Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.     

Catch the kinase conformer

Protein kinases exist in inactive and active states, but little attention has been paid to which state is or should be the target in drug discovery efforts. In this issue of Chemistry & Biology, Okram et al. tackle this issue and show that inhibitors can be designed specifically to bind to inactive Abl.     

Intrinsic integrated optical temperature sensor based on waveguide bend loss

Curvature of a multimode integrated optical waveguide reduces the numerical aperture and induces radiation losses. In this paper, we study this phenomenon and we present a geometrical approach to calculate the local numerical aperture and the intensity attenuation. We exploit the bending effect on the local numerical aperture to make a new intrinsic temperature sensor. The simulation results are validated for the silica/silicone integrated optical case. The principal performances of the silica/silicone temperature sensor are the extended temperatures range (−50 to 200 °C) with an excellent linearity response (1%) between 20 and 200 °C.     

Aqueous Extract of Crataegus azarolus Protects Against DNA Damage in Human Lymphoblast Cell K562 and Enhances Antioxidant Activity

The present study was carried out to characterize the cellular antioxidant effect of the aqueous extract of Crataegus azarolus and its antigenotoxic potential using human myelogenous cells, K562. The antioxidant capacity of this extract was evaluated by determining its cellular antioxidant activity (CAA) in K562 cells. Also, preceding antigenotoxicity assessment, its eventual genotoxicity property was investigated by evaluating its capacity to induce the DNA degradation of treated cell nuclei. As no genotoxicity was detected at different exposure times, its ability to protect cell DNA against H₂O₂ oxidative effect was investigated, using the “comet assay.” It appears that 800 μg/mL of extract inhibited the genotoxicity induced by H₂O₂ with a rate of 41.30 %, after 4 h of incubation. In addition, this extract revealed a significant cellular antioxidant capacity against the reactive oxygen species in K562 cells.     

Sorption and diffusion of carbon dioxide in single-phase polystyrene/poly(vinylmethylether) blends

The sorption and transport properties of CO₂ in miscible PS/PVME blends at 20°C are reported as a function of pressure from 1 to 15 atm. The complex shape of isotherms for glassy blends and the concentration-dependent diffusion coefficient for rubbery blends reveal a plasticization by sorbed CO₂. The significant depression in T_g has to be taken into account in the analysis of the sorption data. Diffusion coefficient for CO₂ passes through a minimum when plotted against the blend composition. Such a behavior can be quantitatively related to the negative volume mixing of the PS/PVME system in the framework of the theories based on unoccupied volume. © 1996 John Wiley & Sons, Inc.     

Factors that influence the surface potential decay on a thin film of polyethylene terephthalate (PET)

The initial potential at the surface of the sample, as well as the temperature and the relative humidity of the ambient air are known to influence the surface-potential decay characteristics of corona-charged thin insulating films. The aim of the present work is to demonstrate the effectiveness of the Experimental Design methodology for evaluating the effects of these factors. Thus, a full factorial experimental design was carried out on a thin film of polyethylene terephthalate (thickness: 0.5 mm; surface: 50 mm × 50 mm). A negative corona discharge produced in a needle–grid–plate electrode system was employed to charge the surface of the film samples. The variation domains for the three factors were respectively: ?1000 V to ?1800 V; 25 to 55 °C; 50% to 80%. The surface-potential decay process was characterized by two output variables: the time needed for the potential to reduce to respectively 50% and 10% of the initial value. It was found that the former is more affected by the temperature, while the latter is more sensitive to the variation of the relative humidity.     

Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design

The cyclin-dependent kinases (CDKs) have been characterized in complex with a variety of inhibitors, but the majority of structures solved are in the inactive form. We have solved the structures of six inhibitors in both the monomeric CDK2 and binary CDK2/cyclinA complexes and demonstrate that significant differences in ligand binding occur depending on the activation state. The binding mode of two ligands in particular varies substantially in active and inactive CDK2. Furthermore, energetic analysis of CDK2/cyclin/inhibitors demonstrates that a good correlation exists between the in vitro potency and the calculated energies of interaction, but no such relationship exists for CDK2/inhibitor structures. These results confirm that monomeric CDK2 ligand complexes do not fully reflect active conformations, revealing significant implications for inhibitor design while also suggesting that the monomeric CDK2 conformation can be selectively inhibited.     

Irregular sampling to reduce the limitations induced by the nonlinearities in wavelength scanning

A new numerical method for reducing the effects of the nonlinearity signal in the distance measurements by the frequency-modulated continuous wave technique is presented. It is shown that the phase shift of the interferogram produced by a light-scanning signal could be efficiently considered as polynomial. In the distance measurement method considered, the information is carried by the first-order polynomial phase signal. Our method eliminates the high orders of the polynomial pulse, which allows an improvement of the resolution. First results are reported in order to illustrate the new technique.     

Structural determinants of CDK4 inhibition and design of selective ATP competitive inhibitors

A number of selective inhibitors of the CDK4/cyclin D1 complex have been reported recently. Due to the absence of an experimental CDK4 structure, the ligand and protein determinants contributing to CDK4 selectivity are poorly understood at present. Here, we report the use of computational methods to elucidate the characteristics of selectivity and to derive the structural basis for specific, high-affinity binding of inhibitors to the CDK4 active site. From these data, the hypothesis emerged that appropriate incorporation of an ionizable function into a CDK2 inhibitor results in more favorable binding to CDK4. This knowledge was applied to the design of compounds in the otherwise CDK2-selective 2-anilino-4-(thiazol-5-yl)pyrimidine pharmacophore that are potent and highly selective ATP antagonists of CDK4/cyclin D1. The findings of this study also have significant implications in the design of CDK4 mimic structures based on CDK2.     

Photophysical studies of the trans to cis isomerization of the push-pull molecule: 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.