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Thomas A Bobik - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell
'American Chemical Society (ACS)', 2018Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Kendall N. Houk, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The,energetic effect is consistent with a lower capacity of a serine side chain, which protrudes into the pore at a point of constriction, to form hydrogen bonds with Propionaldehyde relative to the more freely permeable propanediol. The results highlight the importance of molecular diffusion and transport in a new biological context141sciescopu
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molecular dynamics simulations of selective metabolite transport across the propanediol bacterial microcompartment shell
Journal of Physical Chemistry B, 2017Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica-exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The energetic effect is consiste...
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Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell
2017Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Kendall N. Houk, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica-exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The energetic effect is consistent with a lower capacity of a serine side chain, which protrudes into the pore at a point of constriction, to form hydrogen bonds with Propionaldehyde relative to the more freely permeable propanediol. The results highlight the importance of molecular diffusion and transport in a new biological context
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microcompartments for b12 dependent 1 2 propanediol degradation provide protection from dna and cellular damage by a reactive metabolic intermediate
Journal of Bacteriology, 2008Co-Authors: Edith M Sampson, Thomas A BobikAbstract:Salmonella enterica grows on 1,2-propanediol (1,2-PD) in a coenzyme B12-dependent fashion. Prior studies showed that a bacterial microcompartment (MCP) is involved in this process and that an MCP-minus mutant undergoes a 20-h period of growth arrest during 1,2-PD degradation. It was previously proposed that growth arrest resulted from Propionaldehyde toxicity, but no direct evidence was presented. Here, high-pressure liquid chromatography analyses of culture medium were used to show that the major products of aerobic 1,2-PD degradation are Propionaldehyde, propionate, and 1-propanol. A MCP-minus mutant accumulated a level of Propionaldehyde 10-fold higher than that of the wild type (1.6 mM compared to 15.7 mM), associating this compound with growth arrest. The addition of Propionaldehyde to cultures of S. enterica caused growth arrest from 8 to 20 mM, but not at 4 mM, providing direct evidence for Propionaldehyde toxicity. Studies also indicated that Propionaldehyde was toxic due to the inhibition of respiratory processes, and the growth arrest ended when Propionaldehyde was depleted primarily by conversion to propionate and 1-propanol and secondarily due to volatility. The Ames test was used to show that Propionaldehyde is a mutagen and that mutation frequencies are increased in MCP-minus mutants during 1,2-PD degradation. We propose that a primary function of the MCPs involved in 1,2-PD degradation is the mitigation of toxicity and DNA damage by Propionaldehyde.
Xin Gao - One of the best experts on this subject based on the ideXlab platform.
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reversible reaction assisted intensification process for separating the azeotropic mixture of ethanediol and 1 2 butanediol reactants screening
Industrial & Engineering Chemistry Research, 2018Co-Authors: Rui Wang, Xin GaoAbstract:The feasibility of employing reversible reactions to convert the separation of ethanediol (EG) and 1,2-butanediol (1, 2-BDO) azeotropic system was analyzed in our previous work. This article aims at systematically screening the feasible reactants for the reaction-assisted separation process. A screening principle was brought up and applied. Through preliminary screening, acetic acid, acrylic acid, acetaldehyde, Propionaldehyde, propanol and butanone were obtained as potential reactants. Propionaldehyde was chosen as the proper one after fully comparing the reaction selectivity difference and conversion of EG and 1,2-BDO in reaction process, the separation efficiency in purification process as well as final EG yield. The separation efficiency was predicted based on the relative volatility of EG, 1,2-BDO and their corresponding products and was verified by distillation experiments. The stratification appeared in the reaction was found beneficial to the coupling of reaction and separation.
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Reversible Reaction-Assisted Intensification Process for Separating the Azeotropic Mixture of Ethanediol and 1,2-Butanediol: Reactants Screening
2017Co-Authors: Rui Wang, Xin GaoAbstract:The feasibility of employing reversible reactions to convert the separation of ethanediol (EG) and 1,2-butanediol (1,2-BDO) azeotropic system was analyzed in our previous work. This article aims at systematically screening the feasible reactants for the reaction-assisted separation process. A screening principle was brought up and applied. Through preliminary screening, acetic acid, acrylic acid, acetaldehyde, Propionaldehyde, propanol, and butanone were obtained as potential reactants. Propionaldehyde was chosen as the proper one after fully comparing the reaction selectivity difference and conversion of EG and 1,2-BDO in the reaction process, the separation efficiency in the purification process, and final EG yield. The separation efficiency was predicted based on the relative volatility of EG, 1,2-BDO, and their corresponding products and was verified by distillation experiments. The stratification appeared in the reaction was found beneficial to the coupling of reaction and separation
Todd O Yeates - One of the best experts on this subject based on the ideXlab platform.
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Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell
'American Chemical Society (ACS)', 2018Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Kendall N. Houk, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The,energetic effect is consistent with a lower capacity of a serine side chain, which protrudes into the pore at a point of constriction, to form hydrogen bonds with Propionaldehyde relative to the more freely permeable propanediol. The results highlight the importance of molecular diffusion and transport in a new biological context141sciescopu
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molecular dynamics simulations of selective metabolite transport across the propanediol bacterial microcompartment shell
Journal of Physical Chemistry B, 2017Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica-exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The energetic effect is consiste...
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Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell
2017Co-Authors: Jiyong Park, Sunny Chun, Thomas A Bobik, Kendall N. Houk, Todd O YeatesAbstract:Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell. PduA is a major shell protein in a bacterial microcompartment that metabolizes 1,2-propanediol via a toxic aldehyde intermediate, Propionaldehyde. Using both metadynamics and replica-exchange umbrella sampling, we find that the pore of the PduA hexamer has a lower energy barrier for passage of the propanediol substrate compared to the toxic Propionaldehyde generated within the microcompartment. The energetic effect is consistent with a lower capacity of a serine side chain, which protrudes into the pore at a point of constriction, to form hydrogen bonds with Propionaldehyde relative to the more freely permeable propanediol. The results highlight the importance of molecular diffusion and transport in a new biological context
Chonglin Song - One of the best experts on this subject based on the ideXlab platform.
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evaluation of carbonyl compound emissions from a non road machinery diesel engine fueled with a methanol diesel blend
Applied Thermal Engineering, 2018Co-Authors: Chenyang Fan, Chonglin Song, Guangyao Wang, Hua Zhou, Xiaojun JingAbstract:Abstract The carbonyl emissions from a non-road machinery diesel engine running on diesel fuel (DF) or methanol-diesel blend fuel (M/DF) were investigated under a series of steady-state operating conditions. Carbonyl compounds (CBCs) were collected from the diluted exhaust, employing 2,4-dinitrophenylhydrazine-coated silica gel cartridges, and analyzed using a high-performance liquid chromatography system with a photodiode array detector. The results indicate that formaldehyde and acetaldehyde are the most abundant carbonyls, followed by acrolein, acetone, Propionaldehyde and crotonaldehyde. Each of these compounds exhibit a consistent reduction with increases in the engine load. The M/DF produces much more formaldehyde, acetaldehyde, acrolein, acetone and crotonaldehyde than the DF at low loads, while there are marginal differences in the emission levels of these carbonyls between M/DF and DF at medium and high loads. The use of M/DF decreases Propionaldehyde emissions at all test conditions. Compared with the results obtained using DF, the total CBC emissions increase by 45.3% and the ozone formation potential (OFP) increases by 57.0% when burning M/DF at low engine loads. In general, M/DF increases both OFP and total CBC emissions to a greater extent than biodiesel-blend fuel but to a lesser degree than ethanol- or butanol-containing blends.
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carbonyl compound emissions from a heavy duty diesel engine fueled with diesel fuel and ethanol diesel blend
Chemosphere, 2010Co-Authors: Chonglin Song, Zhuang Zhao, Jinou Song, Lidong Liu, Ruifen ZhaoAbstract:Abstract This paper presents an investigation of the carbonyl emissions from a direct injection heavy-duty diesel engine fueled with pure diesel fuel (DF) and blended fuel containing 15% by volume of ethanol (E/DF). The tests have been conducted under steady-state operating conditions at 1200, 1800, 2600 rpm and idle speed. The experimental results show that acetaldehyde is the most predominant carbonyl, followed by formaldehyde, acrolein, acetone, Propionaldehyde and crotonaldehyde, produced from both fuels. The emission factors of total carbonyls vary in the range 13.8–295.9 mg (kW h)−1 for DF and 17.8–380.2 mg (kW h)−1 for E/DF, respectively. The introduction of ethanol into diesel fuel results in a decrease in acrolein emissions, while the other carbonyls show general increases: at low engine speed (1200 rpm), 0–55% for formaldehyde, 4–44% for acetaldehyde, 38–224% for acetone, and 5–52% for crotonaldehyde; at medium engine speed (1800 rpm), 106–413% for formaldehyde, 4–143% for acetaldehyde, 74–113% for acetone, 114–1216% for Propionaldehyde, and 15–163% for crotonaldehyde; at high engine speed (2600 rpm), 36–431% for formaldehyde, 18–61% for acetaldehyde, 22–241% for acetone, and 6–61% for Propionaldehyde. A gradual reduction in the brake specific emissions of each carbonyl compound from both fuels is observed with increase in engine load. Among three levels of engine speed employed, both DF and E/DF emit most CBC emissions at high engine speed. On the whole, the presence of ethanol in diesel fuel leads to an increase in aldehyde emissions.
Ruifen Zhao - One of the best experts on this subject based on the ideXlab platform.
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carbonyl compound emissions from a heavy duty diesel engine fueled with diesel fuel and ethanol diesel blend
Chemosphere, 2010Co-Authors: Chonglin Song, Zhuang Zhao, Jinou Song, Lidong Liu, Ruifen ZhaoAbstract:Abstract This paper presents an investigation of the carbonyl emissions from a direct injection heavy-duty diesel engine fueled with pure diesel fuel (DF) and blended fuel containing 15% by volume of ethanol (E/DF). The tests have been conducted under steady-state operating conditions at 1200, 1800, 2600 rpm and idle speed. The experimental results show that acetaldehyde is the most predominant carbonyl, followed by formaldehyde, acrolein, acetone, Propionaldehyde and crotonaldehyde, produced from both fuels. The emission factors of total carbonyls vary in the range 13.8–295.9 mg (kW h)−1 for DF and 17.8–380.2 mg (kW h)−1 for E/DF, respectively. The introduction of ethanol into diesel fuel results in a decrease in acrolein emissions, while the other carbonyls show general increases: at low engine speed (1200 rpm), 0–55% for formaldehyde, 4–44% for acetaldehyde, 38–224% for acetone, and 5–52% for crotonaldehyde; at medium engine speed (1800 rpm), 106–413% for formaldehyde, 4–143% for acetaldehyde, 74–113% for acetone, 114–1216% for Propionaldehyde, and 15–163% for crotonaldehyde; at high engine speed (2600 rpm), 36–431% for formaldehyde, 18–61% for acetaldehyde, 22–241% for acetone, and 6–61% for Propionaldehyde. A gradual reduction in the brake specific emissions of each carbonyl compound from both fuels is observed with increase in engine load. Among three levels of engine speed employed, both DF and E/DF emit most CBC emissions at high engine speed. On the whole, the presence of ethanol in diesel fuel leads to an increase in aldehyde emissions.
