Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies

2012 ◽  
Vol 137 (14) ◽  
pp. 145103 ◽  
Author(s):  
Morad M. El-Hendawy ◽  
José-Antonio Garate ◽  
Niall J. English ◽  
Stephen O’Reilly ◽  
Damian A. Mooney
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Active Site ◽  
Quantum Chemical ◽  
Chemical Studies ◽  
Quantum Chemical Studies

scholarly journals Recognition of shorter and longer trimethyllysine analogues by epigenetic reader proteins

2018 ◽  
Vol 54 (19) ◽  
pp. 2409-2412 ◽  
Author(s):  
Abbas H. K. Al Temimi ◽  
Roman Belle ◽  
Kiran Kumar ◽  
Jordi Poater ◽  
Peter Betlem ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermodynamic Data ◽  
Quantum Chemical ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Dynamics Simulations

Combined thermodynamic data, molecular dynamics simulations, and quantum chemical studies reveal that epigenetic reader proteins efficiently bind trimethylornithine and trimethylhomolysine.

scholarly journals Interaction of methanol with the oxygen-evolving complex: atomistic models, channel identification, species dependence, and mechanistic implications

2016 ◽  
Vol 7 (10) ◽  
pp. 6463-6476 ◽  
Author(s):  
Marius Retegan ◽  
Dimitrios A. Pantazis
Keyword(s):  
Photosystem Ii ◽  
Active Site ◽  
Quantum Chemical ◽  
Oxygen Evolving Complex ◽  
Manganese Cluster ◽  
Channel Identification ◽  
Atomistic Models ◽  
Chemical Studies ◽  
Quantum Chemical Studies ◽  
Oxygen Evolving

Spectroscopy-oriented quantum chemical studies establish how methanol is delivered to the water-oxidizing active site of Photosystem II and how it interacts with the manganese cluster.

The reactivation of tabun-inhibited mutant AChE with Ortho-7: steered molecular dynamics and quantum chemical studies

2016 ◽  
Vol 12 (4) ◽  
pp. 1224-1231 ◽  
Author(s):  
Rabindranath Lo ◽  
Nellore Bhanu Chandar ◽  
Shibaji Ghosh ◽  
Bishwajit Ganguly
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Quantum Chemical ◽  
Double Mutant ◽  
Steered Molecular Dynamics ◽  
Wild Type ◽  
Single Mutant ◽  
Chemical Studies ◽  
Quantum Chemical Studies

Tabun inhibited AChE can be reactivated more easily with a single mutant than with a wild-type or double mutant: an in silico study.

scholarly journals Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate

2017 ◽  
Vol 114 (18) ◽  
pp. 4667-4672 ◽  
Author(s):  
Zhihong Zhang ◽  
Tristan J. Smart ◽  
Hwanho Choi ◽  
Florence Hardy ◽  
Christopher T. Lohans ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Carboxylic Acid ◽  
Pseudomonas Syringae ◽  
Ethylene Production ◽  
Quantum Chemical ◽  
High Energy ◽  
Acid Oxidase ◽  
Biochemical Studies ◽  
Chemical Studies ◽  
Quantum Chemical Studies

Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, but via the four-electron oxidation of 2-oxoglutarate to give ethylene in an arginine-dependent reaction. Crystallographic and biochemical studies on the Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate–derived intermediate occurs to give ethylene and carbon dioxide. Crystallographic and quantum chemical studies reveal that fragmentation to give ethylene is promoted by binding of l-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation.

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