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Query: UMLS:C0344329 (collapse)
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To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding.
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PMID:Simulating the minimum core for hydrophobic collapse in globular proteins. 941 9

The oxygen insertion into C-H bonds (of methane, isobutane, and acetone) by dioxiranes (parent dioxirane and dimethyldioxirane) to give alcohols was studied with the DFT theory, using both restricted and unrestricted B3LYP methods, and 6-31G(d) and 6-311+G(d,p) basis sets to evaluate the feasibility of stepwise mechanisms and their competition with the concerted counterpart. Confirming previous results by other authors, we have located, with the RB3LYP method, concerted TSs in which the oxygen bound to be inserted interacts very strongly with the hydrogen atom and very weakly with the carbon atom of the C-H bond. These TSs nicely explain all the experimental observations (e.g., configuration retention at the chiral centers), but all of them exhibit an RHF --> UHF wave function instability that preclude considering them as genuine transition structures. We also were able to characterize, with UB3LYP methods, two alternative two-step processes that can lead to final products (alcohol + carbonyl compound) via singlet radical pair intermediates. For the first step of both processes we located genuine diradicaloid TSs, namely, TSs rad,coll and TSs rad,perp, that have stable wave functions. In TSs rad,coll the alkane C-H bond tends to be collinear with the breaking O(1)- - -O(2) bond while in TSs rad,perp the alkane C-H bond is almost perpendicular to the O(1)- - -O(2) bond. The first step, of both processes, can represent an example of a "molecule induced homolysis" reaction: collision between alkane and dioxirane brings about the homolytic cleavage of the dioxirane O-O bond and the hydrogen abstraction follows afterward to produce the diradicaloid TS that then falls down to a singlet radical pair. This hypothesis was fully confirmed by IRC analysis in the case of TSs rad,coll. The possible pathways that lead from the intermediate radical pair to final products are discussed as well as the hypothesis that the radical collinear TSs may collapse directly to products in a "one-step nonconcerted" process. However, diradical mechanisms cannot explain the experimental data as satisfactorily as the concerted pathway does. As for computational predictions about competition of diradical vs concerted mechanisms, they strongly depend (i) on the alkane C-H type, (ii) on whether gas phase or solution is considered, and (iii) on the basis set used for calculations. In short, the concerted TS benefits, with respect to the corresponding diradicaloid TSs, of alkyl substitution at the C-H center, solvation effects, and basis set extension. Actually, in the case of DMD reactions with methane and acetone, the diradicaloid TSs are always (both in gas phase and in solution and with both the basis sets used) strongly favored over their concerted counterpart. In the case of DMD reaction with isobutane tertiary C-H bond the large favor for the diradicaloid TSs over the concerted TS, predicted in gas phase by the B3LYP/6-31G(d) method, progressively decreases as a result of basis set extension and introduction of solvent effects: the higher theory level [B3LYP/6-311+G(d,p)] suggests that in acetone solution TS conc has almost the same energy as TS rad,perp while TS rad,coll resides only 2 kcal/mol higher.
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PMID:Novel pathways for oxygen insertion into unactivated C-H bonds by dioxiranes. Transition structures for stepwise routes via radical pairs and comparison with the concerted pathway. 1255 3

Collapse, explosion and water pollution by leachate have been three major problems in confining the development of sanitary landfilling technology as an economical method for disposal of municipal refuse. Potential risk factors including settlement of landfilled refuse, the generation of methane, carbon dioxide and other gases from landfill, the dynamic changes in temperature within the landfill and its ambient environment, as well as COD(Cr), BOD5, nutrients (TKN, TP and organic matter), heavy metals (Cu, Pb and Zn) and pH in landfill leachate were simulated using a reactor with high water input. It was indicated that high content of organic components in landfilled refuse is a key risk factor to cause abrupt collapse and accidental explosion in the landfill because they have impact not only on the settlement, but also on the release of methane and other gases. Elevated temperatures coincided with maximum generation of methane and other gases, thus increasing the risk of accidental explosion. Leachate quality was closely related with the release of COD(Cr) and BOD5 and heavy metals such as Cu, Pb and Zn, as well as organic pollutants, there was less release of TKN and TP. The mass balance analysis for the reactor showed that 36% of organic carbon reduction in the refuse during the simulations was discharged into leachate as soluble organic carbon, and 3% was converted to methane and carbon dioxide as gas production. Mixing of refuse with soil and sand particles, the so-called drill-a-hole method and recycling leachate were measures suggested in order to mitigate and avoid potential accidents.
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PMID:A risk factor analysis of municipal domestic refuse landfills using a reactor with high water input. 1453 24

Multireference perturbation theory (MRPT) with multiconfigurational self-consistent field (MCSCF) reference functions is applied to the calculations of core-electron binding energies (CEBEs) of atoms and molecules. Orbital relaxations in a core-ionized state and electron correlation are both taken into account in a conventional MCSCF-MRPT procedure. In the MCSCF calculation, the target core ionized state is directly optimized as an excited state and this treatment can completely prevent a variational collapse. Multireference Moller-Plesset perturbation theory and multiconfigurational self-consistent field reference quasidegenerated perturbation theory were used to treat electron correlation. The present method quite accurately reproduced the 1s CEBEs of CH4, NH3, H2O, and FH; the average deviation from the experimental data is 0.11 eV using Ahlrichs' VTZ basis set. The C 1s and O 1s CEBEs of formic acid and acetic acid were calculated and the results are consistent with the bonding characters of the atoms in these molecules. The present procedure can also be applied to CEBEs of higher angular momentum orbitals by including spin-orbit coupling. The calculated CEBEs of Ar 2p, HCl 2p, Kr 3d, and HBr 3d are in reasonable agreement with the available experimental values. In the calculation of the 3d CEBEs, a relativistic correction significantly improves the agreements. The effect of polarization functions is also discussed.
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PMID:Accurate calculation of core-electron binding energies: multireference perturbation treatment. 1548 18

A recent assessment by the intergovernmental panel on climate change concluded that the Earth's climate would be 2-6 degrees C warmer than in the pre-industrial era by the end of the twenty-first century, due to human-induced increases in greenhouse gases. In the absence of other changes, this would lead to the warmest period on Earth for at least the last 1000 years, and probably the last 100,000 years. The large-scale warming is expected to be accompanied by increased frequency and/or intensity of extreme events, such as heatwaves, heavy rainfall, storms and coastal flooding. There are also several possibilities that this large change could initiate nonlinear climate responses which lead to even more extreme and rapid (on the time-scale of decades) climate change, including the collapse of the ocean 'conveyor belt' circulation, the collapse of major ice sheets or the release of large amounts of methane in high latitudes leading to further global warming. Although these catastrophic events are much more speculative than the direct warming due to increased greenhouse gases, their potential impacts are great and therefore should be included in any risk assessment of the impacts of anthropogenic climate change.
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PMID:Extreme events due to human-induced climate change. 1684 51

Cyclic voltammetry and impedance spectroscopy were employed to probe the responsive properties of polyelectrolyte brushes. Poly[(dimethylamino)ethyl methacrylate] (PDMAEMA) brushes over 100 nm thick on gold substrates were synthesized via surface-initiated atom-transfer radical polymerization and quaternized with methane iodide to obtain cationic brushes (Q-PDMAEMA). Q-PDMAEMA brushes respond to electrolytes by exhibiting swollen and collapsed states. Swollen brushes allow good permeability of electroactive probes, while collapsed states block electron transport. Electrolytes have different impacts on the electrochemical properties of Q-PDMAEMA. Some salts (NaNO3) cause brush collapse due to charge screening, while others such as those with more hydrophobic anions (ClO4-, PF6-, and Tf2N-) induce brush collapse because of solubility changes. The collapsed brushes exhibit intrinsically different resistance as probed with impedance. Charged screened brushes retain good permeability to electroactive probes. Strongly coordinating hydrophobic anions lead to insoluble brushes, resulting in a high resistance. These results show that electrochemical impedance spectroscopy is a powerful technique to probe the properties and structure of polyelectrolyte brushes.
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PMID:Probing the responsive behavior of polyelectrolyte brushes using electrochemical impedance spectroscopy. 1719 36

In modern marine sediments, the anoxic decomposition of organic matter generates a significant flux of methane that is oxidized microbially with sulphate under the seafloor and never reaches the atmosphere. In contrast, prior to ca 2.4Gyr ago, the ocean had little sulphate to support anaerobic oxidation of methane (AOM) and the ocean should have been an important methane source. As atmospheric O2 and seawater sulphate levels rose on the early Earth, AOM would have increasingly throttled the release of methane. We use a biogeochemical model to simulate the response of early atmospheric O2 and CH4 to changes in marine AOM as sulphate levels increased. Semi-empirical relationships are used to parameterize global AOM rates and the evolution of sulphate levels. Despite broad uncertainties in these relationships, atmospheric O2 concentrations generally rise more rapidly and to higher levels (of order approx. 10(-3) bar versus approx. 10(-4) bar) as a result of including AOM in the model. Methane levels collapse prior to any significant rise in O2, but counter-intuitively, methane re-rises after O2 rises to higher levels when AOM is included. As O2 concentrations increase, shielding of the troposphere by stratospheric ozone slows the effective reaction rate between oxygen and methane. This effect dominates over the decrease in the methane source associated with AOM. Thus, even with the inclusion of AOM, the simulated Late Palaeoproterozoic atmosphere has a climatologically significant level of methane of approximately 50ppmv.
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PMID:Anaerobic methanotrophy and the rise of atmospheric oxygen. 1751 57

Volcanoes pose a threat to almost half a billion people; today there are approximately 500 active volcanoes on Earth, and every year there are 10 to 40 volcanic eruptions. Volcanic eruptions produce hazardous effects for the environment, climate, and the health of the exposed persons, and are associated with the deterioration of social and economic conditions. Along with magma and steam (H2O), the following gases surface in the environment: carbon dioxide (CO2) and sulphur dioxide (SO2), carbon monoxide (CO), hydrogen sulphide (H2S), carbon sulphide (CS), carbon disulfide (CS2), hydrogen chloride (HCl), hydrogen (H2), methane (CH4), hydrogen fluoride (HF), hydrogen bromide (HBr) and various organic compounds, as well as heavy metals (mercury, lead, gold).Their unfavourable effects depend on the distance from a volcano, on magma viscosity, and on gas concentrations. The hazards closer to the volcano include pyroclastic flows, flows of mud, gases and steam, earthquakes, blasts of air, and tsunamis. Among the hazards in distant areas are the effects of toxic volcanic ashes and problems of the respiratory system, eyes and skin, as well as psychological effects, injuries, transport and communication problems, waste disposal and water supplies issues, collapse of buildings and power outage. Further effects are the deterioration of water quality, fewer periods of rain, crop damages, and the destruction of vegetation. During volcanic eruptions and their immediate aftermath, increased respiratory system morbidity has been observed as well as mortality among those affected by volcanic eruptions. Unfavourable health effects could partly be prevented by timely application of safety measures.
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PMID:[Effects of volcanic eruptions on environment and health]. 1806 33

We consider a model system of methane molecule and a hemispherical, hydrophobic pocket of an 8 A radius, remaining together in aqueous environment. A spatial map of potential of mean force acting on methane molecule due to presence of pocket is constructed, based on a series of explicit solvent molecular dynamics simulations. A relation between free energy variations associated with methane translocations and accompanying changes in solvent density distribution is analyzed. A funnel-like area where free energy is diminished with respect to bulk is present over the pocket entrance and extends up to 9 A toward the bulk solvent. In order to get into the pocket, however, methane has to cross a free energy barrier, which is more prominent around the circumferential part of pocket entrance, while achieving bulklike free energy values at the very center. As a methane molecule crosses this barrier, the pocket gets completely dehydrated, which leads to "hydrophobic collapse," manifested by a sharp decrease in free energy. We find that the observed free energy changes are closely related to interactions between the methane hydration shell and the surrounding solvent. Results presented here are a continuation of our previous studies of methane-pocket systems.
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PMID:Hydrophobic interactions between methane and a nanoscopic pocket: three dimensional distribution of potential of mean force revealed by computer simulations. 1837 80

It has been suggested that a decrease in atmospheric methane levels triggered the progressive rise of atmospheric oxygen, the so-called Great Oxidation Event, about 2.4 Gyr ago. Oxidative weathering of terrestrial sulphides, increased oceanic sulphate, and the ecological success of sulphate-reducing microorganisms over methanogens has been proposed as a possible cause for the methane collapse, but this explanation is difficult to reconcile with the rock record. Banded iron formations preserve a history of Precambrian oceanic elemental abundance and can provide insights into our understanding of early microbial life and its influence on the evolution of the Earth system. Here we report a decline in the molar nickel to iron ratio recorded in banded iron formations about 2.7 Gyr ago, which we attribute to a reduced flux of nickel to the oceans, a consequence of cooling upper-mantle temperatures and decreased eruption of nickel-rich ultramafic rocks at the time. We measured nickel partition coefficients between simulated Precambrian sea water and diverse iron hydroxides, and subsequently determined that dissolved nickel concentrations may have reached approximately 400 nM throughout much of the Archaean eon, but dropped below approximately 200 nM by 2.5 Gyr ago and to modern day values ( approximately 9 nM) by approximately 550 Myr ago. Nickel is a key metal cofactor in several enzymes of methanogens and we propose that its decline would have stifled their activity in the ancient oceans and disrupted the supply of biogenic methane. A decline in biogenic methane production therefore could have occurred before increasing environmental oxygenation and not necessarily be related to it. The enzymatic reliance of methanogens on a diminishing supply of volcanic nickel links mantle evolution to the redox state of the atmosphere.
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PMID:Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event. 1936 74


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