A quantum mechanics study on the reaction mechanism of chalcone formation from p-coumaroyl-CoA and malonyl-CoA catalyzed by chalcone synthase

2008 ◽  
Vol 122 (3-4) ◽  
pp. 157-166 ◽  
Author(s):  
Dai-lin Li ◽  
Qing-chuan Zheng ◽  
Hong-xing Zhang
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Chalcone Synthase ◽  
Malonyl Coa

High Quality cDNA synthesis and Amplification of Chalcone Synthase Gene (CHS) from Justicia gendarussa Burm. F.

2013 ◽  
Vol 64 (2) ◽  
Author(s):  
Arman Amani Babadi ◽  
Faezah Mohd Salleh
Keyword(s):  
Chalcone Synthase ◽  
High Concentration ◽  
Cdna Synthesis ◽  
Chalcone Synthase Gene ◽  
Malonyl Coa ◽  
Flavonoid Biosynthetic Pathway ◽  
Ctab Method ◽  
Preliminary Study ◽  
The Rich ◽  
Flavonoid Biosynthesis Pathway

Chalcone synthase (CHS) (EC 2.3.1.74) catalyzes the first committed step of flavonoid biosynthesis pathway. It combines 4-coumaroyl-CoA with three C2 units from malonyl-CoA to produce naringenin chalcone which transforms to various numbers of flavonoids. In this work, we attempt to isolate the CHS gene from Gendarusa, which could serve as a preliminary study to elucidate the CHS gene regulation in the flavonoid biosynthetic pathway of Malaysian medicinal plants generally, and in Justicia gendarussa Burm. F. species specifically. The total RNA was isolated from the mature leaves of Justicia gendarussa Burm. F. using the modified CTAB method. Extracted RNA, treated with RQ1 RNase-free DNasekit and cDNA synthesis in order to prepare the rich template of DNA for PCR by using M-MLV Reverse Transcriptase kit. High concentration of cDNA and A260/280 ratio reversely transcribed cDNAs guarantee the quality and quantity of synthesized cDNA. The CHS gene was amplified using the Phusion DNA Polymeraseand showed the same size of the previously amplified CHS gene from Melastoma, 1100bp.

Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations

ACS Catalysis ◽  
2014 ◽  
Vol 4 (11) ◽  
pp. 3869-3876 ◽  
Author(s):  
Ana R. Calixto ◽  
Natércia F. Brás ◽  
Pedro A. Fernandes ◽  
Maria J. Ramos
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Human Renin

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

2020 ◽  
Vol 168 (3) ◽  
pp. 223-229
Author(s):  
Yoshinori Shibanuma ◽  
Naoki Nemoto ◽  
Norifumi Yamamoto ◽  
Gen-Ichi Sampei ◽  
Gota Kawai
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Adenylate Kinase ◽  
Reaction Coordinate ◽  
Amino Acid Residues ◽  
Aeropyrum Pernix ◽  
Adenylate Kinases

Abstract The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism

Biochemistry ◽  
2016 ◽  
Vol 55 (40) ◽  
pp. 5764-5771 ◽  
Author(s):  
Yojiro Hamada ◽  
Yusuke Kanematsu ◽  
Masanori Tachikawa
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics

Two Different Chalcone Synthase Activities from Spinach

1985 ◽  
Vol 40 (3-4) ◽  
pp. 160-165 ◽  
Author(s):  
L. Beerhues ◽  
R. Wiermann
Keyword(s):  
Ion Exchange ◽  
Substrate Specificity ◽  
Chalcone Synthase ◽  
Ion Exchange Chromatography ◽  
Exchange Chromatography ◽  
Enzyme Preparations ◽  
Assay Mixture ◽  
Suitable Substrate ◽  
Malonyl Coa ◽  
Young Leaves

Chalcone synthase activity was found in enzyme preparations from spinach. In homogenates of young leaves two different activities of the enzyme could be separated by DEAE-ion exchange chromatography and chromatofocusing. Both activities formed naringenin with [2-14C] malonyl- CoA and 4-coumaroyl-CoA as substrates. They exhibited only slight differences in substrate specificity. For both activities 4-coumaroyl-CoA proved to be the most suitable substrate at both pH 6.8 and 8.0. Eriodictyol and homoeriodictyol formation from caffeoyl-CoA and feruloyl-CoA, respectively, only occured at pH 6.8. The formation of naringenin by the two activities was maximal at pH 7.5-8.0 and dependent upon the DTE-concentration in the assay mixture.

scholarly journals Reaction mechanism of N-cyclopropylglycine oxidation by monomeric sarcosine oxidase

2020 ◽  
Vol 22 (29) ◽  
pp. 16552-16561
Author(s):  
Mitsuo Shoji ◽  
Yukihiro Abe ◽  
Mauro Boero ◽  
Yasuteru Shigeta ◽  
Yoshiaki Nishiya
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Theoretical Level ◽  
Sarcosine Oxidase

Reaction mechanism of monomeric sarcosine oxidase (MSOX) with N-cyclopropylglycine (CPG) is unravelled at the theoretical level of the hybrid quantum mechanics/molecular mechanical (QM/MM) method.

Quantum mechanics and molecular mechanics study of the reaction mechanism of quorum quenching enzyme: N-acyl homoserine lactonase with C6-HSL

RSC Advances ◽  
2016 ◽  
Vol 6 (28) ◽  
pp. 23396-23402 ◽  
Author(s):  
Shujun Zhang ◽  
Hao Su ◽  
Guangcai Ma ◽  
Yongjun Liu
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Lactone Ring ◽  
Quorum Quenching ◽  
Homoserine Lactone ◽  
Ester Bond ◽  
Acyl Homoserine Lactone

N-Acyl-homoserine lactonase fromOchrobactrumsp. strain (AidH) is a novel AHL (N-acyl-homoserine lactone)-lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs.

Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics

2002 ◽  
Vol 106 (46) ◽  
pp. 12059-12065 ◽  
Author(s):  
Yong S. Lee ◽  
Sharon E. Worthington ◽  
Morris Krauss ◽  
Bernard R. Brooks
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Chorismate Mutase
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