Organic synthesis

Some comments on the problems that are encountered by organic chemists who attempt the total synthesis of a molecule having several asymmetric centers. These difficulties explain the relatively slow progress of that branch of chemistry, although some of its successes merit being considered works of art.     

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

Due to the limited distance data available from the experiments, the structures determined by NMR Spectroscopy may not always be as accurate as desired. Further refinement of the structures is often required and sometimes critical. With the increase of high quality protein structures determined and deposited in PDB Data Bank, commonly shared protein conformational properties can be extracted based on the statistical distributions of the properties in the structural database and used to improve the outcomes of the NMR-determined structures. Here we examine the distributions of protein interatomic distances in known protein structures. We show that based on these distributions, a set of mean-force potentials can be defined for proteins and employed to refine the NMR-determined structures. We report the test results on 70 NMR-determined structures and compare the potential energy, the Ramachandran plot, and the ensemble RMSD of the structures refined with and without using the derived mean-force potentials.     

Histamine and H1 -histamine receptors faster venous circulation

The study has analysed the action of histamine in the rabbit venous system and evaluated its potential role in contraction during increased venous pressure. We have found that a great variety exists in histamine sensitivity and H(1) -histamine receptor expression in various types of rabbit veins. Veins of the extremities (saphenous vein, femoral vein, axillary vein) and abdomen (common iliac vein, inferior vena cava) responded to histamine by a prominent, concentration-dependent force generation, whereas great thoracic veins (subclavian vein, superior vena cavas, intrathoracic part of inferior vena cava) and a pelvic vein (external iliac vein) exhibited slight sensitivity to exogenous histamine. The lack of reactivity to histamine was not due to increased activity of nitric oxide synthase (NOS) or heme oxygenase-1. H(1) -histamine receptor expression of veins correlated well with the histamine-induced contractions. Voltage-dependent calcium channels mediated mainly the histamine-induced force generation of saphenous vein, whereas it did not act in the inferior vena cava. In contrast, the receptor-operated channels were not involved in this response in either vein. Tyrosine phosphorylation occurred markedly in response to histamine in the saphenous vein, but not in the inferior vena cava. Histamine induced a prominent ρ kinase activation in both vessels. Protein kinase C and mitogen-activated protein kinase (MAPK) were not implicated in the histamine-induced intracellular calcium sensitization. Importantly, transient clamping of the femoral vein in animals caused a short-term constriction, which was inhibited by H(1) -histamine receptor antagonist in vivo. Furthermore, a significantly greater histamine immunopositivity was detected in veins after stretching compared to the resting state. We conclude that histamine receptor density adapts to the actual requirements of the circulation, and histamine liberated by the venous wall during increased venous pressure contributes to the contraction of vessels, providing a force for the venous return.     

Sustained activation of extracellular signal-regulated kinase by nerve growth factor regulates c-fos protein stabilization and transactivation in PC12 cells

The duration of intracellular signaling is thought to be a critical component in effecting specific biological responses. This paradigm is demonstrated by growth factor activation of the extracellular signal-regulated kinase (ERK) signaling cascade in the rat pheochromocytoma cell line (PC12 cells). In this model, sustained ERK activation induced by nerve growth factor (NGF) results in differentiation, whereas transient ERK activation induced by epidermal growth factor (EGF) results in proliferation in these cells. Recently, the immediate early gene product c-fos has been proposed to be a sensor for ERK signaling duration in fibroblasts. In this study, we ask whether this is true for NGF and EGF stimulation of PC12 cells. We show that NGF, but not EGF, can regulate both c-fos stability and activation in an ERK-dependent manner in PC12 cells. This is achieved through ERK-dependent phosphorylation of c-fos. Interestingly, distinct sites regulate enhanced stability and transactivation of c-fos. Phosphorylation of Thr325 and Thr331 are required for maximal NGF-dependent transactivation of c-fos. In addition, a consensus ERK binding site (DEF domain) is also required for c-fos transactivation. However, stability is controlled by ERK-dependent phosphorylation of Ser374, while phosphorylation of Ser362 can induce conformational changes in protein structure. We also provide evidence that sustained ERK activation is required for proper post-translational regulation of c-fos following NGF treatment of PC12 cells. Because these ERK-dependent phosphorylations are required for proper c-fos function, and occur sequentially, we propose that c-fos is a sensor for ERK signaling duration in the neuronal-like cell line PC12.     

Re-assessing current extinction rates

There is a widespread belief that we are experiencing a mass extinction event similar in severity to previous mass extinction events in the last 600 million years where up to 95% of species disappeared. This paper reviews evidence for current extinctions and different methods of assessing extinction rates including species–area relationships and loss of tropical forests, changing threat status of species, co-extinction rates and modelling the impact of climate change. For 30 years some have suggested that extinctions through tropical forest loss are occurring at a rate of up to 100 species a day and yet less than 1,200 extinctions have been recorded in the last 400 years. Reasons for low number of identified global extinctions are suggested here and include success in protecting many endangered species, poor monitoring of most of the rest of species and their level of threat, extinction debt where forests have been lost but species still survive, that regrowth forests may be important in retaining ‘old growth’ species, fewer co-extinctions of species than expected, and large differences in the vulnerability of different taxa to extinction threats. More recently, others have suggested similar rates of extinction to earlier estimates but with the key cause of extinction being climate change, and in particular rising temperatures, rather than deforestation alone. Here I suggest that climate change, rather than deforestation is likely to bring about such high levels of extinction since the impacts of climate change are local to global and that climate change is acting synergistically with a range of other threats to biodiversity including deforestation.     

Characterization of Plant Carotenoid Cyclases as Members of the Flavoprotein Family Functioning with No Net Redox Change

The later steps of carotenoid biosynthesis involve the formation of cyclic carotenoids. The reaction is catalyzed by lycopene β-cyclase (LCY-B), which converts lycopene into β-carotene, and by capsanthin-capsorubin synthase (CCS), which is mainly dedicated to the synthesis of κ-cyclic carotenoids (capsanthin and capsorubin) but also has LCY-B activity. Although the peptide sequences of plant LCY-Bs and CCS contain a putative dinucleotide-binding motif, it is believed that these two carotenoid cyclases proceed via protic activation and stabilization of resulting carbocation intermediates. Using pepper (Capsicum annuum) CCS as a prototypic carotenoid cyclase, we show that the monomeric protein contains one noncovalently bound flavin adenine dinucleotide (FAD) that is essential for enzyme activity only in the presence of NADPH, which functions as the FAD reductant. The reaction proceeds without transfer of hydrogen from the dinucleotide cofactors to β-carotene or capsanthin. Using site-directed mutagenesis, amino acids potentially involved in the protic activation were identified. Substitutions of alanine, lysine, and arginine for glutamate-295 in the conserved 293-FLEET-297 motif of pepper CCS or LCY-B abolish the formation of β-carotene and κ-cyclic carotenoids. We also found that mutations of the equivalent glutamate-196 located in the 194-LIEDT-198 domain of structurally divergent bacterial LCY-B abolish the formation of β-carotene. The data herein reveal plant carotenoid cyclases to be novel enzymes that combine characteristics of non-metal-assisted terpene cyclases with those attributes typically found in flavoenzymes that catalyze reactions, with no net redox, such as type 2 isopentenyl diphosphate isomerase. Thus, FAD in its reduced form could be implicated in the stabilization of the carbocation intermediate.Later steps of carotenoid biosynthesis involve the formation of diverse cyclic carotenoids. For example, β-carotene, the vitamin A precursor, is synthesized de novo by photosynthetic organisms, limited nonphototrophic bacteria and fungi, and also by aphids (Moran and Jarvik, 2010) according to a multistep pathway that ends with the cyclization of lycopene by lycopene β-cyclase (LCY-B). Similarly, in pepper (Capsicum annuum) chromoplasts, antheraxanthin and violaxanthin are converted into the κ-cyclic carotenoids capsanthin and capsorubin, respectively, by capsanthin-capsorubin synthase (CCS). In both cases, the proposed mechanism involves a concerted protic attack and stabilization of a transient carbocation without any net redox change (Camara, 1980; Bouvier et al., 1994; Britton, 1998). Several cDNAs for LCY-B have been cloned from bacteria (Misawa et al., 1990; Cunningham et al., 1994; Armstrong, 1997; Cunningham and Gantt, 2001), fungi (Verdoes et al., 1999; Velayos et al., 2000; Arrach et al., 2001), and plants (Hugueney et al., 1995; Ronen et al., 2000) using functional complementation. Information available from primary structures suggest that the cyclization of lycopene is catalyzed by holomeric proteins in photosynthetic organisms (Cunningham et al., 1994; Maresca et al., 2007), by holomeric (Misawa et al., 1990) or heteromeric (Krubasik and Sandmann, 2000; Viveiros et al., 2000) proteins in nonphotosynthetic bacteria, and by holomeric, bifunctional proteins in fungi that combine the activities of phytoene synthase and lycopene cyclase (Verdoes et al., 1999; Velayos et al., 2000; Arrach et al., 2001). This structural diversity of LCY-Bs coupled to a lack of significant amino acid sequence identity between the lycopene cyclases from bacteria, fungi, and plants hinder our understanding of the catalytic mechanism of LCY-Bs and CCS. In addition, the N terminus of plant LCY-B and CCS contains an amino sequence motif characteristic of a polypeptide predicted to adopt a Rossmann fold (Rossmann et al., 1974) and suggests the binding of an as yet unknown dinucleotide prosthetic ligand. It has been shown using recombinant bacterial enzyme that the cyclization of lycopene into β-carotene strictly requires NADPH but proceeds without any net redox change (Schnurr et al., 1996; Hornero-Mendez and Britton, 2002). Under the same conditions, FAD alone could not sustain bacterial LCY-B activity (Schnurr et al., 1996). Much less is known about the dinucleotide requirements of plant carotenoid cyclases, which are highly conserved within plants but are extremely divergent in nonplant organisms. Previously, a crucial acidic domain for lycopene cyclase activity was identified using an affinity-labeling strategy followed by site-directed mutagenesis (Bouvier et al., 1997) in the absence of any crystal structures. This so-called 293-FLEET-297 motif of LCY-B and CCS contained two tandem Glu-295-Glu-296 residues that were essential for LCY-B- and κ-cyclase activities (Bouvier et al., 1997). However, it still remains unclear how the protic mechanism is compatible with the requirement of dinucleotide cofactors.To further explore the mechanism of plant carotenoid cyclases, we first choose pepper CCS as a prototypic enzyme because it displays a strong identity (52%) to pepper LCY-B, and we have shown previously that CCS could also catalyze the cyclization of lycopene into β-carotene (up to 25% of activity compared with LCY-B; Hugueney et al., 1995). Herein, we have shown that monomeric CCS purified to homogeneity from plant chromoplasts or recombinant CCS purified from Escherichia coli-transformed cells are typical flavoproteins containing one noncovalently bound FAD. We also observed that CCS-bound FAD is required for enzyme activity in the presence of NADPH, which functions as a reductant of FAD. During this process, no hydrogen is transferred to β-carotene or κ-cyclic carotenoids. In addition to this cofactor requirement, we also show from extensive site-directed mutagenesis using pepper CCS and LCY-B and Erwinia herbicola LCY-B (Mialoundama, 2009) that Glu-295 of pepper CCS and LCY-B plays a key role in the formation of β-carotene and κ-cyclic carotenoids, and we demonstrate that a similar role is played in structurally divergent bacterial LCY-Bs by Glu-196. These characteristics suggest that plant CCS and LCY-Bs are mechanistically similar to non-metal-assisted terpene cyclases, such as squalene:hopene cyclase and oxidosqualene cyclase, and additionally represent a new subfamily of flavoproteins like isopentenyl diphosphate isomerase type II, which catalyze carotenoid cyclization without any net redox modification of the substrate.     

The requirement of Ras and Rap1 for the activation of ERKs by cAMP, PACAP, and KCl in cerebellar granule cells

In cerebellar granule cells, the mitogen-activated protein kinase (MAPK) or extracellular signal-regulated kinase (ERK) cascade mediates multiple functions, including proliferation, differentiation, and survival. In these cells, ERKs are activated by diverse stimuli, including cyclic adenosine monophosphate (cAMP), pituitary adenylate cyclase activating protein (PACAP), depolarization induced by elevated extracellular potassium (KCl), and the neurotrophin brain-derived neurotrophic factor. Extensive studies in neuronal cell lines have implicated the small G proteins Ras and Rap1 in the activation of ERKs by cAMP, PACAP, and KCl. However, the requirement of Ras and Rap1 in these pathways in cerebellar granule cells has not been addressed. In this study, we utilize multiple biochemical assays to determine the mechanisms of action and requirement of Ras and Rap1 in cultured cerebellar granule cells. We show that both Ras and Rap1 can be activated by cAMP or PACAP via protein kinase (PKA)-dependent mechanisms. KCl activation of Ras also required PKA. Using both adenoviral and transgenic approaches, we show that Ras plays a major role in ERK activation by cAMP, PACAP, and KCl, while Rap1 also mediates activation of a selective membrane-associated pool of ERKs. Furthermore, Rap1, but not Ras, activation by PKA appears to require the action of Src family kinases.     

The specialization and structure of antagonistic and mutualistic networks of beetles on rainforest canopy trees

Different kinds of species interactions can lead to different structures within ecological networks. Antagonistic interactions (such as between herbivores and host plants) often promote increasing host specificity within a compartmentalized network structure, whereas mutualistic networks (such as pollination networks) are associated with higher levels of generalization and form nested network structures. However, we recently showed that the host specificity of flower‐visiting beetles from three different feeding guilds (herbivores, fungivores, and predators) in an Australian rainforest canopy was equal to that of herbivores on leaves, suggesting that antagonistic herbivores on leaves are no more specialized than flower‐visitors. We therefore set out to test whether similarities in the host specificity of these different assemblages reflect similarities in underlying network structures. As shown before at the species level, mutualistic communities on flowers showed levels of specialization at the network scale similar to those of the antagonistic herbivore community on leaves. However, the network structure differed, with flower‐visiting assemblages displaying a significantly more nested structure than folivores, and folivores displaying a significantly more compartmentalized structure than flower‐visitors. These results, which need further testing in other forest systems, demonstrate that both antagonistic and mutualistic interactions can result in equally high levels of host specialization among beetle assemblages in tropical rainforests. If this is a widespread phenomenon, it may alter our current perceptions of food web dynamics, species diversity patterns, and co‐evolution in tropical rainforests. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 287–295.     

Neuropeptide S-mediated facilitation of synaptic transmission enforces subthreshold theta oscillations within the lateral amygdala

The neuropeptide S (NPS) receptor system modulates neuronal circuit activity in the amygdala in conjunction with fear, anxiety and the expression and extinction of previously acquired fear memories. Using in vitro brain slice preparations of transgenic GAD67-GFP (Δneo) mice, we investigated the effects of NPS on neural activity in the lateral amygdala as a key region for the formation and extinction of fear memories. We are able to demonstrate that NPS augments excitatory glutamatergic synaptic input onto both projection neurons and interneurons of the lateral amygdala, resulting in enhanced spike activity of both types of cells. These effects were at least in part mediated by presynaptic mechanisms. In turn, inhibition of projection neurons by local interneurons was augmented by NPS, and subthreshold oscillations were strengthened, leading to their shift into the theta frequency range. These data suggest that the multifaceted effects of NPS on amygdaloid circuitry may shape behavior-related network activity patterns in the amygdala and reflect the peptide's potent activity in various forms of affective behavior and emotional memory.