Dynamic hydrogen-bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase

cd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme cofactor, found only in this class of enzymes, where the substrate, nitrite, binds and is converted to NO. For a long time, it was believed that NO must be released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of ferrous-nitroso complex, which was considered as a dead-end product. However, recently an enhanced rate of NO dissociation from the ferrous form, not observed in standard b-type hemes, has been reported and attributed to the unique d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J. Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the spatial and electronic structure of the ferrous d(1)-heme NO complex from Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in solution, searching for the unique properties that are responsible for the relatively fast release. There are three residues at the "distal" side of the heme (Tyr(10), His(327), and His(369)), and in this work we focus on the identification and characterization of possible H-bonds they can form with the NO, thereby affecting the stability of the complex. For this purpose, we have used high field pulse electron-nuclear double resonance (ENDOR) combined with density functional theory (DFT) calculations. The DFT calculations were essential for assigning and interpreting the ENDOR spectra in terms of geometric structure. We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms H-bonds with Tyr(10) and His(369), whereas the second conserved histidine, His(327), appears to be less involved in NO H-bonding. This is in contrast to the crystal structure that shows that Tyr(10) is removed from the NO. We have also observed a larger solvent accessibility to the distal pocket in the mutants as compared to the wild-type. Moreover, it was shown that the H-bonding network within the active site is dynamic and that a change in the protonation state of one of the residues does affect the strength and position of the H-bonds formed by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation of both distal histidines displaces Tyr(10), removing its H-bond. The implications of the H-bonding network found in terms of the complex stability and catalysis are discussed.     

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.     

Efficient synthesis of purines by inverse electron-demand Diels-Alder reactions of 1-substituted-1H-imidazol-5-amines with 1,3,5-triazines

The reaction of 1,3,5-triazine and 2,4,6-tri(trifluoromethyl)-1,3,5-triazine with in situ generated 1-substituted 5-amino-1H-imidazoles led to a set of functionalized purines. The developed practical route could serve as a fundament for the preparation of related ADA inhibitors.     

Evolution of amide stacking in larger γ-peptides: triamide H-bonded cycles

The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecule's midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.     

Synthesis of fluorinated purine and 1-deazapurine glycosides as potential inhibitors of adenosine deaminase

The synthesis of 2- and 6-trifluoromethylated purines and 1-deazapurines was performed by formal [3 + 3]-cyclization reactions of 5-aminoimidazoles with a set of trifluoromethyl-substituted 1,3-CCC- and 1,3-CNC-dielectrophiles. The corresponding fluorinated nucleosides were synthesized by glycosylation of 9-unsubstituted purines and 1-deazapurines with peracetylated β-ribose, β-glucose, and rhamnose and subsequent deprotection. These scaffolds can be considered as potential inhibitors of adenosine deaminase (ADA) and inosine monophosphate dehydrogenase (IMPDH) enzymes.     

Radical cations of disubstituted cyclopropanes: stereoelectronic effects on hyperfine coupling

The positive hyperfine coupling constants of the geminal ¹H nuclei in cis‐1,2‐dimethyl‐ and cis‐1,2‐diphenylcyclopropane radical cations show a significant stereoelectronic effect: the ¹H nuclei trans (anti) to the substituents are coupled much more strongly than the corresponding nuclei cis (syn) to them. Theoretical calculations on these radical cations and on bismethano[2,2]paracylophane as well as new ¹H‐CIDNP experiments at 200 Mz elucidate the general features of these systems. Copyright © 2014 John Wiley & Sons, Ltd.     

Total Synthesis of (18S)‐ and (18R)‐Homolargazole by Rhodium‐Catalyzed Hydrocarboxylation

Homolargazole derivatives, in which the macrocycle of natural largazole is extended by one methylene group, were prepared by the recently developed rhodium‐catalyzed hydrocarboxylation reaction onto allenes. This strategy gives access to both the (18S)‐ and (18R)‐stereoisomers in high stereoselectivity under ligand control.     

Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+

The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O-->Mg and Mg<--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.     

Evolution of a heavy rigid body rotation under the action of unsteady restoring and perturbation torques

The paper develops an approximate solution to the system of Euler’s equations with additional perturbation term for dynamically symmetric rotating rigid body. The perturbed motions of a rigid body, close to Lagrange’s case, under the action of restoring and perturbation torques that are slowly varying in time are investigated. We describe an averaging procedure for slow variables of a rigid body perturbed motion, similar to Lagrange top. Conditions for the possibility of averaging the equations of motion with respect to the nutation phase angle are presented. The averaging technique reduces the system order from 6 to 3 and does not contain fast oscillations. An example of motion of the body using linearly dissipative torques is worked out to demonstrate the use of general equations. The numerical integration of the averaged system of equations is conducted of the body motion. The graphical presentations of the solutions are represented and discussed. A new class of rotations of a dynamically symmetric rigid body about a fixed point with account for a nonstationary perturbation torque, as well as for a restoring torque that slowly varies with time, is studied. The main objective of this paper is to extend the previous results for problem of the dynamic motion of a symmetric rigid body subjected to perturbation and restoring torques. The proposed averaging method is implemented to receive the averaging system of equations of motion. The graphical representations of the solutions are presented and discussed. The attained results are a generalization of our former works where µ and M_i are independent of the slow time τ and M_i depend on the slow time only.

     

Synthesis, structural and hydrogenation properties of Mg-rich MgH2-TiH2 nanocomposites prepared by reactive ball milling under hydrogen gas

MgH(2)-TiH(2) nanocomposites have been obtained by reactive ball milling of elemental powders under 8 MPa of hydrogen pressure. The composites consist of a mixture of β-rutile MgH(2), γ-orthorhombic high pressure MgH(2) and ε-tetragonal TiH(2) phases with nanosized crystallites ranging from 4 to 12 nm. In situ hydrogen absorption curves on milling reveal that nanocomposite formation occurs in less than 50 min through the consecutive synthesis of the TiH(2) and MgH(2) phases. The abrasive and catalytic properties of TiH(2) speed up the formation of the MgH(2) phase. Thermodynamic, kinetic and cycling hydrogenation properties have been determined for the 0.7MgH(2)-0.3TiH(2) composite and compared to nanometric MgH(2). Only the MgH(2) phase desorbs hydrogen reversibly at moderate temperature (523 to 598 K) and pressure (10(-3) to 1 MPa). The presence of TiH(2) does not modify the thermodynamic properties of the Mg/MgH(2) system. However, the MgH(2)-TiH(2) nanocomposite exhibits outstanding kinetic properties and cycling stability. At 573 K, H-sorption takes place in less than 100 s. This is 20 times faster than for a pure nanometric MgH(2) powder. We demonstrate that the TiH(2) phase inhibits grain coarsening of Mg, which allows extended nucleation of the MgH(2) phase in Mg nanoparticles before a continuous and blocking MgH(2) hydride layer is formed. The low crystallinity of the TiH(2) phase and its hydrogenation properties are also compatible with a gateway mechanism for hydrogen transfer from the gas phase to Mg. Mg-rich MgH(2)-TiH(2) nanocomposites are an excellent media for hydrogen storage at moderate temperatures.