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  • Etna  (2)
  • Hartree-Fock calculations  (2)
  • Organic Chemistry  (2)
  • SO2  (2)
  • Active site residues
  • Conformational analysis
  • 1
    ISSN: 1573-4951
    Keywords: Cytochromes P450 ; P450 2D6 ; P450 101 ; 3D model ; Active site residues ; Homology building
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching α-helices (C, D, G, I, J, K and L) and β-sheets (β3/β4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, α-helices B, B′ and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val370, Pro371, Leu372, Trp316, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp100 or Asp301 was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-4951
    Keywords: G-protein-coupled receptor ; Hartree-Fock calculations ; Histamine H2 receptor ; Molecular mechanics ; Receptor models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In the first part (pp. 461–478 in this issue) of this study regarding the histamine H2 receptor agonistic binding site, the best possible interactions of histamine with an α-helical oligopeptide, mimicking a part of the fifth transmembrane α-helical domain (TM5) of the histamine H2 receptor, were considered. It was established that histamine can only bind via two H-bonds with a pure α-helical TM5, when the binding site consists of Tyr182/Asp186 and not of the Asp186/Thr190 couple. In this second part, two particular three-dimensional models of G-protein-coupled receptors previously reported in the literature are compared in relation to agonist binding at the histamine H2 receptor. The differences between these two receptor models are discussed in relation to the general benefits and limitations of such receptor models. Also the pros and cons of simplifying receptor models to a relatively easy-to-deal-with oligopeptide for mimicking agonistic binding to an agonistic binding site are addressed. Within complete receptor models, the simultaneous interaction of histamine with both TM3 and TM5 can be analysed. The earlier suggested three-point interaction of histamine with the histamine H2 receptor can be explored. Our results demonstrate that a three-point interaction cannot be established for the Asp98/Asp186/Thr190 binding site in either of the investigated receptor models, whereas histamine can form three H-bonds in case the agonistic binding site is constituted by the Asp98/Tyr182/Asp186 triplet. Furthermore this latter triplet is seen to be able to accommodate a series of substituted histamine analogues with known histamine H2 agonistic activity as well.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1573-4951
    Keywords: α-helical model system ; Conformational analysis ; Counterpoise method ; Hartree-Fock calculations ; Histamine H2 receptor ; Molecular mechanics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Mutation studies on the histamine H2 receptor were reported by Gantz et al. [J. Biol. Chem., 267 (1992) 20840], which indicate that both the mutation of the fifth transmembrane Asp186 (to Ala186) alone or in combination with Thr190 (to Ala190) maintained, albeit partially, the cAMP response to histamine. Recently, we have shown that histamine binds to the histamine H2 receptor as a monocation in its proximal tautomeric form, and, moreover, we suggested that a proton is donated from the receptor towards the tele-position of the agonist, thereby triggering the biological effect [Nederkoorn et al., J. Mol. Graph., 12 (1994) 242; Eriks et al., Mol. Pharmacol., 44 (1993) 886]. These findings result in a close resemblance with the catalytic triad (consisting of Ser, His and Asp) found in serine proteases. Thr190 resembles a triad's serine residue closely, and could also act as a proton donor. However, the mutation of Thr190 to Ala190 — the latter is unable to function as a proton donor — does not completely abolish the agonistic cAMP response. At the fifth transmembrane α-helix of the histamine H2 receptor near the extracellular surface, another amino acid is present, i.e. Tyr182, so an alternative couple of amino acids, Tyr182 and Asp186, could constitute the histamine binding site at the fifth α-helix instead of the (mutated) couple Asp186 and Thr190. In the first part of our present study, this hypothesis is investigated with the aid of an oligopeptide with an α-helical backbone, which represents a part of the fifth transmembrane helix. Both molecular mechanics and ab initio data lead to the conclusion that the Tyr182/Asp186 couple is most likely to act as the binding site for the imidazole ring present in histamine.
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  • 4
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 17 (1836), S. 191-192 
    ISSN: 0365-5490
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 20 (1836), S. 71-73 
    ISSN: 0365-5490
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Publication Date: 2019-01-24
    Description: The advent of UV cameras has recently paved the way to volcanic SO2 flux observations of much improved temporal and spatial resolution, and has thus contributed to expanding use and utility of SO2 fluxes in volcano monitoring. Recently, the first examples of permanent UV camera systems have appeared that are now opening the way to routine fully automated monitoring of the volcanic SO2 flux at high-rate, and continuously (daily hours only). In 2014, using funding from the FP7-ERC project “Bridge” (http://www.bridge.unipa.it/), we deployed a network of 4 permanent UV cameras at Etna and Stromboli volcanoes (Sicily) that has been operating regularly since then. Using a suite of custom-built codes, data streamed by the UV camera are automatically processed and telemetered, allowing nearly real-time visualization and analysis of SO2 fluxes. Here, we summarise the key results obtained during the last 5 years of continuous observations (2014-2018) to demonstrate potentials and challenges in real-time continuous SO2 flux monitoring with UV cameras. We show that the spatially resolved SO2 flux time-series delivered by the UV camera allow effectively tracking migration in volcanic activity from the Central to New South-East Crater (Etna), and shifts in degassing activity along the crater terrace (Stromboli). At both volcanoes, the high temporal of UV cameras allows capturing the escalation in active (strombolian) SO2 degassing that typically precedes onset of paroxysmal (Etna in 2014-2016) or effusive (Stromboli in 2014) activity, and to quantify for the first time the syn- explosive SO2 budget for larger-scale explosions, including 2 paroxysmal lava fountains (Etna) and 1 major explosion (Stromboli). We finally demonstrate the ability of our automatic camera systems to capture temporal changes in SO2 flux regime, and thus to “live” monitoring degassing and eruptive behaviors at active volcanoes.
    Description: Published
    Description: Napoli
    Description: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Keywords: UV Camera ; SO2 Flux Monitoring ; Etna ; Stromboli
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 7
    Publication Date: 2019-01-24
    Description: The persistent open-vent activity of basaltic volcanoes is periodically interrupted by spectacular but hazardous paroxysmal explosions. The rapid transition from quiescence to explosive eruption poses a significant challenge for volcanic hazard assessment and mitigation, and improving our understanding of the processes that trigger these paroxysmal events is critical. Although magmatic gas is unquestionably the driver, direct measurements of a paroxysm's gas flux budget have remained challenging, to date. A particularly violent paroxysmal sequence took place on Etna on December 2015, intermittently involving all summit craters, especially the Voragine (VOR) that had previously displayed no activity for several years. Here, we characterize the volcano's SO2 degassing budget prior to, during and after this paroxysmal sequence, using ground-based (UV-Camera) and satellite (OMI) observations, complemented with ground- and space-borne thermal measurements. We make use of the high spatial resolution of UV-cameras to resolve SO2 emissions from the erupting VOR crater for the first time, and to characterize temporal switches in degassing activity from VOR to the nearby New Southeast Crater (NSEC). Our data show that onset of paroxysmal activity on December 3–5 was marked by visible escalation in VOR SO2 fluxes (4,700–8,900 tons/day), in satellite-derived thermal emissions (2,000 MW vs. ~2–11 MW in July-November 2015), and in OMI-derived daily SO2 masses (5.4 ± 0.7 to 10.0 ± 1.3 kilotonnes, kt; 0.5 kt was the average in the pre-eruptive period). Switch in volcanic activity from VOR to NSEC on December 6 was detected by increasing SO2 fluxes at the NSEC crater, and by decaying SO2 emissions at VOR, until activity termination on December 19. Taken together, our observations infer the total degassed SO2 mass for the entire VOR paroxysmal sequence at 21,000 ± 2,730 t, corresponding to complete degassing of ~1.9 ± 0.3 Mm3 of magma, or significantly less than the measured erupted magma volumes (5.1–12 Mm3). From this mismatch we propose that only a small fraction of the erupted magma was actually emplaced in the shallow plumbing system during (or shortly prior) the paroxysmal sequence. Rather, the majority of the erupted magma was likely stored conduit magma, having gone through extensive degassing for days to weeks prior to the paroxysm.
    Description: Published
    Description: id 239
    Description: 6V. Pericolosità vulcanica e contributi alla stima del rischio
    Description: JCR Journal
    Keywords: volcanic SO2 ; UV camera ; thermal remote sensing ; Etna ; basaltic paroxysms ; OMI
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 8
    Publication Date: 2021-12-23
    Description: At open-vent basaltic volcanoes, resolving the activity escalation that heralds larger, potentially harmful eruptions is challenged by the persistent mild ordinary activity, which often masks the precursory unrest signals related to heightened magma transport from depth. Gas (SO2 and CO2) fluxes at surface are controlled by rate of magma transport and degassing within the magma plumbing system, and thus constitute key parameters to infer deep magma budget and dynamics. Here, we use several year-long (2014-present) gas observations at Etna and Stromboli volcanoes, in Sicily, to provide new evidence for the utility of long-term instrumental gas monitoring in real-time detecting the early phase of unrest prior eruption, and for characterizing syn-eruptive dynamics. To this aim, we use information from a gas monitoring network of permanent ultraviolet (UV) cameras and automatic Multi-Gas instruments that, combined with geophysical observations, allow characterizing changes in degassing and eruptive dynamics at high temporal/spatial resolution. Our results show that the paroxysmal (lava fountaining) explosions that periodically interrupted persistent open-vent activity on Etna (during 2014-2020) were accompanied by systematic, repetitive SO2 emission patterns prior, during, and after eruptions. These allow us identifying the characteristic pre- syn- and post- eruptive degassing regimes, and to establish thresholds in the SO2 flux record that mark phases of unrest. On Stromboli, the much improved temporal/spatial resolution of UV cameras allows resolving the escalation of regular strombolian activity, and its concentration toward its North-east crater, that heralds onset of effusive eruptions. During effusive eruption, although magma level drops in the conduit and explosive summit activity ceases, UV camera observations can still detect explosive gas bursts deep in the conduit while no infrasonic activity is detected. Combining the UV camera-derived SO2 fluxes with CO2/SO2 ratio records measured by the Multi-Gas, the CO2 flux can be inferred. We find that such CO2 flux time-series can allow tracking degassing of deeply stored mafic magma months before Stromboli"s eruptions. We finally show that remotely sensed gas emission and thermal activity can be combined together to characterize the dynamics of shallow magmatic system prior to and during unrest, ultimately helping to define timing of magma re-charging events driving the eruptions.
    Description: Published
    Description: Virtual
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Keywords: Open vent volcanism ; SO2 ; UV cameras
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 9
    Publication Date: 2024-01-26
    Description: We used two and a half years long SO2 flux record, obtained using permanent ultraviolet cameras, to characterize changes in degassing dynamics at Mt. Etna volcano from summer 2014 to the end of 2016. Volcanic activity at Mt. Etna was characterized by persistent open-vent degassing periodically interrupted by intense paroxysmal lava fountaining events (in August 2014, December 2015, and May 2016). Results revealed systematic SO2 emission patterns prior, during, and after Etna’s paroxysmal phases, allowing us to identify thresholds between pre-syn-and post-eruptive degassing regimes. The SO2 flux typically peaked during a lava fountain: in the 18 May 2016 example, the averaged SO2 degassing rate was ~158 kg/s, the peak emission was ~260 kg/s, and the total released SO2 mass was ~1700 tons (in 3h). Paroxysmal explosive activity at NSE crater on 11-15 August 2014 was also associated with intense syneruptive SO2 degassing (at 30-40 kg/s levels on a daily average), and was preceded by onset in degassing activity at the same crater 4 days before. During paroxysmal activity on 3-5 December 2015, the SO2 fluxes peaked at 54-103 kg/s from VOR crater, and was preceded by a sizable increase from 10 kg/s (end of November) up to 45.5 kg/s, two days before. The May 16-25 2016 paroxysmal activity was characterized by intense degassing ~2 times higher than the 2016 average (~18 kg/s) and preceded by mild but detectable SO2 flux increases more than one month before its onset. Taken together, our observations, when combined with independent geophysical (thermal and seismic) evidence, allow us to fully characterize the Etna’s degassing dynamics and contribute to our understanding of its shallow plumbing system.
    Description: Published
    Description: Catania
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Keywords: SO2 ; Mt. Etna volcano ; permanent ultraviolet cameras
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Abstract
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