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The title compound, C20H22O2, crystallizes with two independent molecules in the asymmetric unit. In each molecule, all the non-H atoms lie in a common plane (r.m.s. deviations of 0.098 and 0.079 Å). There is a [pi]-[pi] stacking interaction in the crystal structure. The central aromatic rings of the two molecules, which are stacked head-to-tail one above the other, are separated by centroid-to-centroid distances of 3.872 (13) and 3.999 (10) Å. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.003 A° ; R factor = 0.044; wR factor = 0.101; data-to-parameter ratio = 14.6.
The title compound, C14H20O3, is a synthetic analogue with a long aliphatic side chain of the important food additive and flavoring agent, vanillin. There are two independent molecules in the asymmetric unit, each having an essentially planar conformation (r.m.s. deviations of 0.023 and 0.051Å for all non-H atoms of the two molecules in the asymmetric unit). Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.049; wR factor = 0.144; data-to-parameter ratio = 15.9.
The utilization of Ginkgo biloba in medicinal practice dates back to 1505 A.D. Ironically, the mechanisms of action of Ginkgo are not fully clarified till now. Nowadays, Ginkgo biloba leaf extracts are mainly indicated for mild to moderate cerebrovascular insufficiency and different forms of dementia. The fact that it is an herbal extract composed of several different components indeed adds to the intricacy of finding its mechanisms of actions. Indisputably, many scientists tried to elucidate the mechanisms of actions of Ginkgo. The first step to achieve this goal was to standardize the leaf extract. The standardized Ginkgo leaf extract contains 22-27 % flavonol glycosides, 2.8-3.4 % of ginkgolide A, B and C, as well as approximately 2.6-3.2 % bilobalide and below 5 ppm ginkgolic acids. A widespread standardized Ginkgo extract is the EGb 761, which was utilized in the current work. One of the earliest proposed mechanisms is the ability of the Ginkgo extract to act as an anti-oxidant, which could be explained by its high flavonoid contents. However, without doubt EGb 761 encompasses other characteristics which distinguish it from other herbal extracts that are also rich in flavonoids. Since free radicals and reactive oxygen species are highly associated with the mitochondrial functions, examination of the effect of EGb 761 on mitochondrial functions was lately addressed. Moreover, this was encouraged as the link between Alzheimer’s disease [AD] and the mitochondria started to emerge. Previously, our group observed mitochondrial protective actions of EGb 761 on cell culture in vitro. Furthermore, anti-apoptotic effects were previously described for EGb 761. However, only very few studies addressed the single constituents and their effect on mitochondrial functions. Flavonoids were studied in several other plant extracts and their radical scavenging activity is unquestionable, but EGb 761 has anti-apoptotic actions which may be attributed to its terpenoid fraction. Exclusively found in the Ginkgo plant, are the ginkgolides and therefore their actions are not yet fully elucidated. Moreover, those who attempted to address these constituents concentrated on one or two candidates, for example bilobalide or ginkgolide B and ignored the rest. Unfortunately, this led to incomplete results, and one couldn’t compare the relative activities of all EGb 761 components in order to state whether all the components are effective or not. ...
We study the beam-energy and system-size dependence of \phi meson production (using the hadronic decay mode \phi -- K+K-) by comparing the new results from Cu+Cu collisions and previously reported Au+Au collisions at \sqrt{s_NN} = 62.4 and 200 GeV measured in the STAR experiment at RHIC. Data presented are from mid-rapidity (|y|<0.5) for 0.4 < pT < 5 GeV/c. At a given beam energy, the transverse momentum distributions for \phi mesons are observed to be similar in yield and shape for Cu+Cu and Au+Au colliding systems with similar average numbers of participating nucleons. The \phi meson yields in nucleus-nucleus collisions, normalised by the average number of participating nucleons, are found to be enhanced relative to those from p+p collisions with a different trend compared to strange baryons. The enhancement for \phi mesons is observed to be higher at \sqrt{s_NN} = 200 GeV compared to 62.4 GeV. These observations for the produced \phi(s\bar{s}) mesons clearly suggest that, at these collision energies, the source of enhancement of strange hadrons is related to the formation of a dense partonic medium in high energy nucleus-nucleus collisions and cannot be alone due to canonical suppression of their production in smaller systems.
The STAR Collaboration at the Relativistic Heavy Ion Collider presents measurements of 𝐽/𝜓→𝑒+𝑒− at midrapidity and high transverse momentum (𝑝𝑇>5 GeV/𝑐) in 𝑝+𝑝 and central Cu+Cu collisions at √𝑠𝑁𝑁=200 GeV. The inclusive 𝐽/𝜓 production cross section for Cu+Cu collisions is found to be consistent at high 𝑝𝑇 with the binary collision-scaled cross section for 𝑝+𝑝 collisions. At a confidence level of 97%, this is in contrast to a suppression of 𝐽/𝜓 production observed at lower 𝑝𝑇. Azimuthal correlations of 𝐽/𝜓 with charged hadrons in 𝑝+𝑝 collisions provide an estimate of the contribution of 𝐵-hadron decays to 𝐽/𝜓 production of 13%±5%.
Specific functions of biological systems often require conformational transitions of macromolecules. Thus, being able to describe and predict conformational changes of biological macromolecules is not only important for understanding their impact on biological function, but will also have implications for the modelling of (macro)molecular complex formation and in structure-based drug design approaches. The “conformational selection model” provides the foundation for computational investigations of conformational fluctuations of the unbound protein state. These fluctuations may reveal conformational states adopted by the bound proteins. The aim of this work is to incorporate directional information in a geometry-based approach, in order to sample biologically relevant conformational space extensively. Interestingly, coarse-grained normal mode (CGNM) approaches, e.g., the elastic network model (ENM) and rigid cluster normal mode analysis (RCNMA), have emerged recently and provide directions of intrinsic motions in terms of harmonic modes (also called normal modes). In my previous work and in other studies it has been shown that conformational changes upon ligand binding occur along a few low-energy modes of unbound proteins and can be efficiently calculated by CGNM approaches. In order to explore the validity and the applicability of CGNM approaches, a large-scale comparison of essential dynamics (ED) modes from molecular dynamics (MD) simulations and normal modes from CGNM was performed over a dataset of 335 proteins. Despite high coarse-graining, low frequency normal modes from CGNM correlate very well with ED modes in terms of directions of motions (average maximal overlap is 0.65) and relative amplitudes of motions (average maximal overlap is 0.73). In order to exploit the potential of CGNM approaches, I have developed a three-step approach for efficient exploration of intrinsic motions of proteins. The first two steps are based on recent developments in rigidity and elastic network theory. Initially, static properties of the protein are determined by decomposing the protein into rigid clusters using the graph-theoretical approach FIRST at an all-atom representation of the protein. In a second step, dynamic properties of the molecule are revealed by the rotations-translations of blocks approach (RTB) using an elastic network model representation of the coarse-grained protein. In the final step, the recently introduced idea of constrained geometric simulations of diffusive motions in proteins is extended for efficient sampling of conformational space. Here, the low-energy (frequency) normal modes provided by the RCNMA approach are used to guide the backbone motions. The NMSim approach was validated on hen egg white lysozyme by comparing it to previously mentioned simulation methods in terms of residue fluctuations, conformational space explorations, essential dynamics, sampling of side-chain rotamers, and structural quality. Residue fluctuations in NMSim generated ensemble is found to be in good agreement with MD fluctuations with a correlation coefficient of around 0.79. A comparison of different geometry-based simulation approaches shows that FRODA is restricted in sampling the backbone conformational space. CONCOORD is restricted in sampling the side-chain conformational space. NMSim sufficiently samples both the backbone and the side-chain conformations taking experimental structures and conformations from the state of the art MD simulation as reference. The NMSim approach is also applied to a dataset of proteins where conformational changes have been observed experimentally, either in domain or functionally important loop regions. The NMSim simulations starting from the unbound structures are able to reach conformations similar to ligand bound conformations (RMSD < 2.4 Å) in 4 out of 5 cases of domain moving proteins. In these four cases, good correlation coefficients (R > 0.7) between the RMS fluctuations derived from NMSim generated structures and two experimental structures are observed. Furthermore, intrinsic fluctuations in NMSim simulation correlate with the region of loop conformational changes observed upon ligand binding in 2 out of 3 cases. The NMSim generated pathway of conformational change from the unbound structure to the ligand bound structure of adenylate kinase is validated by a comparison to experimental structures reflecting different states of the pathway as proposed by previous studies. Interestingly, the generated pathway confirms that the LID domain closure precedes the closing of the NMPbind domain, even if no target conformation is provided in NMSim. Hence, the results in this study show that, incorporating directional information in the geometry-based approach NMSim improves the sampling of biologically relevant conformational space and provides a computationally efficient alternative to state of the art MD simulations.
Modelling protein flexibility and plasticity is computationally challenging but important for understanding the function of biological systems. Furthermore, it has great implications for the prediction of (macro) molecular complex formation. Recently, coarse-grained normal mode approaches have emerged as efficient alternatives for investigating large-scale conformational changes for which more accurate methods like MD simulation are limited due to their computational burden. We have developed a Normal Mode based Simulation (NMSim) approach for efficient conformation generation of macromolecules. Combinations of low energy normal modes are used to guide a simulation pathway, whereas an efficient constraints correction approach is applied to generate stereochemically allowed conformations. Non-covalent bonds like hydrogen bonds and hydrophobic tethers and phi-psi favourable regions are also modelled as constraints. Conformations from our approach were compared with a 10 ns MD trajectory of lysozyme. A 2-D RMSD plot shows a good overlap of conformational space, and rms fluctuations of residues show a correlation coefficient of 0.78 between the two sets of conformations. Furthermore, a comparison of NMSim simulations starting from apo structures of different proteins show that ligand-bound conformations can be sampled for those cases where conformational changes are mainly correlated, e.g., domain-like motion in adenylate kinase. Efforts are currently being made to also model localized but functionally important motions for protein binding pockets and protein-protein interfaces using relevant normal mode selection criteria and implicit rotamer basin creation.
Background Endothelium-derived nitric oxide plays an important role for the bone marrow microenvironment. Since several important effects of nitric oxide are mediated by cGMP-dependent pathways, we investigated the role of the cGMP downstream effector cGMP-dependent protein kinase I (cGKI) on postnatal neovascularization. Methodology/Principal Findings In a disc neovascularization model, cGKI -/- mice showed an impaired neovascularization as compared to their wild-type (WT) littermates. Infusion of WT, but not cGKI -/- bone marrow progenitors rescued the impaired ingrowth of new vessels in cGKI-deficient mice. Bone marrow progenitors from cGKI -/- mice showed reduced proliferation and survival rates. In addition, we used cGKI alpha leucine zipper mutant (LZM) mice as model for cGKI deficiency. LZM mice harbor a mutation in the cGKI alpha leucine zipper that prevents interaction with downstream signaling molecules. Consistently, LZM mice exhibited reduced numbers of vasculogenic progenitors and impaired neovascularization following hindlimb ischemia compared to WT mice. Conclusions/Significance Our findings demonstrate that the cGMP-cGKI pathway is critical for postnatal neovascularization and establish a new role for cGKI in vasculogenesis, which is mediated by bone marrow-derived progenitors.
4-(4-Nitrophenoxy)biphenyl
(2009)
The two phenyl rings of the biphenyl unit of the title compound, C18H13NO3, are almost coplanar [dihedral angle 6.70 (9)°]. The nitrophenyl ring, on the other hand, is significantly twisted out of the plane of the these two rings, making dihedral angles of 68.83 (4)° with the middle ring and 62.86 (4)° with the end ring. The nitro group is twisted by 12.1 (2)° out of the plane of the phenyl ring to which it is attached. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A° ; R factor = 0.040; wR factor = 0.118; data-to-parameter ratio = 12.8.
The Wages of Corruption
(2009)
Corruption is endemic in Cameroon. Twice, Transparency International have accorded the country the infamous first place in corruption. As one of many concerned Cameroonians, Sammy Oke Akombi was moved and they realized that something was in fact wrong somewhere and something had to be done somehow. This collection of short stories is his contribution to the collective resolve by concerned Cameroonians to wage a war against this most unusual friend of fairness. The stories seek to elicit awareness about a social ill that is ironically championed by the very politicians, functionaries, educator, leaders and power elite whose duty it is to keep society healthy and on the rails. The stories are on corruption in different segments of society and about the people who perpetrate it. Almost everyone is immersed in it and so must make every effort to resurface from it. It takes only the will to stay alive because the wages of corruption like any other sin can only be death.