Measurement of the alpha-secondary kinetic isotope effect for the reaction catalyzed by mammalian protein farnesyltransferase

Protein farnesytransferase (FTase) catalyzes the transfer of a 15-carbon prenyl group from farnesyl diphosphate (FPP) to the cysteine residue of target proteins and is a member of the newest class of zinc metalloenzymes that catalyze sulfur alkylation. Common substrates of FTase include oncogenic Ras proteins, and therefore inhibitors are under development for the treatment of various cancers. An increased understanding of the salient features of the chemical transition state of FTase may aid in the design of potent inhibitors and enhance our understanding of the mechanism of this class of zinc enzymes. To investigate the transition state of FTase we have used transient kinetics to measure the alpha-secondary 3H kinetic isotope effect at the sensitive C1 position of FPP. The isotope effect for the FTase single turnover reaction using a peptide substrate that is farnesylated rapidly is near unity, indicating that a conformational change, rather than farnesylation, is the rate-limiting step. To look at the chemical step, the kinetic isotope effect was measured as 1.154 +/- 0.006 for a peptide that is farnesylated slowly, and these data suggest that FTase proceeds via a concerted mechanism with dissociative character.     

Structural characterization of the zinc site in protein farnesyltransferase

X-ray absorption spectroscopy has been used to determine the structure of the Zn site in protein farnesyltransferase. Extended X-ray absorption fine structure (EXAFS) data are consistent with a Zn site that is ligated to three low-Z (oxygen or nitrogen) ligands and one cysteine sulfur, as predicted from the crystal structures that are available for farnesyltransferase. However, in contrast with the crystallographic results the EXAFS data do not show evidence for significant distortions in the Zn-ligand distances. The average Zn-(N/O) and Zn-S distances are 2.04 and 2.31 A, respectively. Addition of a farnesyl diphosphate analogue causes no detectable change in the structure of the Zn site. However, addition of peptide substrate causes a change in ligation from ZnS(N/O)(3) to ZnS(2)(N/O)(2), consistent with ligation of the C-terminal cysteine to the Zn. There is no significant change in Zn-ligand distances when a substrate binds, demonstrating that the Zn remains four-coordinate. Addition of both peptide and farnesyl diphosphate to give the product complex causes the Zn to return to ZnS(N/O)(3) ligation, indicating that the product thioether is not tightly coordinated to the Zn. These spectroscopic experiments provide insight into the catalytic mechanism of FTase.     

Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism

Protein farnesyltransferase (FTase) is very promising anticancer drug target, with several drugs in advanced stages of clinical testing. However, in spite of the thrilling achievements in the development of farnesyltransferase inhibitors (FTIs) over the past few years, the farnesylation mechanism remains, to some degree, a mystery. This work reports the determination and validation of three sets of molecular mechanical parameters specifically tailored to accurately account for the very specific nature of the several Zn coordination spheres formed during the unclear catalytic pathway of this puzzling metalloenzyme, and built on the top of recent experimental and theoretical results that have dramatically changed the way how the farnesylation mechanism is perceived. Extensive validation studies with 14 FTase crystallographic structures, EXAFS data, DFT, and QM/MM theoretical calculations are presented.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Evidence for the role of tetramethylethylenediamine in aqueous Negishi cross-coupling: synthesis of nonproteinogenic phenylalanine derivatives on water

The structure of the alkylzinc-tetramethylethyl-enediamine (TMEDA) cluster cation 3 has been determined in the gas phase by a combination of tandem mass spectrometry, infrared multiphoton dissociation (IRMPD) spectroscopy, and DFT calculations. Both sets of experimental results establish the existence of a strongly stabilizing interaction of TMEDA with the zinc cation. High-level DFT calculations on the alkylzinc-TMEDA cluster cation 3 allowed the identification of two low energy conformers, each featuring a four-coordinate zinc atom with a bidentate TMEDA ligand, and internal coordination from the carbonyl group of the Boc group to zinc. The experimental IRMPD spectrum is reproduced with an appropriately weighted combination of the IR spectra of the two conformers identified by theory. DFT calculations on the structure of the alkylzinc halide 2 with coordinated TMEDA using the PCM model of water solvent suggest that TMEDA can promote ionization of the zinc-iodine bond in organozinc iodides under aqueous conditions, providing a credible explanation for the role of TMEDA in stabilizing the carbon-zinc bond. Reaction of the serine-derived iodide 1 with aryl iodides "on water", promoted by nano zinc in the presence of PdCl(2)(Amphos)(2) (5 mol %) and TMEDA, leads to the formation of protected phenylalanine derivatives 4 in reasonable yields. In the case of ortho-substituted aryl iodides and aryl iodides that are solids at room temperature, conducting the reaction at 65 °C gives improved results. In all cases, the product 5 of reductive dimerization of the iodide 1 is also isolated.     

Solid State Synthesis and Characterization of Zinc Oxide (ZnO) Microflakes by [Bis(acetylacetonato)zinc(II)] and Sodium Hydroxide at Room Temperature

A novel and simple one-step solid state reaction in the presence of a suitable surfactant, sodium dodecyl sulfate (SDS), and a novel precursor, [bis(acetylacetonato)zinc(II)]; [Zn(acac)₂]; has been developed to synthesize uniform zinc oxide microflakes with an average thickness of 0.3–2.4 μm. In the absence of SDS the product samples contained microrods. The formation of zinc oxide microflakes depends on the molar ratio of Zn(II)/SDS and the experimental procedure. The products were characterized by X-ray diffraction, photoluminescence spectroscopy, FT-IR spectroscopy, surface area, scanning electron microscopy and transmission electron microscopy to depict the phase and morphology. The synthesized ZnO microflakes have a hexagonal zincite structure.     

Experimental and theoretical evidence for the formation of zinc tricarbonyl in solid argon

Zinc carbonyls are extremely rare. Here we report experimental and theoretical evidence of unprecedented zinc tricarbonyl, Zn(CO)3, the next member of the series of 18-electron metal carbonyls Cr(CO)6 --> Fe(CO)5 --> Ni(CO)4, whereas there is no evidence for the formation of the zinc mono- and dicarbonyls Zn(CO)n (n = 1, 2). DFT calculations predict that the Zn(CO)3 molecule has a singlet ground state with D3h symmetry. The formation of Zn(CO)3 involves 4s --> 4p promotion of the Zn atom, which increases the Zn-CO bonding by decreasing the sigma repulsion and significantly increasing the Zn 4sp hybrid orbitals --> CO pi* back-donation.     

X-ray absorption near edge structure study on Acutolysin-C,a zinc-metalloproteinase from Agkistrodon acutus venom: Insight into the acid-inactive mechanism

Acutolysin-C, a snake-venom zinc metalloproteinase, displays a distinct pH-dependent proteolytic activity, which has been tentatively assigned to a structural change of the zinc-containing catalytic center. In this work we compare X-ray absorption near-edge structure (XANES) experimental spectra at the Zn K-edge and theoretical calculations of solutions at different pH values. The experimental data show clear differences confirmed by a best fit using the MXAN procedure. The results show that, when pH decreases from pH 8.0 to pH 3.0, the zinc-coordinating catalytic water molecule moves far from the Glu143 residue that is considered to play an essential role in the proteolytic process. Data suggests that this is the possible mechanism that deactivates the metalloproteinase.     

Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase

Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD⁺), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH^? and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxyacetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.     

Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases

X-ray analyses of matrix metalloproteinases (MMPs) have shown that the catalytic zinc ion (Zn1) can bind to one to three water molecules in addition to three conserved histidine residues. To estimate the relative stability of the possible Zn1 coordination structures in the active site of the MMPs, we carry out computational analyses on the coordination environment of the Zn1 ion in the gelatinase A enzyme (or matrix metalloproteinase 2; MMP-2). Four-, five-, and six-coordinated complexes representative of the Zn1 site are fully characterized by means of quantum mechanical (QM) methodologies. On one hand, B3LYP/LACVP* minimizations of various cluster models of the MMP-2 active site show that the trigonal bipyramidal geometry is energetically favored in the gas phase and that continuum solvent effects stabilize preferentially the tetrahedral complexes. On the other hand, B3LYP/OPLS-AA hybrid QM/molecular mechanical calculations in the solvated catalytic domain of the MMP-2 enzyme complemented with electrostatic Poisson-Boltzmann calculations show that the mature enzyme presents most likely a Zn1 ion coordinated by three histidine residues and two water molecules, while the active site glutamic acid is negatively charged. In consonance with X-ray diffraction data, other possible Zn1 configurations, a six-coordinated structure with Zn1-water as well as four- and five-coordinated complexes with a Zn1-bound hydroxide, are predicted to be very close in energy.     

Synthesis and crystal structure of two new discrete, neutral complexes of manganese and zinc using a rigid organic clip

Two discrete neutral dimanganese(II) and tetrazinc(II) complexes were synthesized from a rigid organic clip and the corresponding metal acetates. The compounds were characterized by elemental analysis and single crystal X-ray diffraction study. The manganese species is a dinuclear discrete product with two disordered acetates bridging two manganese centers, while the zinc one consists of two octahedral and two tetrahedral Zn(II) centers with both bridging acetates and triply micro(3)-hydroxides. Variable temperature magnetic measurement reveals the existence of weak antiferromagnetic interaction (J = -1.6 cm(-)(1); H = -2JS(1).S(2)) within the manganese complex.     

温度对ZnO薄膜电沉积的影响

通过0.1 mol·L-1 Zn(NO3)2体系在不同温度下的电势-pH图、组分的分布系数和ZnO/Zn(OH)2沉淀的溶解度热力学计算得出最佳电沉积实验条件及最终沉积产物. 随后用沉积过程的循环伏安曲线、电流密度-时间曲线、薄膜的X射线粉末衍射(XRD)、扫描电子显微镜(SEM)和热重-差热(TG-DSC)实验结果验证了热力学理论分析. 光学研究发现, ZnO薄膜在可见光区具有高透光度(>80%)和较为陡峭的吸收边缘. 提出硝酸锌水溶液中电沉积ZnO的反应机理.     

Helical structure of tercyclopropanedimethanol in solution

Oligocyclopropanes with repetitive stereochemistry occur in two unusual natural products with interesting bioactivity. X-ray crystal structures are available for these compounds but with partially contradicting results. Because the 1H and 13C NMR spectra of oligocyclopropanes are far from trivial to be assigned even at highest magnetic fields, we have prepared a specifically deuterated sample and have applied high field NMR spectroscopy and DFT calculations to determine its conformation. The helix with equal handedness shown in the stereopicture was found for tercyclopropanedimethanol. A dihedral angle of around +40 degrees is the best representation of the experimental data and characterizes, therefore, the dominating helical conformation of tercyclopropanedimethanol with a single repetitive (+)-gauche interunit dihedral angle. This is in full agreement with the crystal structure of the all syn,trans-quinquecyclopropanedimethanol with an R configuration at the termini that also adopted an all (+)-gauche conformation. However, the crystal structure of the title compound and the solution structure are different.     

Synthesis, Characterization and Weak Intramolecular Interactions of Porphyrins Bearing Nucleobases

5,10, 15-Triphenyl-20-{2- [α- (adenine-9 ) acetylamino]} phenyl porphyrin ( 1 ), 5,10, 15-triphenyl-20-{2-[α-(cytosine-1)acetylamino]} phenyl porphyrin (2), 5, 10, 15-triphenyl-20-{4-[α-(cytosine-1)ethoxy]} phenyl porphyrin (3) and their zinc complexes Zn-1, Zn-2 and Zn-3 have been prepared and characterized by ^1H NMR spectra, elemental analyses, electronic absorption spectra and mass spectra (FAB). Intramolecular π-π interactions and intramolecular metal-~ interaction for 1, 2, Zn-1,and Zn-2 have been investigated by several methods. ^1H NMR studies demonstrate that the porphyrin π-system in 1 and 2 is parallel to the adenine and the cytosine aromatic ring, respectively. The electronic absorption spectral properties of free porphyrin derivatives and their zinc complexes have been compared with those of H2TPP and ZnTPP. The results show that the UV-vis spectra of 1 and 2 are the same as that of H2TPP,whereas the spectra of their zinc complexes show 7 nm red shifts of the Soret bands compared to that of ZnTPP. The emission spectra of Zn-1 and Zn-2 are independent of excitation wavelength. From combination of the evidence of absorption and emission spectra it is suggested the existence of intramolecular metal-π interaction in Zn-1 and Zn-2. The results of conformational analysis agreed quite nicely with that of experiments, thus it was further to validate the experimental conclusions.     

Topological features of both electron density and electrostatic potential in the bis(thiosemicarbazide)zinc(II) dinitrate complex

The experimental electron density of the bis(thiosemicarbazide)zinc(II) dinitrate complex, [Zn(CH5N3S)2](NO3)2,was studied. The Hansen-Coppens multipole model was used to extract the electron density from high-resolution X-ray diffraction data collected at 100 K. Careful strategies were designed for the electron density refinements regarding the charge transfer between the anionic and the cationic parts of the complex. Particular attention was also paid to the treatment of the electron density of the zinc atom interacting with two thiosemicarbazide ligands in a tetrahedral coordination. Nevertheless, the filled 3d valence shell of Zn was found unperturbed, and only the 4s shell was engaged in the metal-ligand interaction. Topological properties of both electron density and electrostatic potential, including kinetic and potential energy densities, and atomic charges were reported to quantify a metal-ligand complex with particular Zn-S and Zn-N bonds and hydrogen-bonding features. Chemical activities were screened through the molecular surface on which the three-dimensional electrostatic potential function was projected. The experimental results were compared to those obtained from gas-phase quantum calculations, and a good agreement was reached between these two approaches. Finally, among other electrostatic potential critical points, the values at the maxima corresponding to the nuclear sites were used as indices of the hydrogen-bonding capacity of the thiosemicarbazide ligand.     

Structures, electronic states, and electroluminescent properties of a zinc(II) 2-(2-hydroxyphenyl)benzothiazolate complex

Bis(2-(2-hydroxyphenyl)benzothiazolate)zinc (Zn(BTZ)(2)) is one of the best white electroluminescent materials used in organic light-emitting diodes (LEDs). Despite a large number of studies devoted to this complex, very little is known about its basic molecular and electronic structures and electron transport properties in LEDs. Therefore, we investigate the structures and electroluminescent properties. The unsolvated single crystal of Zn(BTZ)(2) was grown and its crystalline structure was determined from X-ray diffraction data. The crystal is triclinic, space group P-1, a = 9.4890(19) A, b = 9.5687(19) A, c = 11.685(2) A, alpha = 84.38(3) degrees, beta = 78.94(3) degrees, gamma = 83.32(3) degrees. The structure of the chelate is dimeric [Zn(BTZ)(2)](2) with two isotropic Zn(2+) ion centers having five-coordinate geometry. The present study provides direct evidence for the sole existence of dimeric structure in the powder and the thin film. The dimer is energetically more stable than the monomer. Analysis of the electronic structure of [Zn(BTZ)(2)](2) calculated by density functional theory reveals a localization of orbital and the distribution of four orbital "tetrads". The structural stabilities of both anion and cation and the distribution of the hole in the cation and that of the excess electron in the anion are discussed in terms of theoretical calculations. Strong intermolecular interaction may be expected to enable good electron transport properties as compared with tris(8-hydroxyquinolinato)aluminum.     

Chemical effects in diffusion and structure of zinc chloride in aqueous solution

In the absence of neutron data, we have examined existing experimental data for X-ray, Raman scattering, EXAFS and thermodynamic activity studies in order to build up a consistent model of the structure of ZnCl₂ in aqueous solution in the range of molality from 2 up to saturation. The structure that emerges is that Zn is tetrahedrally coordinated and that in these coordination complexes the number of Cl ions per Zn ion increases with increasing molality, this implying the existence of extended Zn structures as the saturation concentration is approached. Relevant evidence in support of these structural models has been obtained by measuring the diffusion constants of Zn. Cl and H₂O when the stoichiometry of the solution is varied by replacing Zn by Li. This evidence strongly supports the model in which available Cl ions form complexes with Zn up to at least four Cl ions per Zn ion.     

Antibiotic deactivation by a dizinc beta-lactamase: mechanistic insights from QM/MM and DFT studies

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods and density functional theory (DFT) were used to investigate the initial ring-opening step in the hydrolysis of moxalactam catalyzed by the dizinc L1 beta-lactamase from Stenotrophomonas maltophilia. Anchored at the enzyme active site via direct metal binding as suggested by a recent X-ray structure of an enzyme-product complex (Spencer, J.; et al. J. Am. Chem. Soc. 2005, 127, 14439), the substrate is well aligned with the nucleophilic hydroxide that bridges the two zinc ions. Both QM/MM and DFT results indicate that the addition of the hydroxide nucleophile to the carbonyl carbon in the substrate lactam ring leads to a metastable intermediate via a dominant nucleophilic addition barrier. The potential of mean force obtained by SCC-DFTB/MM simulations and corrected by DFT/MM calculations yields a reaction free energy barrier of 23.5 kcal/mol, in reasonable agreement with the experimental value of 18.5 kcal/mol derived from kcat of 0.15 s(-1). It is further shown that zinc-bound Asp120 plays an important role in aligning the nucleophile, but accepts the hydroxide proton only after the nucleophilic addition. The two zinc ions are found to participate intimately in the catalysis, consistent with the proposed mechanism. In particular, the Zn(1) ion is likely to serve as an "oxyanion hole" in stabilizing the carbonyl oxygen, while the Zn(2) ion acts as an electrophilic catalyst to stabilize the anionic nitrogen leaving group.     

Synthesis, Characterization, and Theoretical Study of Sulfur-Containing Donor-Acceptor DCNQI Derivatives with Photoinduced Intramolecular Electron Transfer

The donor-acceptor compounds N,N'-dicyanobenzo[b]naphtho[2,3-e][1,4]dithiin-6,11-quinonediimine (9a) and N,N'-dicyanobenzo[b]naphtho[2,3-e][1,4]oxathiin-6,11-quinonediimine (10a) and their methyl-substituted derivatives (9b and 10b-d, respectively) have been prepared, and their structural and electronic properties have been characterized by both experimental techniques and quantum-chemical calculations. The (1)H-NMR spectra evidence the existence of a syn/anti isomerism in solution. Both experimental and theoretical data suggest that the preferred configuration of the N-CN groups corresponds to a syn isomer for 9 and to an anti isomer for 10. The X-ray analysis performed for 9b reveals that molecules are not planar and pack in vertical stacks showing an overlap between donor and acceptor moieties of adjacent molecules. In agreement with X-ray data, theoretical calculations predict that both for 9 and 10 the acceptor DCNQI moiety is folded and adopts a butterfly-type structure and the donor moiety is bent along the line passing through the heteroatoms. The energy difference between planar and butterfly structures is calculated to be < 3 kcal/mol at the ab initio 6-31G level. The UV-vis spectra present a broad absorption in the visible which corresponds to a photoinduced intramolecular electron transfer from the high-energy HOMO furnished by the donor moiety to the low-energy LUMO located on the DCNQI fragment. Cyclic voltammetry displays one oxidation peak to the cation and two one-electron reduction waves to the anion and dianion. Theoretical calculations show the planarization of the acceptor/donor moiety induced by reduction/oxidation. The formation of stable radical anions is corroborated by the intense EPR signals recorded for reduced 9. The assignment of the hyperfine coupling constants of the EPR spectra is consistent with the existence of a preferred syn configuration.     

Catalytic mechanism of glyoxalase I: a theoretical study

Hybrid density functional theory is used to study the catalytic mechanism of human glyoxalase I (GlxI). This zinc enzyme catalyzes the conversion of the hemithioacetal of toxic methylglyoxal and glutathione to nontoxic (S)-D-lactoylglutathione. GlxI can process both diastereomeric forms of the substrate, yielding the same form of the product. As a starting point for the calculations, we use a recent crystal structure of the enzyme in complex with a transition-state analogue, where it was found that the inhibitor is bound directly to the zinc by its hydroxycarbamoyl functions. It is shown that the Zn ligand Glu172 can abstract the substrate C1 proton from the S enantiomer of the substrate, without being displaced from the Zn ion. The calculated activation barrier is in excellent agreement with experimental rates. Analogously, the Zn ligand Glu99 can abstract the proton from the R form of the substrate. To account for the stereochemical findings, it is argued that the S and R reactions cannot be fully symmetric. A detailed mechanistic scheme is proposed.     

Effect of Zn...Zn separation on the hydrolytic activity of model dizinc phosphodiesterases

From the study of highly preorganized model systems, experimental support has been obtained for a possible functional role of the Zn-(H)O...HO(H)-Zn motif in oligozinc hydrolases. The mechanistic relevance of such an array, which may be described as a hydrated form of a pseudo-terminal Zn-bound hydroxide, has recently been supported by DFT calculations on various metallohydrolase active sites. In the present targeted approach, the Zn...Zn distance in two related dizinc complexes has been controlled through the use of multifunctional pyrazolate-based ligand scaffolds, giving either a tightly bridged Zn-O(H)-Zn or a more loosely bridged Zn-(H)O...HO(H)-Zn species in the solid state. Zn-bound water has been found to exhibit comparable acidity irrespective of whether the resulting hydroxide is supported by strong hydrogen-bonding in the O(2)H(3) moiety or is in a bridging position between two zinc ions, indicating that water does not necessarily have to adopt a bridging position in order for its pK(a) to be sufficiently lowered so as to provide a Zn-bound hydroxide at physiological pH. Comparative reactivity studies on the cleavage of bis(4-nitrophenyl)phosphate (BNPP) mediated by the two dizinc complexes have revealed that the system with the larger Zn...Zn separation is hydrolytically more potent, both in the hydrolysis and the transesterification of BNPP. The extent of active site inhibition by the reaction products has also been found to be governed by the Zn...Zn distance, since phosphate diester coordination in a bridging mode within the clamp of two zinc ions is only favored for Zn...Zn distances well above 4 A. Different binding affinities are rationalized in terms of the structural characteristics of the product-inhibited complexes for the two different ligand scaffolds, with dimethyl phosphate found as a bridging ligand within the bimetallic pocket.