Structural Study of the Partially Disordered Full‐Length δ Subunit of RNA Polymerase from Bacillus subtilis

The partially disordered δ subunit of RNA polymerase was studied by various NMR techniques. The structure of the well‐folded N‐terminal domain was determined based on inter‐proton distances in NOESY spectra. The obtained structural model was compared to the previously determined structure of a truncated construct (lacking the C‐terminal domain). Only marginal differences were identified, thus indicating that the first structural model was not significantly compromised by the absence of the C‐terminal domain. Various ¹⁵N relaxation experiments were employed to describe the flexibility of both domains. The relaxation data revealed that the C‐terminal domain is more flexible, but its flexibility is not uniform. By using paramagnetic labels, transient contacts of the C‐terminal tail with the N‐terminal domain and with itself were identified. A propensity of the C‐terminal domain to form β‐type structures was obtained by chemical shift analysis. Comparison with the paramagnetic relaxation enhancement indicated a well‐balanced interplay of repulsive and attractive electrostatic interactions governing the conformational behavior of the C‐terminal domain. The results showed that the δ subunit consists of a well‐ordered N‐terminal domain and a flexible C‐terminal domain that exhibits a complex hierarchy of partial ordering.     

Base‐Pairing Behavior of a Carbocyclic Janus‐AT Nucleoside Analogue Capable of Recognizing A and T within a DNA Duplex

Janus‐type nucleosides are heterocycles with two faces, each of which is designed to complement the H‐bonding interactions of natural nucleosides comprising a canonical Watson–Crick base pair. By intercepting all of the hydrogen bonds contained within the base pair, oligomeric Janus nucleosides are expected to achieve sequence‐specific DNA recognition through the formation of J‐loops that will be more stable than D‐loops, which simply replaces one base‐pair with another. Herein, we report the synthesis of a novel Janus‐AT nucleoside analogue, J_AT, affixed on a carbocyclic analogue of deoxyribose that was converted to the corresponding phosphoramidite. A single J_AT was successfully incorporated into a DNA strand by solid phase for targeting both A and T bases, and characterized through biophysical and computational methods. Experimental UV‐melting and circular dichroism data demonstrated that within the context of a standard duplex, J_AT associates preferentially with T over A, and much more poorly with C and G. Density functional theory calculations confirm that the J_AT structure is well suited to associate only with A and T thereby highlighting the importance of the electronic structure in terms of H‐bonding. Finally, molecular dynamics simulations validated the observation that J_AT can substitute more effectively as an A‐analogue than as a T‐analogue without substantial distortion of the B‐helix. Overall, this new Janus nucleotide is a promising tool for the targeting of A–T base pairs in DNA, and will lead to the development of oligo‐Janus‐nucleotide strands for sequence‐specific DNA recognition.     

Structural Basis for the Improved Potency of Peroxisome Proliferator‐Activated Receptor (PPAR) Agonists

The need to develop safer and more effective antidiabetic drugs is essential owing to the growth worldwide of the diabetic population. Targeting the PPAR receptor is one strategy for the treatment of diabetes; the PPAR agonists rosiglitazone and pioglitazone are already on the market. Here we report the identification of a potent PPAR agonist, 15 , whose PPARγ activation was more than 20 times better than that of rosiglitazone. Compound 15 was designed to incorporate an indole head with a carboxylic acid group, and 4‐phenylbenzophenone tail to achieve a PPARγ EC₅₀ of 10 nM . Compound 15 showed the most potent PPARγ agonist activity among the compounds we investigated. To gain molecular insight into the improved potency of 15 , a structural biology study and binding energy calculations were carried out. Superimposition of the X‐ray structures of 15 and agonist 10 revealed that, even though they have the same indole head part, they adopt different conformations. The head part of 15 showed stronger interactions toward PPARγ; this could be due to the presence of the novel tail part 4‐phenylbenzophenone, which could enhance the binding efficiency of 15 to PPARγ.     

Monooxime‐monocarbamoyl Bispyridinium Xylene‐Linked Reactivators of Acetylcholinesterase—Synthesis,In vitro and Toxicity Evaluation,and Docking Studies

Acetylcholinesterase (AChE) reactivators are crucial antidotes to organophosphate intoxication. A new series of 26 monooxime‐monocarbamoyl xylene‐linked bispyridinium compounds was prepared and tested in vitro, along with known reactivators (pralidoxime, HI‐6, obidoxime, trimedoxime, methoxime, K107, K108 and K203), on a model of tabun‐ and paraoxon‐, methylparaoxon‐ and DFP‐inhibited human erythrocyte AChE. Although their ability to reactivate tabun‐inhibited AChE did not exceed that of the previously known compounds, some newly prepared compounds showed promising reactivation of pesticide‐inhibited AChE. The acute toxicity of the novel compounds was also determined. Docking studies using tabun‐inhibited AChE were performed for three compounds of interest. The structure–activity relationship (SAR) study confirmed the apparent influence of the xylene linkage and carbamoyl moiety on the reactivation ability and toxicity of the agents.     

Decoupled Roles for the Atypical,Bifurcated Binding Pocket of the ybfF Hydrolase

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate‐binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc‐ybfF) by using a 21‐member library of fluorogenic ester substrates. We assigned the roles of the two substrate‐binding clefts in controlling the substrate selectivity and folded stability of Vc‐ybfF by comprehensive substitution analysis. The overall substrate preference of Vc‐ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc‐ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc‐ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc‐ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.     

Supercritical water for environmental technologies

OVERVIEW: Supercritical water is a great medium in which to perform chemical reactions and to develop processes. Due to its unique thermo‐physico‐chemical properties, supercritical water is able to play the role of solvent of organic compounds and/or to react with them. These specific properties have been used since the 1990s to develop new technologies dedicated to the environment and energy. IMPACT: Supercritical water based technologies are innovative and efficient processes having a strong impact on society, the environment and the economy, and is termed a sustainable technology. APPLICATIONS: Three main applications for supercritical water technology are under development: (i) supercritical water oxidation (SCWO); (ii) supercritical water biomass gasification (SCBG); and (iii) hydrolysis of polymers in supercritical water (HPSCW) for composites/plastics recycling. In this paper some fundamentals of supercritical water are first presented to introduce the above three major developments. Then these technologies are reviewed in terms of their present and future industrial development and their impact on the environment and on energy production. Copyright © 2010 Society of Chemical Industry