solutions ((3)MLCT 485 nm), all 2-4 heteropolynuclear complexes display intense emissions in the solid state and in glassy solutions. Time-dependent density functional theory (TD-DFT) is used to elucidate the origin of the electronic transitions in the heteronuclear complexes 2 and 3. The low energy absorption and intense orange emission for cluster 2 (solid 77 K and glass) are attributed to metal-metal to ligand charge transfer (MM'LCT) with a minor L'LCT contribution. For 3 and 4 two different bands are developed: the high energy band (602-630 nm) observed for 4 at 77 K (solid, glass) and in diluted glasses for 3 is ascribed to emission from discrete Pt2Tl units of mixed (3)L'LCT/(3)LM'CT origin. However, the low energy band (670-690 nm) observed at room temperature (solid) for both complexes and also in concentrated glasses for 3 is assigned to (3)ππ excited states arising from intermolecular interactions.

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.

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 Cß-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 Cß and Cγ positions. We also captured, at 2.25 Å resolution, the X-ray structure for the state just after the substrate's Cß-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.

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.

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.

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.

Three quinolone compounds featuring O...I halogen bonding.

Ethyl 1-ethyl-6-iodo-4-oxo-1,4-dihydroquinoline-3-carboxylate, C14H14INO3, (I), and ethyl 1-cyclopropyl-6-iodo-4-oxo-1,4-dihydroquinoline-3-carboxylate, C15H14INO3, (II), have isomorphous crystal structures, while ethyl 1-dimethylamino-6-iodo-4-oxo-1,4-dihydroquinoline-3-carboxylate, C14H15IN2O3, (III), possesses a different solid-state supramolecular architecture. In all three structures, O...I halogen-bonding interactions connect the quinolone molecules into infinite chains parallel to the unique crystallographic b axis. In (I) and (II), these molecular chains are arranged in (101) layers, via pi-pi stacking and C-H...pi interactions, and these layers are then interlinked by C-H...O interactions. The structural fragments involved in the C-H...O interactions differ between (I) and (II), accounting for the observed difference in planarity of the quinolone moieties in the two isomorphous structures. In (III), C-H...O and C-H...pi interactions form (100) molecular layers, which are crosslinked by O...I and C-H...I interactions.

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 Calpha 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-A 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 beta-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 Calpha proton.

Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions.

Tyrosine phenol-lyase, a tetrameric pyridoxal 5'-phosphate dependent enzyme, catalyzes the reversible hydrolytic cleavage of L-tyrosine to phenol and ammonium pyruvate. Here we describe the crystal structure of the Citrobacter freundii holoenzyme at 1.9 A resolution. The structure reveals a network of protein interactions with the cofactor, pyridoxal 5'-phosphate, and details of coordination of the catalytically important K+ ion. We also present the structure of the apoenzyme at 1.85 A resolution. Both structures were determined using crystals grown at pH 8.0, which is close to the pH of the maximal enzymatic activity (8.2). Comparison of the apoenzyme structure with the one previously determined at pH 6.0 reveals significant differences. The data suggest that the decrease of the enzymatic activity at pH 6.0 may be caused by conformational changes in the active site residues Tyr71, Tyr291, and Arg381 and in the monovalent cation binding residue Glu69. Moreover, at pH 8.0 we observe two different active site conformations: open, which was characterized before, and closed, which is observed for the first time in beta-eliminating lyases. In the closed conformation a significant part of the small domain undergoes an extraordinary motion of up to 12 A toward the large domain, closing the active site cleft and bringing the catalytically important Arg381 and Phe448 into the active site. The closed conformation allows rationalization of the results of previous mutational studies and suggests that the observed active site closure is critical for the course of the enzymatic reaction and for the enzyme's specificity toward its physiological substrate. Finally, the closed conformation allows us to model keto(imino)quinonoid, the key transition intermediate.