The mechanistic insight of a specific interaction between 15d-Prostaglandin-J2 and eIF4A suggests an evolutionary conserved role across species

15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is an anti-inflammatory/anti-neoplastic prostaglandin that functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A (Kim et al., 2007). Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A, which leads to the formation of stress granules (SGs), which then cluster mRNAs with inhibited translation. Here, we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail plays a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets may uncover new therapeutic approaches in anti-inflammatory drug discovery.

Drivers of hibernation in the brown bear

BACKGROUND

Hibernation has been a key area of research for several decades, essentially in small mammals in the laboratory, yet we know very little about what triggers or ends it in the wild. Do climatic factors, an internal biological clock, or physiological processes dominate? Using state-of-the-art tracking and monitoring technology on fourteen free-ranging brown bears over three winters, we recorded movement, heart rate (HR), heart rate variability (HRV), body temperature (Tb), physical activity, ambient temperature (TA), and snow depth to identify the drivers of the start and end of hibernation. We used behavioral change point analyses to estimate the start and end of hibernation and convergent cross mapping to identify the causal interactions between the ecological and physiological variables over time.

RESULTS

To our knowledge, we have built the first chronology of both ecological and physiological events from before the start to the end of hibernation in the field. Activity, HR, and Tb started to drop slowly several weeks before den entry. Bears entered the den when snow arrived and when ambient temperature reached 0 °C. HRV, taken as a proxy of sympathetic nervous system activity, dropped dramatically once the bear entered the den. This indirectly suggests that denning is tightly coupled to metabolic suppression. During arousal, the unexpected early rise in Tb (two months before den exit) was driven by TA, but was independent of HRV. The difference between Tb and TA decreased gradually suggesting that bears were not thermoconforming. HRV increased only three weeks before exit, indicating that late activation of the sympathetic nervous system likely finalized restoration of euthermic metabolism. Interestingly, it was not until TA reached the presumed lower critical temperature, likely indicating that the bears were seeking thermoneutrality, that they exited the den.

CONCLUSIONS

We conclude that brown bear hibernation was initiated primarily by environmental cues, but terminated by physiological cues.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Calix[n]imidazolium as a new class of positively charged homo-calix compounds

Macrocycles based on neutral calixarenes and calixpyrroles have been extensively explored for ion binding, molecular assembly and related applications. Given that only these two types of calix compounds and their analogs are available, the introduction of new forms of widely usable calix macrocycles is an outstanding challenge. Here we report the quadruply/quintuply charged imidazole-based homo-calix compounds, calix[4/5]imidazolium. The noncovalent (C-H)⁺/π⁺-anion interactions of the imidazolium rings with anions inside and outside the cone are the stabilizing factors for crystal packing, resulting in self-assembled arrays of cone-shaped calix-imidazolium molecules. Calix[4]imidazolium senses fluoride selectively even in aqueous solutions. Calix[5]imidazolium recognizes neutral fullerenes through π⁺–π interactions and makes them soluble in water, which could be useful in fullerene chemistry. Not only derivatization and ring expansion of calix[n]imidazolium, but also their utilization in ionic liquids, carbene chemistry and nanographite/graphene exfoliation could be exploited.

Only two types of neutral homo-calix compounds, including analogues, have been reported. Chun et al. now describe a new class of positively charged calix[n]imidazolium, which is synthesized in one pot and is able to recognize anions and fullerenes in aqueous media.

Mechanistic studies on the oxidation of ascorbic acid and hydroquinone by a {Mn4O6}4+ core in aqueous media

Described in this work is the kinetics of oxidation of ascorbic acid and hydroquinone by a tetranuclear Mn(IV) oxidant, [Mn(4)(μ-O)(6)(bipy)(6)](4+) (1(4+), bipy =2,2(/)-bipyridine), in aqueous solution over a wide pH range 1.5-6.0. In particular, below pH 3.0, protonation on the oxo-bridge of 1(4+) results in the formation of [Mn(4)(μ-O)(5)(μ-OH)(bipy)(6)](5+) (1H(5+)) as an additional oxidant over 1(4+). Both ascorbic acid and ascorbate whereas only hydroquinone and none of its protolytic species were found to be reactive reducing agents in these reactions. Analysis of the rate data clearly established that the oxo-bridge protonated oxidant 1H(5+) is kinetically far more superior to 1(4+) in oxidizing ascorbic acid and hydroquinone. Rates of these reactions are substantially lowered in D(2)O-enriched media in comparison to that in H(2)O media. An initial one electron one proton transfer electroprotic rate step could be mechanistically conceived. DFT studies established that among the two sets of terminal and central Mn(IV) atoms in the tetranuclear oxidant, one of the two terminal Mn(IV) is reduced to Mn(III) at the rate step that we can intuitively predict considering the probable positive charge distribution on the Mn(IV) atoms.

Antigen-activated T cells induce IL-12p75 production from dendritic cells in an IFN-γ-independent manner

The addition of IL-12p75 to naïve CD4(+) T cells promotes their differentiation towards a TH1-type cytokine pattern. Dendritic cells stimulated by LPS generate IL-12p75, but only if the environment also contains IFN-γ. Thus, it appears that IFN-γ is needed to start the response that will result in further production of IFN-γ. We previously reported that paradoxically DCs produce IL-12p75 only after engaging primed, but not naïve T cells. This study examines the mechanism by which primed T cells trigger IL-12p75 secretion and asks whether this induction is also dependent on the presence of IFN-γ. Here, we show that, in contrast to LPS, primed T cells induce IL-12p75 in an IFN-γ-independent manner. Addition of rIFN-γ to cocultures of naïve T cells with DCs did not induce IL-12p75. Moreover, antigen-activated CD4(+) T cells from wild type or IFN-γ-deficient mice both initiated IL-12p75 production from DCs. Surprisingly, we found that synergies between three T-cell-derived factors - CD40 Ligand, IL-4 and GM-CSF - were necessary and sufficient for IL-12p75 production. These results suggest that there are at least two distinct pathways for IL-12p75 production in vivo. Furthermore, the T-cell-dependent pathway of IL-12p75 production employs molecules that are not classically associated with a TH1-type response.

Quencher-free molecular beacon: Enhancement of the signal-to-background ratio with graphene oxide

We report the highly improved version of quencher-free molecular beacon (QF-MB) system by using graphene oxide (GO) as an external quencher. This QF-MB/GO system provided a higher S/B ratio (31.0) relative to that (2.2) of the same system in the absence of GO, while retaining a high selectivity for fully matched over single-base-mismatched targets.

Chiral transformation in protonated and deprotonated adipic acids through multistep internal proton transfer

Protonated and deprotonated adipic acids (PAA: HOOC-(CH(2))(4)--COOH(2) (+) and DAA: HOOC-(CH(2))(4)-COO(-)) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H(2)O...H...OH(2))(+) Zundel-like symmetric hydrogen bonding, whereas that of DAA has H(3)O(+) Eigen-like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel-like ions for PAA and Eigen-like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH...O short hydrogen-bond stretching peaks are predicted in the range of 1000-1700 cm(-1) in the Car-Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen-bond peaks. The O-H-O stretching peaks in the range of 1800-2700 cm(-1) become insignificant above around 150 K and are almost washed out at about 300 K.

Unique sandwich stacking of pyrene-adenine-pyrene for selective and ratiometric fluorescent sensing of ATP at physiological pH

A pincer-like benzene-bridged sensor 1 with a pyrene excimer as a signal source and imidazolium as a phosphate anion receptor was synthesized and investigated for ATP sensing. A unique switch of excimer vs monomer pyrene fluorescence of 1 is observed in the presence of ATP due to the charcteristic sandwich pi-pi stacking of pyrene-adenine-pyrene. On the other hand, four other bases of nucleoside triphosphates such as GTP, CTP, UTP, and TTP can interact only from the outside with the already stabilized stacked pyrene-pyrene dimer of 1, resulting in excimer fluorescence quenching. The fluorescent intensity ratio of monomer-to-excimer for 1 upon binding with ATP (I(375)/I(487)) is much larger than that upon binding with ADP and AMP. This difference is large enough to discriminate ATP from ADP and AMP. As one of the biological applications, sensor 1 is successfully applied to the ATP staining experiments. Sensor 1 is also applied to monitor the hydrolysis of ATP and ADP by apyrase. The results indicate that 1 is a useful fluorescent sensor for investigations of ATP-relevant biological processes.

Eigen and Zundel Forms of Small Protonated Water Clusters: Structures and Infrared Spectra

The spectral properties of protonated water clusters, especially the difference between Eigen (H3O+) and Zundel (H5O2+) conformers and the difference between their unhydrated and dominant hydrated forms are investigated with the first principles molecular dynamics simulations as well as with the high level ab initio calculations. The vibrational modes of the excess proton in H3O+ are sensitive to the hydration, while those in H5O2+ are sensitive to the messenger atom such as Ar (which was assumed to be weakly bound to the water cluster during acquisitions of experimental spectra). The spectral feature around approximately 2700 cm-1 (experimental value: 2665 cm-1) for the Eigen moiety appears when H3O+ is hydrated. This feature corresponds to the hydrating water interacting with H3O+, so it cannot appear in the Eigen core. Thus, H3O+ alone would be somewhat different from the Eigen forms in water. For the Zundel form (in particular, H5O2+), there have been some differences in spectral features among different experiments as well as between experiments and theory. When an Ar messenger atom is introduced at a specific temperature corresponding to the experimental condition, the calculated vibrational spectra for H5O2+.Ar are in good agreement with the experimental infrared spectra showing the characteristic Zundel frequency at approximately 1770 cm-1. Thus, the effect of hydration, messenger atom Ar, and temperature are crucial to elucidating the nature of vibrational spectra of Eigen and Zundel forms and to assigning the vibrational modes of small protonated water clusters.

2-dimensional analytic approach for anion differentiation with chromofluorogenic receptors

By linking the urea moiety at the 1,8 positions of the carbazole fragment, we synthesized host systems 1, 2, and 3 having both chromogenic and fluorogenic signaling subunits. The spectral changes in both the signaling subunits could be easily analyzed via a simple 2-dimensional (2D) analytic approach described here, which enables us to differentiate the given set of anions. Structural studies are also reported.

A Color Version of the Hinsberg Test: 1°–3° Amine Indicator

The Hinsberg test to recognize the type of amine (1 degrees -3 degrees amines), which has been established for more than 100 years and well documented in textbooks, is not possible without conducting complicated organic reactions. We report for the first time unique chemosensors that are capable of showing selective color changes toward 1 degrees -3 degrees amines as a color version of the Hinsberg test. This simple and straightforward qualitative analysis, using the synthesized novel compounds herein, can be considered a new innovative tool for discriminating 1 degrees -3 degrees amines as an alternative to the historical Hinsberg test.

Quinoxaline−Imidazolium Receptors for Unique Sensing of Pyrophosphate and Acetate by Charge Transfer

[structure: see text] Quinoxaline derivatives (1-4) bearing two imidazolium moieties are found to strongly bind anions and show unique charge-transfer fluorescent responses to pyrophosphate and acetate, whereas they show excimer formation with other anions. Anion-binding studies are investigated with fluorescence and 1H NMR analysis, single-crystal X-ray analysis, and theoretical calculations.

Homology modeling and molecular dynamics study of chorismate synthase from Shigella flexneri

Shigellosis is a major public health problem in many developing countries. Antibiotic therapy can reduce the severity of the dysentery and prevent potentially lethal complication. However, owing to the increased resistance to most of the widely used and inexpensive antibiotics, there is an urgent need for new antibacterial agents, particularly those that act on novel targets. Chorismate synthase (CS) is a key enzyme in the shikimic acid pathway, which is essential for the synthesis of aromatic amino acids in bacteria. As an anti-bacterial drug target, CS has been well validated. A homology model of Shigella-CS with the flavin mononucleotide (FMN) binding was constructed using the crystal structure of CS from other species. The substrate 5-enolpyruvylshikimate 3-phosphate (EPSP) was subsequently docked into the active site based on previous theoretical studies. Molecular dynamics (MD) was used to refine the starting ternary model. The model was well conserved during the 1.8 ns MD simulation with the equilibrium root mean square deviation (RMSD) value of 3.5 angstrom. The substrate binding energy was calculated and the electrostatic energy was found to be the most important term for binding. Decomposition of binding energies revealed that R129, R125, R327, R134 and R48 are important residues involved in substrate binding, which is useful for further site-directed mutagenesis experiments. In the absence of crystal structure, our study provides an early insight into the structure of CS from Shigella flexneri and its binding to the substrate and cofactor, thus facilitating the inhibitor design.

Homology modeling and molecular dynamics study of West Nile virus NS3 protease: A molecular basis for the catalytic activity increased by the NS2B cofactor

The West Nile virus (WNV) NS3 serine protease, which plays an important role in assembly of infective virion, is an attractive target for anti-WNV drug development. Cofactors NS2B and NS4A increase the catalytic activity of NS3 in dengue virus and Hepatitis C virus, respectively. Recent studies on the WNV-NS3 characterize the catalytically active form of NS3 by tethering the 40-residue cofactor NS2B. It is suggested that NS2B is essential for the NS3 activity in WNV, while there is no information of the WNV-NS3-related crystal structure. To understand the role of NS2B/substrate in the NS3 catalytic activity, we built a series of models: WNV-NS3 and WNV-NS3-NS2B and WNV-NS3-NS2B-substrate using homology modeling and molecular modeling techniques. Molecular dynamics (MD) simulations were performed for 2.75 ns on each model, to investigate the structural stabilization and catalytic triad motion of the WNV NS3 protease with and without NS2B/substrate. The simulations show that the NS3 rearrangement occurs upon the NS2B binding, resulting in the stable D75-OD1...H51-NH hydrogen bonding. After the substrate binds to the NS3-NS2B active site, the NS3 protease becomes more stable, and the catalytic triad is formed. These results provide a structural basis for the activation and stabilization of the enzyme by its cofactor and substrate.

Organic-inorganic hybrid compounds of Li with bisimidazole derivatives: Li ion binding study and topochemical properties

The imidazole-based ligands, bis(imidazol-1-yl)methane (Bizm, 1a) and (pyrenyl)bis(imidazol-1-yl) methane (Pbizm,2a) were prepared. With LiClO4, these two compounds formed two novel organic-inorganic hybrid materials: a 3D network polymer Li(Bizm).ClO4 (1b) and a 1D chain polymer Li(Pbizm)2.ClO4 (2b). The intriguing topological and physiochemical characteristics of 1b and 2b are reported on the basis of the X-ray single-crystal structure analysis and Li ion binding studies.

Imidazolium receptors for the recognition of anions

This tutorial review covers imidazolium receptors for anion recognition according to their topological and structural classification, and includes benzene tripodal, cyclophane and calix-imidazolium, fluorescent imidazolium, ferrocenyl imidazolium, cavitand and calixarene, and polymeric imidazolium systems.