Model for ring closure in ER tubular network dynamics

Tubular networks of endoplasmic reticulum (ER) are dynamic structures whose steady-state conformations are maintained by a dynamic balance between the persistent generation and vanishing of the network elements. While factors producing the ER tubules and inter-tubular junctions have been investigated, the mechanisms behind their elimination remained unknown. Here we addressed the ER ring closure, the process resulting in the tubule and junction removal through constriction of the network unit-cells into junctional knots followed by the knot remodeling into regular junctions. We considered the ring closure to be driven by the tension existing in ER membranes. We modeled, computationally, the structures of the junctional knots containing internal nanopores and analyzed their tension dependence. We predicted an effective interaction between the nanopores facilitating the knot tightening and collapse of additional network unit cells. We analyzed the process of the pore sealing through membrane fission resulting in formation of regular junctions. Considering the hemi-fission as the rate-limiting stage of the fission reaction, we evaluated the membrane tensions guarantying the spontaneous character of the pore sealing. We concluded that feasible membrane tensions explain all stages of the ER ring closure.

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Modelling methanogenesis during anaerobic conversion of complex organic matter at low temperatures

Water Science & Technology ◽

10.2166/wst.1997.0633 ◽

1997 ◽

Vol 36 (6-7) ◽

pp. 531-538 ◽

Cited By ~ 8

Author(s):

V. A. Vavilin ◽

L. Ya. Lokshina ◽

S. V. Rytov ◽

O. R. Kotsyurbenko ◽

A. N. Nozhevnikova ◽

...

Keyword(s):

Organic Matter ◽

Low Temperature ◽

Wetland Soil ◽

Methane Formation ◽

Tundra Soil ◽

Alternative Pathways ◽

Wide Range ◽

Limiting Stage ◽

Acetoclastic Methanogenesis ◽

Rate Limiting

Low temperature consumption of H2/CO2 by microflora of tundra wetland soil and pond silt were simulated using the modified <METHANE> model with consideration of homoacetogens or hydrogen consuming methanogens as hydrogenotrophs. Simulations show that the model with homoacetogens was able to fit the data closely. Under the conditions of high initial hydrogen concentrations acetate was the main precursor of methane. Inhibition of acetoclasic methanogens proved to be significant for tundra soil samples. Methane formation from organic matter contained in the samples of tundra soil was modeled in the wide range of temperature conditions. It was concluded that hydrolysis is the rate-limiting step at 10–28°C, but at 6°C the rate of acetoclastic methanogenesis becomes the rate-limiting stage in methane production. To describe the low temperature methane formation from organic matter by microflora of pond silt, cattle's and pig's manure the alternative pathways with participation of homoacetogens or hydrogenotrophic methanogens were verified. It was shown that the both pathways fit the measured data comparatively well.

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Activation of the Hydrogen-Terminated Diamond [100] by Hydrogen Atoms and Hydroxyl Groups

Materials Science Forum ◽

10.4028/www.scientific.net/msf.996.151 ◽

2020 ◽

Vol 996 ◽

pp. 151-156

Author(s):

Xiao Gang Jian ◽

Ji Bo Hu ◽

Xin Huang ◽

Pei Kang Yang ◽

Jun Peng Wang

Keyword(s):

Hydrogen Atom ◽

Low Temperature ◽

Density Functional ◽

Diamond Surface ◽

Hydroxyl Group ◽

Hydroxyl Groups ◽

Hydrogen Atoms ◽

Activation Rate ◽

Limiting Stage ◽

Rate Limiting

The process of producing active vacancies on a hydrogen-terminated diamond surface is the most important rate-limiting stage in CH4/H2 and CH4/H2/CO2 atmospheres. Hydrogen atom and the hydroxyl group can bone to the hydrogen atom on the diamond surface and create an active vacancy. Density functional theory (DFT) was used to study the extraction reaction by two reactants both hydrogen atom and the hydroxyl group. The result indicated that the hydroxyl group could reduce the energy required for diamond surface activation. What is more, the activation rate of the surface by the hydroxyl group was livelier at low temperature, while the activation rate of the hydrogen atom predicts on the contrary. The scanning electron microscope (SEM) and Raman spectra demonstrated that the introduction of CO2 in the CH4/H2 atmosphere could reduce the deposition temperature and raise the deposition rate at low temperature.

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Stereoelectronic effects in ring closure reactions: the 2′-hydroxychalcone – flavanone equilibrium, and related systems

Canadian Journal of Chemistry ◽

10.1139/v90-277 ◽

1990 ◽

Vol 68 (10) ◽

pp. 1780-1785 ◽

Cited By ~ 29

Author(s):

Colin M. Brennan ◽

Ian Hunt ◽

Terence C. Jarvis ◽

C. David Johnson ◽

Peter D. McDonnell

Keyword(s):

Double Bond ◽

Michael Addition ◽

Protonated Form ◽

Ring Closure ◽

Rate Limiting Step ◽

Michael Adducts ◽

Main Pathway ◽

Rate Limiting ◽

Bond Character ◽

Influence Of Substituents

The 2′-hydroxychalcone (2-HOC6H4COCH=CHC6H4X)–flavanone equilibrium in trifluoroacetic acid (TFA) has been examined. The influence of substituents X on the rate of attainment of equilibrium shows that the 6-endo-trig mode of ring closure by Michael addition is disallowed, by demonstrating a negative ρ value for the reaction rate when X is varied. Reaction therefore proceeds either on the carbonyl-protonated form, which allows twisting about the 2,3 bond, its double bond character being reduced by resonance, or through direct rate-limiting protonation on the 2,3 double bond. Either pathway permits the allowed 6-exo-trig mode of ring closure to be followed. Alternative mechanisms involving intermolecular Michael addition of trifluoroacetate, followed by intramolecular 6-exo-tet displacement are considered. Such Michael adducts can be detected in the ring closures of 2-crotonyl-4-methylphenol and 4,4-dimethyl-1-(2-hydroxyphenyl)-2-penten-1-one in TFA, but they do not appear to lie on the main pathway, because the reactions proceed with equal facility in methanesulphonic acid/chloroform medium, which does not contain a suitable nucleophile for such a mechanism. Further important mechanistic information is given by studying the reactions in TFA-d, together with measurements on the (E)-2-methyl-3-oxo-5-arylpent-4-en-2-ol and 3′-methoxychalcone systems. These isotope effect studies, which yield kH/kD values of about 3, indicate that the proton is in flight during the rate-limiting step, and provide evidence against the mechanism involving a preequilibrium carbonyl protonation, such as in the Nazarov rearrangement of 3′-methoxychalcones, where kH/kD is ca. 0.7. Some results are also reported for ring closure of the 2-aminochalcones in TFA. Keywords: 2′-hydroxychalcones, flavanones, 3′methoxychalcones, 3-aryl-6-methoxyindanones, 2′-aminochalcones, 2-aryl-1, 2, 3, 4-tetrahydroquinolines, Baldwin's rules.

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Investigation of carbon and energy metabolic mechanism of mixotrophy in Chromochloris zofingiensis

Biotechnology for Biofuels ◽

10.1186/s13068-021-01890-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Zhao Zhang ◽

Dongzhe Sun ◽

Ka-Wing Cheng ◽

Feng Chen

Keyword(s):

Dynamic Balance ◽

Carbon Sources ◽

Photosynthesis Rate ◽

Biodiesel Production ◽

Photochemical Quenching ◽

Metabolic Mechanism ◽

Glucose Decomposition ◽

Non Photochemical Quenching ◽

Rate Limiting ◽

Chromochloris Zofingiensis

Abstract Background Mixotrophy can confer a higher growth rate than the sum of photoautotrophy and heterotrophy in many microalgal species. Thus, it has been applied to biodiesel production and wastewater utilization. However, its carbon and energy metabolic mechanism is currently poorly understood. Results To elucidate underlying carbon and energy metabolic mechanism of mixotrophy, Chromochloris zofingiensis was employed in the present study. Photosynthesis and glucose metabolism were found to operate in a dynamic balance during mixotrophic cultivation, the enhancement of one led to the lowering of the other. Furthermore, compared with photoautotrophy, non-photochemical quenching and photorespiration, considered by many as energy dissipation processes, were significantly reduced under mixotrophy. Comparative transcriptome analysis suggested that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO2 to provide carbon sources for chloroplast organic carbon metabolism under mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped, allowing for more efficient utilization of photoreaction-derived energy. Besides, compared with heterotrophy, photoreaction-derived ATP reduced the need for TCA-derived ATP, so the glucose decomposition was reduced, which led to higher biomass yield on glucose. Based on these results, a mixotrophic metabolic mechanism was identified. Conclusions Our results demonstrate that the intermediates of glycolysis could directly enter the chloroplast and replace RuBisCO-fixed CO2 to provide carbon for photosynthesis in mixotrophy. Therefore, the photosynthesis rate-limiting enzyme, RuBisCO, was skipped in mixotrophy, which could reduce energy waste of photosynthesis while promote cell growth. This finding provides a foundation for future studies on mixotrophic biomass production and photosynthetic metabolism.

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Hydrolysis of a monocyclic oxyphosphorane containing a five-membered ring

Canadian Journal of Chemistry ◽

10.1139/v91-300 ◽

1991 ◽

Vol 69 (12) ◽

pp. 2075-2083 ◽

Cited By ~ 1

Author(s):

Glenn H. McGall ◽

Robert A. McClelland

Keyword(s):

Rate Constant ◽

Methoxy Group ◽

Ring Closure ◽

Rate Limiting Step ◽

Acid Base Equilibrium ◽

Reaction With Water ◽

Effective Molarity ◽

Rate Limiting ◽

Hydrolysis Of ◽

Good Agreement

A kinetic study is reported for the hydrolysis of 2,2-diphenyl-2-methoxy-1,3,2-dioxaphospholane 1. This phosphorane exists in aqueous solution in a pseudo acid–base equilibrium with an observable phosphonium ion, the ring-opened (2′-hydroxyethoxy)diphenylmethoxyphosphonium ion 5. The equilibrium constant Ka ([1][H+]/[5]) is 9 × 10−9, values determined by kinetic and spectroscopic methods being in good agreement. This phosphonium ion is, however, not involved in the overall hydrolysis reaction, which proceeds via the thermodynamically less stable cyclic five-membered phosphonium ion derived by loss of the exocyclic methoxy group from the phosphorane, the 2,2-diphenyl-1,3,2-dioxaphospholan-2-ylium ion 6. This route for the overall hydrolysis is established by analysis of the products, and by the observation that the rate constant for the disappearance of 5 in acid solutions is 40 000 times greater than that for an analog that differs only in not being able to cyclize, the (2′-methoxyethoxy)diphenylmethoxyphosphonium ion 7. At all pH, the phosphorane 1 and the ring-opened phosphonium ion 5 exist in equilibrium, and the rate-limiting step in the overall hydrolysis is the cleavage of the exocyclic methoxy group to give the cyclic phosphonium ion 6, which is rapidly converted to products by reaction with water. The actual equilibration reaction involving 1 and 5 cannot be observed at any pH, even with stopped-flow spectroscopy. The non-catalyzed ring closure of the phosphonium ion 5 reforming the phosphorane 1 occurs with a rate constant of 200–500 s−1, corresponding to an effective molarity of (2–5) × 107 M for the intramolecular hydroxy group in this reaction. The rate-limiting exocyclic cleavage is assisted by H+, with a very large rate constant 2 × 109 M−1 s−1. Catalysis by general acids is also observed. The Brønsted plot has a slope α of 1.0 for the weaker acids, with a break for acids with pKa < 3. This "Eigen"-type behavior is proposed to arise from a transition state with little phosphonium ion character, in which the proton is almost completely transferred for the weaker acids. Key words: phosphorane, phosphate, phosphonium, hydrolysis.

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Upward movement of IS4 and IIIS4 is a rate-limiting stage in Cav1.2 activation

Pflügers Archiv - European Journal of Physiology ◽

10.1007/s00424-016-1895-5 ◽

2016 ◽

Vol 468 (11-12) ◽

pp. 1895-1907 ◽

Cited By ~ 7

Author(s):

Stanislav Beyl ◽

Annette Hohaus ◽

Stanislav Andranovits ◽

Eugen Timin ◽

Steffen Hering

Keyword(s):

Upward Movement ◽

Limiting Stage ◽

Rate Limiting

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Uncoupling of dynamin polymerization and GTPase activity revealed by the conformation-specific nanobody dynab

eLife ◽

10.7554/elife.25197 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 6

Author(s):

Valentina Galli ◽

Rafael Sebastian ◽

Sandrine Moutel ◽

Jason Ecard ◽

Franck Perez ◽

...

Keyword(s):

Real Time ◽

Gtpase Activity ◽

Fission Reaction ◽

Gtp Hydrolysis ◽

Membrane Fission

Dynamin is a large GTPase that forms a helical collar at the neck of endocytic pits, and catalyzes membrane fission (Schmid and Frolov, 2011; Ferguson and De Camilli, 2012). Dynamin fission reaction is strictly dependent on GTP hydrolysis, but how fission is mediated is still debated (Antonny et al., 2016): GTP energy could be spent in membrane constriction required for fission, or in disassembly of the dynamin polymer to trigger fission. To follow dynamin GTP hydrolysis at endocytic pits, we generated a conformation-specific nanobody called dynab, that binds preferentially to the GTP hydrolytic state of dynamin-1. Dynab allowed us to follow the GTPase activity of dynamin-1 in real-time. We show that in fibroblasts, dynamin GTP hydrolysis occurs as stochastic bursts, which are randomly distributed relatively to the peak of dynamin assembly. Thus, dynamin disassembly is not coupled to GTPase activity, supporting that the GTP energy is primarily spent in constriction.

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Anti-inflammation biomaterial platforms for chronic wound healing

Biomaterials Science ◽

10.1039/d1bm00637a ◽

2021 ◽

Author(s):

Zejun Xu ◽

Biao Liang ◽

Junzhang Tian ◽

Jun Wu

Keyword(s):

Wound Healing ◽

Chronic Wounds ◽

Chronic Wound ◽

Health Problems ◽

Limiting Stage ◽

Rate Limiting ◽

Anti Inflammation

Nowadays, there has been an increase in the number of people with chronic wounds, which has resulted in serious health problems worldwide. The rate-limiting stage of chronic wound healing has...

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Dynamic constriction and fission of ER membranes by reticulon

10.1101/472829 ◽

2018 ◽

Author(s):

Javier Espadas ◽

Diana Pendin ◽

Rebeca Bocanegra ◽

Artur Escalada ◽

Giulia Misticoni ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Network Formation ◽

Dynamic Balance ◽

Ectopic Expression ◽

Membrane Curvature ◽

Fragmentation Mechanism ◽

Membrane Fission ◽

Pulling Force ◽

Organelle Morphology

AbstractThe endoplasmic reticulum (ER) is a continuous cell-wide membrane network. Network formation has been widely associated with proteins producing membrane curvature and fusion, such as reticulons and atlastin. Regulated network fragmentation, occurring in different physiological contexts, is less understood. We found that the ER network has an embedded fragmentation mechanism based upon the ability of reticulons to produce fission of elongating network branches. In Drosophila, fission is counterbalanced by atlastin-driven fusion, with their imbalance leading to ER fragmentation. Live imaging of ER network dynamics upon ectopic expression of Drosophila reticulon linked fission to augmented membrane friction. Consistently, in vitro analysis revealed that purified reticulon produced velocity-dependent constriction and fission of lipid nanotubes pulled from a flat reservoir membrane. Fission occurred at elongation rates and pulling force ranges intrinsic to the ER network, thus suggesting a novel principle of organelle morphology regulation where the dynamic balance between fusion and fission is governed by membrane motility.

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