In vitro and in silico studies of chalcone synthase variant 2 in Boesenbergia rotunda and its substrate specificity
In this study, transformation of BrCHS var 2 into B. rotunda cell suspension culture, followed by chalcone synthase enzymatic assay and HPLC analysis was conducted to investigate whether the substrate specificity for BrCHS var 2 is either cinnamoyl-CoA or p-coumaroyl-CoA. The HPLC profile showed an increase in the amount of pinocembrin chalcone when cinnamoyl-CoA and malonyl-CoA were added but not p-coumaroyl-CoA. Molecular docking was performed to explore the binding of cinnamoyl-CoA and p-coumaroyl-CoA to BrCHS var 2 receptor and the docking results showed that cinnamoyl-CoA formed numerous hydrogen bonds
and more negative docked energy than p-coumaroyl-CoA. Cinnamoyl-CoA showed good interactions with Cys 164 to initiate the subsequent formation of pinocembrin chalcone, whereas the hydroxyl group of p-coumaroyl-CoA formed an unfavorable interaction with Gln 161 that caused steric hindrance to subsequent formation of naringenin chalcone. Docked conformation analysis results also showed that malonyl-CoA formed hydrogen bonding with Cys 164, His 303, and Asn 336 residues in BrCHS var 2. The results show that cinnamoyl-CoA is the preferred substrate for BrCHS var 2.
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- Abe T, Morita H, Noma H, Kohno T, Noguchi H, Abe I (2007).
Structure function analysis of benzalacetone synthase from
Rheum palmatum
. Bioorg Med Chem Lett 17: 3161-3166.
- Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B,
Lindahl E (2015). GROMACS: high performance molecular
simulations through multi-level parallelism from laptops to
supercomputers. SoftwareX 1-2: 19-25.
- Awasthi P, Jamwal VL, Kapoor N, Rasool S, Bahler J (2016).
Homology modeling and docking study of chalcone synthase
gene (CfCHS) from
Coleus forskohlii
. Cogent Biology 2:
1175332.
- Carpentier SC, Witters E, Laukens K, Deckers P, Swennen R, Panis B
(2005). Preparation of protein extracts from recalcitrant plant
tissues: an evaluation of different methods for two-dimensional
gel electrophoresis analysis. Proteomics 5: 2497-2507.
- Christensen AB, Gregersen PL, Schröder J, Collinge DB (1998). A
chalcone synthase with an unusual substrate preference is
expressed in barley leaves in response to UV light and pathogen
attack. Plant Mol Biol 37: 849-857.
- de Vries SJ, van Dijk M, Bonvin AM (2010). The HADDOCK web
server for data-driven biomolecular docking. Nat Prot 5: 883-
897.
- Feinbaum RL, Ausubel FM (1988). Transcriptional regulation of the
Arabidopsis thaliana
chalcone synthase gene. Mol Cell Biol 8:
1985-1992.
- Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP (1999). Structure
of chalcone synthase and the molecular basis of plant polyketide
biosynthesis. Nature Struct Biol 6: 775-784.
- Fliegmann J, Schröder G, Schanz S, Britsch L, Schröder J (1992).
Molecular analysis of chalcone and dihydropinosylvin synthase
from Scots pine (
Pinus sylvestris
), and differential regulation of
these and related enzyme activities in stressed plants. Plant Mol
Biol 18: 489-503.
- Goto-Yamamoto N, Wan GH, Masaki K, Kobayashi S (2002).
Structure and transcription of three chalcone synthase genes of
grapevine (
Vitis vinifera
). Plant Sci 162: 867-872.
- Hatayama M, Ono E, Yonekura-Sakakibara K, Tanaka Y, Nishino
T, Nakayama T (2006). Biochemical characterization and
mutational studies of a chalcone synthase from yellow
snapdragon (
Antirrhinum majus
) flowers. Plant Biotechnol 23:
373-378.
- Jez JM, Bowman ME, Noel JP (2002). Expanding the biosynthetic
repertoire of plant type III polyketide synthases by altering
starter molecule specificity. P Natl Acad Sci USA 99: 5319-
5324.
- Jez JM, Noel JP (2000). Mechanism of chalcone synthase. pKa of the
catalytic cysteine and the role of the conserved histidine in a
plant polyketide synthase. J Biol Chem 275: 39640-39646.
- Kiat TS, Pippen R, Yusof R, Ib
rahim H, Khalid N, Rahman NA
(2006). Inhibitory activity of cyclohexenyl chalcone derivatives
and flavonoids of fingerroot,
Boesenbergia rotunda
(L.),
towards dengue-2 virus NS3 protease. Bioorg Med Chem Lett
16: 3337-3340.
- Kirana C, Jones GP, Record IR, McIntosh GH (2007). Anticancer
properties of panduratin A isolated from
Boesenbergia
pandurata
(Zingiberaceae). J Nat Med 61: 131-137.
- Koduri PK, Gordon GS, Barker EI, Colpitts CC, Ashton NW, Suh
DY (2010). Genome-wide analysis of the chalcone synthase
superfamily genes of
Physcomitrella patens
. Plant Mol Biol 72:
247-263.
- Koo HJ, McDowell ET, Ma X, Greer KA, Kapteyn J, Xie Z, Descour A,
Kim H, Yu Y, Kudrna D (2013). Ginger and turmeric expressed
sequence tags identify signature genes for rhizome identity and
development and the biosynthesis of curcuminoids, gingerols
and terpenoids. BMC Plant Biol 13: 27.
- Kreuzaler F, Hahlbrock K (1975). Enzymic synthesis of an aromatic
ring from acetate units. Partial purification and some
properties of flavanone synthase from cell-suspension cultures
of
Petroselinum hortense
. Eur J Biochem 56: 205-213.
- Krieger E, Koraimann G, Vriend G (2002). Increasing the precision
of comparative models with YASARA NOVA—a self-
parameterizing force field. Proteins 47: 393-402.
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993).
PROCHECK: a program to check the stereochemical quality
of protein structures. J Appl Crystallogr 26: 283-291.
- Laskowski RA, Swindells MB (2011). LigPlot+: multiple ligand–
protein interaction diagrams for drug discovery. J Chem Inf
Model 51: 2778-2786.
- Lo C, Coolbaugh RC, Nicholson RL (2002). Molecular
characterization and in silico expression analysis of a chalcone
synthase gene family in
Sorghum bicolor
. Physiol Mol Plant P
61: 179-188.
- Mallika V, Aiswarya G, Gincy PT, Remakanthan A, Soniya EV (2016).
Type III polyketide synthase repertoire in Zingiberaceae:
computational insights into the sequence, structure and
evolution. Dev Genes Evol 226: 269-285.
- Mazumdar AB, Chattopadhyay S (2015). Sequencing, de novo
assembly, functional annotation and analysis of
Phyllanthus
amarus
leaf transcriptome using the illumina platform. Front
Plant Sci 6: 1199.
- Morita H, Takahashi Y, Noguchi H, Abe I (2000). Enzymatic
formation of unnatural aromatic polyketides by chalcone
synthase. Biochem Bioph Res Co 279: 190-195.
- Samappito S, Page J, Schmidt J, De-Eknamkul W, Kutchan TM
(2002). Molecular characterization of root-specific chalcone
synthases from
Cassia alata
. Planta 216: 64-71.
- Shen YF, Chen GH, Lin SH, Lin G (2016). Molecular modeling
and docking calculations of 4-acyloxy-biphenyl-4
′
-
N-butylcarbamates as potential inhibitors of human
butyrylcholinesterase. Can J Chem 94: 72-77.
- Schüz R, Heller W, Hahlbrock K (1983). Substrate specificity of
chalcone synthase from
Petroselinum hortense
: formation of
phloroglucinol derivatives from aliphatic substrates. J Biol
Chem 258: 6730-6734.
- Sohn JH, Han KL, Lee SH, Hwang JK (2005). Protective
effects of panduratin A against oxidative damage of tert-
butylhydroperoxide in human HepG2 Cells. Biol Pharm Bull
28: 1083-1086.
- Sun W, Meng X, Liang L, Jiang W, Huang Y, He J, Hu H, Almqvist J,
Gao X, Wang L (2015). Molecular and biochemical analysis of
chalcone synthase from
Freesia hybrid
in flavonoid biosynthetic
pathway. PLoS One 10: e0119054.
- Tsou LK, Chen CH, Dutschman GE, Cheng YC, Hamilton AD
(2012). Blocking HIV-1 entry by a gp120 surface binding
inhibitor. Bioorg Med Chem Lett 22: 3358-3361.
- Tuteja JH, Clough SJ, Chan WC, Vodkin LO (2004). Tissue-specific
gene silencing mediated by a naturally occurring chalcone
synthase gene cluster in
Glycine max
. Plant Cell 16: 819-835.
- Voravuthikunchai SP, Limsuwan S, Supapol O, Subhadhirasakul
S (2006). Antibacterial activity of extracts from family
zingiberaceae against foodborne pathogens. J Food Safety 26:
325-334.
- Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G,
de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A,
Ferella L et al. (2012). WeNMR: structural biology on the grid.
J Grid Comput 10: 743-767.
- Yamazaki Y, Suh DY, Sitthithaworn W, Ishiguro K, Kobayashi Y,
Shibuya M, Ebizuka
Y, Sankawa U (2001). Diverse chalcone synthase superfamily
enzymes from the most primitive vascular plant,
Psilotum
nudum
. Planta 214: 75-84
- Yu B, Zhai H, Wang Y, Zang N, He S, Liu Q (2007). Efficient
Agrobacterium tumefaciens
-mediated transformation using
embryogenic suspension cultures in sweetpotato,
Ipomoea
batatas
(L.) Lam. Plant Cell Tiss Org 90: 265-273.