ArticleThe journal of physical chemistry. B2011
Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophile.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed, 21 citations in OpenAlex.
- How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study.The journal of physical chemistry. A · 2014Article
- A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations.PloS one · 2012Article
- Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.The journal of physical chemistry. B · 2011Article
- On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines.Journal of the American Chemical Society · 2011Article
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5 authors at 3 institutions in 2 countries.
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Abstract
The first step of the hydrolytic deimination of L-arginine catalyzed by arginine deiminase is examined using ab initio quantum mechanical/molecular mechanical molecular dynamics simulations. Two possible protonation states of the nucleophilic Cys406 residue were investigated, and the corresponding activation free energies were obtained via umbrella sampling. Our calculations indicated a reaction free-energy barrier of 21.3 kcal/mol for the neutral cysteine, which is in reasonably good agreement with the experimental k(cat) value of 6.3 s(-1), i.e., a barrier of 16.7 kcal/mol. On the other hand, the deprotonated Cys nucleophile yields a free-energy barrier of 6.7 kcal/mol, much lower than the experimental result. The reaction free-energy barriers along with other data suggest that the Cys nucleophile is dominated by its protonated state in the Michaelis complex, and the reaction barrier corresponds largely to its deprotonation.
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