The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease,a Nickel Enzyme

Urease uses a cluster of two Ni^II ions to activate a water molecule for urea hydrolysis. The key to this unsurpassed enzyme is a change in the conformation of a flexible structural motif, the mobile flap, which must be able to move from an open to a closed conformation to stabilize the chelating interaction of urea with the Ni^II cluster. This conformational change brings the imidazole side chain functionality of a critical histidine residue, αHis323, in close proximity to the site that holds the transition state structure of the reaction, facilitating its evolution to the products. Herein, we describe the influence of the solution pH in modulating the conformation of the mobile flap. High-resolution crystal structures of urease inhibited in the presence of N-(n-butyl)phosphoric triamide (NBPTO) at pH 6.5 and pH 7.5 are described and compared to the analogous structure obtained at pH 7.0. The kinetics of urease in the absence and presence of NBPTO are investigated by a calorimetric assay in the pH 6.0–8.0 range. The results indicate that pH modulates the protonation state of αHis323, which was revealed to have pK_a=6.6, and consequently the conformation of the mobile flap. Two additional residues (αAsp224 and αArg339) are shown to be key factors for the conformational change. The role of pH in modulating the catalysis of urea hydrolysis is clarified through the molecular and structural details of the interplay between protein conformation and solution acidity in the paradigmatic case of a metalloenzyme.     

Regio‐ and Enantio‐selective Chemo‐enzymatic C−H‐Lactonization of Decanoic Acid to (S)‐δ‐Decalactone

The conversion of saturated fatty acids to high value chiral hydroxy‐acids and lactones poses a number of synthetic challenges: the activation of unreactive C?H bonds and the need for regio‐ and stereoselectivity. Here the first example of a wild‐type cytochrome P450 monooxygenase (CYP116B46 from Tepidiphilus thermophilus) capable of enantio‐ and regioselective C5 hydroxylation of decanoic acid 1 to (S)‐5‐hydroxydecanoic acid 2 is reported. Subsequent lactonization yields (S)‐δ‐decalactone 3 , a high value fragrance compound, with greater than 90 % ee. Docking studies provide a rationale for the high regio‐ and enantioselectivity of the reaction.     

Nature of the oxomolybdenum-thiolate pi-bond: implications for Mo-S bonding in sulfite oxidase and xanthine oxidase

The electronic structure of cis,trans-(L-N(2)S(2))MoO(X) (where L-N(2)S(2) = N,N'-dimethyl-N,N'-bis(2-mercaptophenyl)ethylenediamine and X = Cl, SCH(2)C(6)H(5), SC(6)H(4)-OCH(3), or SC(6)H(4)CF(3)) has been probed by electronic absorption, magnetic circular dichroism, and resonance Raman spectroscopies to determine the nature of oxomolybdenum-thiolate bonding in complexes possessing three equatorial sulfur ligands. One of the phenyl mercaptide sulfur donors of the tetradentate L-N(2)S(2) chelating ligand, denoted S(180), coordinates to molybdenum in the equatorial plane such that the OMo-S(180)-C(phenyl) dihedral angle is approximately 180 degrees, resulting in a highly covalent pi-bonding interaction between an S(180) p orbital and the molybdenum d(xy) orbital. This highly covalent bonding scheme is the origin of an intense low-energy S --> Mo d(xy) bonding-to-antibonding LMCT transition (E(max) approximately 16000 cm(-)(1), epsilon approximately 4000 M(-)(1) cm(-)(1)). Spectroscopically calibrated bonding calculations performed at the DFT level of theory reveal that S(180) contributes approximately 22% to the HOMO, which is predominantly a pi antibonding molecular orbital between Mo d(xy) and the S(180) p orbital oriented in the same plane. The second sulfur donor of the L-N(2)S(2) ligand is essentially nonbonding with Mo d(xy) due to an OMo-S-C(phenyl) dihedral angle of approximately 90 degrees. Because the formal Mo d(xy) orbital is the electroactive or redox orbital, these Mo d(xy)-S 3p interactions are important with respect to defining key covalency contributions to the reduction potential in monooxomolybdenum thiolates, including the one- and two-electron reduced forms of sulfite oxidase. Interestingly, the highly covalent Mo-S(180) pi bonding interaction observed in these complexes is analogous to the well-known Cu-S(Cys) pi bond in type 1 blue copper proteins, which display electronic absorption and resonance Raman spectra that are remarkably similar to these monooxomolybdenum thiolate complexes. Finally, the presence of a covalent Mo-S pi interaction oriented orthogonal to the MOO bond is discussed with respect to electron-transfer regeneration in sulfite oxidase and Mo=S(sulfido) bonding in xanthine oxidase.     

Thiazolidin-4-one formation. Mechanistic and synthetic aspects of the reaction of imines and mercaptoacetic acid under microwave and conventional heating

Microwave irradiation of a mixture of benzylidene-anilines and mercaptoacetic acid in benzene gives 1,3-thiazolidin-4-ones in very high yield (65-90%), whereas the same reaction performed through using the conventional method, at reflux temperature, requires a much longer time and gives a much lower yield (25-69%). This difference seems to be due to some intermediates and by-products formed during the conventional reaction. On the basis of 1H NMR studies, two different mechanisms, acting in benzene and in DMF, respectively, have been hypothesized for the thiazolidin-4-one system formation.     

Does a Reinforced Kinetic Macrocyclic Effect Exist? The Demetallation in Strong Acid of Copper(II) Complexes with Open and Cyclic Tetramines Containing a Piperazine Fragment

The demetallation in acidic solution of the Cu(II) complexes with open-chain and cyclic tetramines containing a piperazine unit (2 and 3) has been investigated in terms of its kinetic aspects and compared with the behaviour of unsubstituted counterparts (tetramines 1 and 4). The presence of the piperazine fragment slows demetallation of the open-chain-ligand complex owing to the activation barrier associated with the conformational change from boat-to-half-boat; however, it does not affect the demetallation of the macrocyclic complex, which involves the spontaneous boat-to-twist conformational change. Thus, lateral reinforcement of a cyclam-like ligand does not add any further contribution to the typical inertness in demetallation of macrocyclic complexes.     

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

The denatured state of a protein contains important information about the determinants of the folding process. By combining site-directed spin-labeling NMR experiments and restrained computer simulations, we have determined ensembles of conformations that represent the denatured state of the bovine acyl-coenzyme A binding protein (ACBP) at three different concentrations of guanidine hydrochloride. As the experimentally determined distance information corresponds to weighted averages over a broad ensemble of structures, we applied the experimental restraints to a system of noninteracting replicas of the protein by using a Monte Carlo sampling scheme. This procedure permits us to sample ensembles of conformations that are compatible with the experimental data and thus to obtain information regarding the distribution of structures in the denatured state. Our results show that the denatured state of ACBP is highly heterogeneous. The high sensitivity of the computational method that we present, however, enabled us to identify long-range interactions between two regions, located near the N- and C-termini, that include both native and non-native elements. The preferential formation of these contacts suggests that the sequence-dependent patterns of helical propensity and hydrophobicity are important determinants of the structure in the denatured state of ACBP.     

Interface induced crystal structures of dioctyl-terthiophene thin films

Temperature dependent structural and morphological investigations on semiconducting dioctyl-terthiophene (DOTT) thin films prepared on silica surfaces reveals the coexistence of surface induce order and distinct crystalline/liquid crystalline bulk polymorphs. X-ray diffraction and scanning force microscopy measurements indicate that at room temperature two polymorphs are present: the surface induced phase grows directly on the silica interface and the bulk phase on top. At elevated temperatures the long-range order gradually decreases, and the crystal G (340 K), smectic F (348 K), and smectic C (360 K) phases are observed. Indexation of diffraction peaks reveals that an up-right standing conformation of DOTT molecules is present within all phases. A temperature stable interfacial layer close to the silica-DOTT interface acts as template for the formation of the different phases. Rapid cooling of the DOTT sample from the smectic C phase to room temperature results in freezing into a metastable crystalline state with an intermediated unit cell between the room temperature crystalline phase and the smectic C phase. The understanding of such interfacial induced phases in thin semiconducting liquid crystal films allows tuning of crystallographic and therefore physical properties within organic thin films.     

GC-MS analysis of aroma of Medemia argun (mama-n-khanen or mama-n-xanin), an ancient Egyptian fruit palm

The fruits of the edible and medicinal Egyptian palm, Medemia argun, were collected from Aswan in Egypt and the essential oil (EO) from fruits and headspace (HS) of the seeds and fleshy mesocarps were analyzed by GC and GC-MS. Results obtained by GC-MS analysis indicated a high variability in the oil and in the headspace from seeds and mesocarps. Sesquiterpene derivatives were the main group of volatiles in the EO from fruits and in the HS from seeds (45.0 and 64.0%, respectively), while oxygenated hydrocarbon derivatives were the main constituents in the HS obtained from fleshy mesocarps (96.5%). The different chemical composition of the headspace obtained from the seeds and mesocarps of M. argun can be correlated with the different roles that the different constituents play in the prevention of dehydration of the fruits in the desert region from where the plant was collected.