Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

Somboon, Tuanjai; Ochiai, Jun; Treesuwan, Witcha; Gleeson, M. Paul; Hannongbua, Supa; Mori, Susumu

doi:10.1016/j.jmgm.2014.05.012

Cited by 5 publications

(3 citation statements)

References 57 publications

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“…Therefore, in this study, a combined quantum mechanics and molecular mechanics (QM/MM) approach has been employed to explore the reaction mechanisms of CH‐Fkbo and CH‐Hyg5. The QM/MM method has been successfully applied in exploring the enzymatic mechanisms in the past years . On the basis of our calculations, the detailed energetic profile, and the structures of intermediates and transition states were presented, and the different mechanisms of CH‐Fkbo and CH‐Hyg5 were elucidated as well.…”

Section: Introductionsupporting

confidence: 68%

Comparative studies of the catalytic mechanisms of two chorismatases: CH‐fkbo and CH‐Hyg5

Dong

Liu

2017

Proteins

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Chorismatase is an important enzyme involved in Shikimate pathway, which catalyzes the conversion of chorismate into pyruvate and (dihydro)-benzoic acid derivatives. According to the outcomes of catalytic reactions, chorismatases can be divided into three subfamilies: CH-Fkbo, CH-Hyg5 and CH-XanB2. Recently, the crystal structures of CH-Fkbo and CH-Hyg5 from Streptomyces hygroscopicus have been successfully obtained, allowing us to perform QM/MM calculations to explore the reaction details. Our calculation results support the proposal that CH-Fkbo and CH-Hyg5 employ different catalytic mechanisms and gave the mechanistic details. Fkbo follows a typical hydrolytic mechanism, which contains three consecutive steps, including the protonation step of the methylene group of substrate, the nucleophilic attack of the resulted carbocation by activated water and cleavage of C2'-O8 bond of tetrahedral intermediate (hemiketal). The protonation of methylene group and the C2'-O8 cleavage correspond to similar energy barriers (26.5 and 24.8 kcal/mol), suggesting both steps to be rate-limiting. Whereas Hyg5 employs an intramolecular mechanism, in which the oxygen from C4 migrates to C3 via an arene oxide intermediate. The first step of Hyg5, which corresponds to the concerted protonation of methylene group and the cleavage of C3-O8, is calculated to be rate-limiting with an energy barrier of 26.3 kcal/mol. The nonconserved active site residue G240 (or A244 °) is suggested to be responsible for leading to different reaction mechanism in CH-Fkbo and CH-Hyg5. During the catalytic reaction, residue C327 plays an important role in directing the product selectivity in Hyg5 enzyme. Proteins 2017; 85:1146-1158. © 2017 Wiley Periodicals, Inc.

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Section: Introductionsupporting

confidence: 68%

Comparative studies of the catalytic mechanisms of two chorismatases: CH‐fkbo and CH‐Hyg5

Dong

Liu

2017

Proteins

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“…In the last decade there had been tremendous developments in nanotechnology science, which resulted in the establishment of several new techniques for research. Nanotechnology has achieved the rate of combing all living organisms-plants, animal and microorganisms [1][2][3][4][5][6][7]. It includes multidisciplinary research interest like Biochemistry, Material Science, Polymer Science and etc.…”

Section: Introductionmentioning

confidence: 99%

Biosynthesis and Characterization of Silver Nanoparticles (Snps) by using Leaf Extracts of Ocimum Sanctum L (Tulsi) and Study of its Antibacterial Activities

Bindhani¹,

Panigrahi²

2015

J Nanomedic Nanotechnol

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The present study aimed to synthesis of SNPs (Silver Nanoparticles) or (Green-Silver) in aqueous medium using leaf extracts of Ocimum sanctum L. The synthesized silver nanoparticles (SNPs) were characterized by the different techniques such as UV-vis Spectrophotometer, XRD, FTIR and TEM. The synthesis of silver nanoparticles were confirmed due to the SPR optical absorption band peak at ~440 nm by UV-vis spectrophotometer, nearly 15-45 nm in diameter with spherical in shape by TEM, high crystalline with the Bragg peaks of (111), (200), (220) and (311) plane as the predominant orientation by XRD and FTIR confirmed the presence of methoxy and allyl groups in SNPs. The reduction of Ag metal ions was performed due to the presence of various types of anti-oxidants in the leaves of Ocimum sanctum L. and each having a unique structure and functions. The formations of silver nanoparticles through aqueous medium were fairly stable and which can be incubated up to 4 months in refrigerator. At last, the antimicrobial activities of AgNPs were evaluated using different bacteria strain. It was found that, this biosynthesizing of silver nanoparticles may inhibit the all types of bacterial pathogenic organisms competently. This recent research study opens an innovative design to progress our understanding of how SNPs behave can be optimized to improve human antimicrobial activities.Citation: Bindhani BK, Panigrahi AK (2015) Biosynthesis and Characterization of Silver Nanoparticles (SNPs) by using Leaf Extracts of Ocimum Sanctum L (Tulsi) and Study of its Antibacterial Activities.

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“…45 Preparation was achieved using the following procedure: (1) hydrogen atoms alone were optimized in the first iteration, (2) with the backbone fixed, amino side chains, the substrate, counterions and water molecules were optimized, and (3) the backbone of the protein was harmonically restrained and the system underwent 1 ns of molecular dynamics (MD) under NPT conditions (heating 0.2 ps (0-300 K), equilibration 0.5 ps and production 0.2 ps). 46 The heavy atom RMSD between the initial X-ray structure and the protein following the MD preparation sequence was 2.1 Å.…”

Section: Model Setupmentioning

confidence: 99%

Application of QM/MM and QM methods to investigate histone deacetylase 8

Gleeson

2015

Med. Chem. Commun.

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Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

Cited by 5 publications

References 57 publications

Comparative studies of the catalytic mechanisms of two chorismatases: CH‐fkbo and CH‐Hyg5

Comparative studies of the catalytic mechanisms of two chorismatases: CH‐fkbo and CH‐Hyg5

Biosynthesis and Characterization of Silver Nanoparticles (Snps) by using Leaf Extracts of Ocimum Sanctum L (Tulsi) and Study of its Antibacterial Activities

Application of QM/MM and QM methods to investigate histone deacetylase 8

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