Evidence for substrate preorganization in the peptidylglycine α-amidating monooxygenase reaction describing the contribution of ground state structure to hydrogen tunneling

Peptidylglycine α-amidating monooxygenase (PAM) is a bifunctional enzyme which catalyzes the post-translational modification of inactive C-terminal glycine-extended peptide precursors to the corresponding bioactive α-amidated peptide hormone. This conversion involves two sequential reactions both of which are catalyzed by the separate catalytic domains of PAM. The first step, the copper-, ascorbate-, and O(2)-dependent stereospecific hydroxylation at the α-carbon of the C-terminal glycine, is catalyzed by peptidylglycine α-hydroxylating monooxygenase (PHM). The second step, the zinc-dependent dealkylation of the carbinolamide intermediate, is catalyzed by peptidylglycine amidoglycolate lyase. Quantum mechanical tunneling dominates PHM-dependent C(α)-H bond activation. This study probes the substrate structure dependence of this chemistry using a set of N-acylglycine substrates of varying hydrophobicity. Primary deuterium kinetic isotope effects (KIEs), molecular mechanical docking, alchemical free energy perturbation, and equilibrium molecular dynamics were used to study the role played by ground-state substrate structure on PHM catalysis. Our data show that all Ν-acylglycines bind sequentially to PHM in an equilibrium-ordered fashion. The primary deuterium KIE displays a linear decrease with respect to acyl chain length for straight-chain N-acylglycine substrates. Docking orientation of these substrates displayed increased dissociation energy proportional to hydrophobic pocket interaction. The decrease in KIE with hydrophobicity was attributed to a preorganization event which decreased reorganization energy by decreasing the conformational sampling associated with ground state substrate binding. This is the first example of preorganization in the family of noncoupled copper monooxygenases.     

Neutralization of solvated protons and formation of noble-gas hydride molecules: matrix-isolation indications of tunneling mechanisms?

The (NgHNg)+ cations (Ng = Ar and Kr) produced via the photolysis of HFAr, HFKr, and HBrKr solid mixtures are studied, with emphasis on their decay mechanisms. The present experiments provide a large variety of parameters connected to this decay phenomenon, which allows us to reconsider various models for the decay of the (NgHNg)+ cations in noble-gas matrices. As a result, we propose that this phenomenon could be explained by the neutralization of the solvated protons by electrons. The mechanism of this neutralization reaction probably involves tunneling of an electron from an electronegative fragment or another trap to the (NgHNg)+ cation. The proposed electron-tunneling mechanism should be considered as a possible alternative to the literature models based on tunneling-assisted or radiation-induced diffusion of protons in noble-gas solids. As a novel experimental observation of this work, the efficient formation of HArF molecules occurs at 8 K in a photolyzed HFAr matrix. It is probable that the low-temperature formation of HArF involves local tunneling of the H atom to the Ar-F center, which in turn supports the locality of HF photolysis in solid Ar. In this model, the decay of (ArHAr)+ ions and the formation of HArF molecules observed at low temperatures are generally unconnected processes; however, the decaying (ArHAr)+ ions may contribute to some extent to the formation of HArF molecules.     

Multidimensional tunneling in the [1,5] shift in (Z)-1,3-pentadiene: how useful are Swain-Schaad exponents at detecting tunneling?

Rates, kinetic isotope effects (KIE), and Swain-Schaad exponents (SSE) have been calculated for a variety of isotopologues for the [1,5] shift in (Z)-1,3-pentadiene using mPW1K/6-31+G(d,p). Quantum mechanical effects along the reaction coordinate were incorporated with the zero-curvature tunneling (ZCT) model and with the multidimensional small curvature tunneling (SCT) model, which allows for coupling of modes perpendicular to the reaction coordinate. The latter model gives the best agreement with experimental rates and primary KIEs. The small quasiclassical primary KIE (2.6) is rationalized in terms of a nonlinear transition state. For sp3 to sp2 rehybridization, the quasiclassical alpha-secondary KIE shows an unusual inverse effect due to compression of the nonbonding hydrogens in the suprafacial transition state. SCT transmission coefficients (kappa) increase the rates by as much as one order of magnitude. Tunneling allows the reactant to evade 1-2.5 kcal/mol of the barrier depending on the isotope. Inclusion of tunneling in the secondary KIE increases it beyond the equilibrium isotope effect and converts the inverse effect (0.95) into a normal KIE (1.12). Tunneling was found to deflate the primary y SSE but by an amount too small to distinguish it from the quasiclassical SSE. On the other hand, when a specific labeling pattern is used, the difference between the quasiclassical secondary SSE (4.1) and the tunneling secondary SSE (2.3) may be sufficiently large to detect tunneling. The mixed secondary SSE shows even larger differences.     

Anionic polymerization of ϵ-caprolactam-lix effect of the ratio of reacting components,of the medium and of the ring size on the initial stage of the anionic polymerization of lactams

Effects of the concentrations and ratio of reacting components and of temperature on the kinetics of reaction of N-propionyllactam (I) with potassium salt of lactam (KL) were studied for derivatives of ϵ-caprolactam, 8-octanelactam and 12-dodecanelactam. For ϵ-caprolactam, the initial rates of propagation, acylation of open-chain amide groups and condensation of growth centres were estimated. At the ratio of the starting components [I]₀/[KL]₀ = 0.5-3, the participation of the polymerization reaction is constant, amounting to ca 45% of the overall consumption of 1. The condensation reaction is 14–36% of the total consumption of I; its initial rate passes through a maximum at [I]₀/[KL]₀ = 2. With increasing permittivity of the medium, the total rate of consumption of I increases; in two media with the same bulk permittivity, however, the rates may differ by as much as one order of magnitude.     

Construction of the Skeleton of Phthalascidin, Mechanism of the Formation of the Key Tricyclic Lactam Intermediate

Phthalascidin is a structurally simplified version of Et-743, which is a potent anti-tumor marine natural product isolated from Ecteinascidia turbinata. Its antiproliferative activity is greater than that of the agents taxol, camptothecin, adriamycin, mitomycin C, cisplatin, bleomycin, and etoposide by 1-3 orders of magnitude. An elegant synthesis of Et-743 and phthalascidin has been reported by E. J. Corey and co-workers1,2. As part of our continuing program, we have also engaged in dev…     

Synthesis of two peptides of α-bungarotoxin and the participation of the amino acid residue Trp-28 of the neurotoxin in the antigenicity of the molecule

Using the method of solid-phase peptide synthesis, two peptides have been synthesized, one of which corresponds to the central ring structure of -bungarotoxin (-BTX), while the second has in position 28 a Gly residue in place of the Trp in the first peptide, and their interrelationship with antitoxin antibodies has been investigated. It has been shown that the amino acid residue Trp-28 of -BTX, which is the contact residue in binding with the acetylcholine receptor, also participates directly in binding with the active centers of antibodies to -BTX.Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 628–631, July–August, 1997.     

Studies of the dissociation and the protonation of TB-chlorosulphophenol

The dissociation constant of each step for TB-chlorosulphophenol has been determined by potentiometric method, and the thermodynamic constants, △G°, △H° and △S°, of the dissociation process have been calculated. The protonation constants were measured by the spectrophotometric method. The pH values of various forms of anions of the chromogenic reagent at their concentrations were also calculated.     

Determination of the equilibrium melting point of the β-form of polypropylene

The melting behavior of the -form of isotactic polypropylene (-iPP) was investigated as a function of crystallization time and temperature. Calcium suberate, a selective -nucleating agent was used to produce samples that consist entirely of -form i-PP. The experimental melting points were recorded at different crystallization times and were extrapolated to the start of the crystallization process in order to eliminate the effect of lamellar thickening. Using the non-linear Hoffman—Weeks approach to correlate these extrapolated experimental melting temperatures with the corresponding crystallization temperatures, an equilibrium melting point of 209°C was obtained for -iPP. The equilibrium melting point estimated through the non-linear Hoffman—Weeks analysis is about 30°C higher than that (T _m ⁰=177°C) obtained on the basis of the linear extrapolation. These results are consistent with earlier claims that a linear extrapolation of T _m–T _c data leads to an underestimation of the equilibrium melting point. The results obtained for -iPP exemplify the importance of accounting for both the isothermal lamellar thickening effects and the non-linearity in the T _m–T _c correlation, when the determination of an equilibrium melting point is carried out using a procedure based on the predictions of the Lauritzen—Hoffman secondary nucleation theory.This revised version was published online in November 2005 with corrections to the Cover Date.     

Can the transition from tunneling to hopping in molecular junctions be predicted by theoretical calculation?

The electron transport mechanism changes from tunneling to hopping as molecular length increases. To validate the theoretical simulation after the transition point and clarify influence of electronic structures on the transition, we calculated the conductance of a series of conjugated molecules by density functional theory together with the nonequilibrium Green's function. We found that the highest occupied molecular orbital energy level, transmission spectrum, and the reorganization energy are good indicators for the transition of the electron transport mechanism. The calculated resistances of short junctions (<50 Å, before the transition point) are consistent with the experimental result, following the tunneling mechanism. However, the theoretical predication failed for long molecules, indicating the limitation of the theoretical framework of elastic scattering when the electron transport mechanism changes to hopping. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

The applicability of the “straight-line method” of asmus in the determination of the composition of polynuclear complexes

The straight-line method of Asmus was originally developed for the determination of n in mononuclear complexes of the general form AB_n (n≧ 1). In the present investigation it is demonstrated that the method also can be used for determining the value of n in polynuclear complexes of the form A[_mB_n (m > 1). The method as suggested by Asmus, is, however, not capable of distinguishing between mono- and polynuclear species. It is further shown, that the straight-line method can be applied for the determination of the value of m.     

The effect of the primary structure of the polypeptide catalyst on the enantioselectivity of the Juliá-Colonna asymmetric epoxidation of enones

Epoxidation of chalcone (1), using basic hydrogen peroxide, catalysed by polypeptides with defined primary structures demonstrates that the residues in the chain near to the N-terminus determine the stereochemical outcome of the reaction.     

Addition of γ-silyloxyallyltins on ethyl glyoxylate: evaluation of the influence of the experimental conditions on the stereochemical course of the reaction

Ethyl glyoxylate was reacted with α-substituted γ-(t-butyldimethylsilyloxy)-allyltributyltin in order to obtain selectively each diastereomer of ethyl 3-(t-butyldimethylsilyloxy)-2-hydroxyhex-4-enoate and subsequently the corresponding diols. Diastereomers syn-E, anti-E and anti-Z were obtained in good yields with good to high selectivities and the obtained results were rationalized by consideration of cyclic or open transition states in agreement with the experimental conditions and with the structure of the starting reagents.     

The kinetics of the polymorphic transition of the α-form of 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane

The α → γ polymorphic transition in hexanitrohexaazaisowurtzitane was studied by optical microscopy, calorimetry, IR spectroscopy, thermogravimetry, and X-ray diffraction. The thermal effect of the transition was determined. The kinetics of the process is complex because of the relation between structural rearrangement and transition with the removal of water stabilizing the structure of the α polymorph. Depending on the morphological characteristics of the initial sample, the polymorphic transition can follow a frontal-heterogeneous mechanism (single crystal → polycrystalline aggregate) or a quasi-homogeneous mechanism (single crystal → single crystal).     

Application of the Mössbauer spectroscopy to the study of the oxidation state of azaferrocene derivatives

Azaferrocene has two active sites of iron and nitrogen atoms. Drastic change of the oxidation state in iodine oxidation of azaferrocene is observed by introducing the methyl substituents into the pyrrole ring, while all the N-methylates show a similar electronic state. It was revealed that an introduction of methyl substituent to the pyrrole ring promotes the oxidation of nitrogen atom in pyrrole ring more than the central iron atom.     

Effect of the Composition of the Water–Dimethyl Sulfoxide Solvent on the Thermodynamics of the Formation of the [Ag(18-Crown-6)]+Complex

The effect of a water–dimethyl sulfoxide solvent (X _DMSO= 0–0.97, where X _DMSOis the mole fraction of DMSO) on the thermodynamics of complexation between Ag⁺and 18-crown-6 and the solvation of all reagents involved in this equilibrium were studied. In aqueous solutions, the complex is stable mainly because of the enthalpy contribution to _r G°. For X _DMSO> 0.3, the contributions from entropy and enthalpy become comparable in magnitude, but they are opposite in sign. In the binary solvent, the complex is most stable at X _DMSO= 0.2 to 0.3. Analysis of the enthalpy characteristics of reagent solvation showed that this solvent effect was due to the superposition of two opposite solvation contributions occurring with an increase in the DMSO concentration in the binary solvent, namely, the destabilization of the ligand solvate sphere and the formation of stable Ag⁺complexes with DMSO.