Homology modeling, molecular docking and molecular dynamics studies of the catalytic domain of chitin deacetylase from Cryptococcus laurentii strain RY1

Sarkar, Soumyadev; Gupta, Sayan; Chakraborty, Writachit; Senapati, Sanjib; Gachhui, Ratan

doi:10.1016/j.ijbiomac.2017.03.057

Cited by 24 publications

(10 citation statements)

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“…(Siqueira et al, 2016), Musa paradisiaca (Hemmati, 2016). Recently, similar kind of studies is also reported in A. paniculata (Alexander et al, 2015) and Cryptococcus laurentii strain RY1 (Sarkar et al, 2017). …”

Section: Prediction Of Secondary Tertiary (3d) Structure and Validationsupporting

confidence: 74%

Comparative protein profile studies and in silicostructural/functional analysis of HMGR (ApHMGR)in Andrographispaniculata (Burm.f.) Wall. ex Nees

Bindu¹,

Srinath²,

Shailaja³

et al. 2017

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Andrographis paniculata (Burm.f.) Wall. ex Nees (Ap) contains andrographolide, i.e., synthesized via cytosolic MVA and plastidial MEP pathways using IPP and DMAPP as precursor molecules. HMGR catalyzes the first committed and rate-limiting step in MVA pathway. Limited information is available on structural and functional aspects of key enzyme HMGR. In a preliminary study, the in vivo leaves and light/dark grown callus was used for protein profile analysis. The callus growth and andrographolide content through HPLC analysis was carried out. SDS-PAGE total protein profile of in vivo leaves, light, and dark grown callus was investigated. A high intensity band of 62.3 KD protein indicating its proximity with HMGR enzyme was observed in leaves and light callus compared to dark grown callus. On this background, the present communication reports bioinformatics analysis of HMGR enzyme to decipher its functional and structural properties. The isoelectric point (pI), molecular weight and hydrophobicity were calculated using Expasy tools. The secondary (2D) and tertiary (3D) structures were predicted and validated using PROCHECK SAVES algorithm. Our finding on the allowed percentage (88.2%) of amino acid residues in the Ramachandran plot indicated that the simulated 3D structure was reliable. Phylogenetic analysis of A. paniculata HMGR (ApHMGR) with different plants and other organisms including humans revealed close relationships and common lineage. The protein-protein interaction studies using STRING 10 tool revealed a close association of HMGR and nine other proteins in MVA and MEP pathways. The present analyzed data will give an insight on the structural and function attributes corresponding to this important HMGR protein. The molecular and biochemical understanding of HMGR protein will be advantageous for andrographolide yield enhancement through metabolic engineering.

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Section: Prediction Of Secondary Tertiary (3d) Structure and Validationsupporting

confidence: 74%

Comparative protein profile studies and in silicostructural/functional analysis of HMGR (ApHMGR)in Andrographispaniculata (Burm.f.) Wall. ex Nees

Bindu¹,

Srinath²,

Shailaja³

et al. 2017

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“…The quality of the models was evaluated with QMean, ProQ, and RAMPAGE ( Table 1 , Figures S1–S26 ), and LGscore and MaxSub values implied that the obtained models were good [ 32 ]. The QMean Z -score uses structures that are solved by X-ray crystallography as a reference to estimate the absolute quality of a model [ 33 ]. For the models in this study, the QMean Z -score was in the range of −10.99 to −4.70, showing that these models varied in quality; conversely, however, the results obtained with RAMPAGE and ProQ suggested that the models had the appropriate quality [ 34 , 35 , 36 ].…”

Section: Discussionmentioning

confidence: 99%

“…Three-dimensional structures of carboxylic ester hydrolase, carboxylic ester hydrolase 2, gamma-aminobutyric acid (GABA)-RDL, GABA-GRD, GABA-gated ion channel LCCH3, glutamate-gated chloride channel, histamine-gated chloride channel 1, histamine-gated chloride channel 2, hormone receptor in 39-like, nicotinic acetylcholine receptor subunit alpha1, nicotinic acetylcholine receptor subunit alpha2, pH sensitive chloride channel, and putative octopamine/tyramine receptor proteins were constructed by homology modeling using (PS)2-v2: Protein Structure Prediction Server [ 49 , 50 ], Phyre2 [ 51 ], and I-Tasser [ 52 ]. The best model generated by each prediction server was selected to validate the model quality [ 33 ]. The quality of the models was evaluated using the RAMPAGE [ 53 ], ProQ (Protein Quality Predictor), and QMEAN [ 31 , 54 ].…”

Section: Methodsmentioning

confidence: 99%

“…The quality of the models was evaluated using the RAMPAGE [ 53 ], ProQ (Protein Quality Predictor), and QMEAN [ 31 , 54 ]. The best structure of each protein obtained after the validation procedure was subjected to structural analysis using the molecular graphics system PyMOL [ 33 ] and saved in the Protein Model DataBase (PMDB) [ 32 ]. PM0081096, PM0081123, PM0081100, PM0081098, PM0081126, PM0081097, PM0081124, PM0081099, PM0081101, PM0081125, PM0081129, PM0081127, and PM0081128 were assigned as the identifiers for the structures carboxylic ester hydrolase, carboxylic ester hydrolase2, GABA-RDL, GABA-GRD, GABA-gated ion channel LCCH3, glutamate-gated chloride channel, histamine-gated chloride channel 1, histamine-gated chloride channel 2, hormone receptor in 39-like, nicotinic acetylcholine receptor subunit alpha1, nicotinic acetylcholine receptor subunit alpha2, pH sensitive chloride channel, and putative octopamine/tyramine receptor, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Neurotoxic Effects of Linalool and β-Pinene on Tribolium castaneum Herbst

2017

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Effective, ethical pest control requires the use of chemicals that are highly specific, safe, and ecofriendly. Linalool and β-pinene occur naturally as major constituents of the essential oils of many plant species distributed throughout the world, and thus meet these requirements. These monoterpenes were tested as repellents against Tribolium castaneum, using the area preference method, after four hours of exposure and the effect transcriptional of genes associated with neurotransmission. Changes in gene expression of acetylcholinesterase (Ace1), GABA-gated anion channel splice variant 3a6a (Rdl), GABA-gated ion channel (Grd), glutamate-gated chloride channel (Glucl), and histamine-gated chloride channel 2 (Hiscl2) were assessed and the interaction with proteins important for the insect using in silico methods was also studied. For linalool and β-pinene, the repellent concentration 50 (RC50) values were 0.11 µL/cm2 and 0.03 µL/cm2, respectively. Both compounds induced overexpression of Hiscl2 gen in adult insects, and β-pinene also promoted the overexpression of Grd and the Ace1 gene. However, β-pinene and linalool had little potential to dock on computer-generated models for GABA-gated ion channel LCCH3, nicotinic acetylcholine receptor subunits alpha1 and alpha2, and putative octopamine/tyramine receptor proteins from T. castaneum as their respective binding affinities were marginal, and therefore the repellent action probably involved mechanisms other than direct interaction with these targets. Results indicated that β-pinene was more potent than linalool in inducing insect repellency, and also had a greater capacity to generate changes in the expression of genes involved in neuronal transmission.

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“…Evolutionary history was inferred using the maximum likelihood method based on a JTT matrix-based model 52 . The amino acid sequences used in this tree were reported in [37][38][39][40][41][42][43][44][45][46][47] . Clustal-X2 (Version 1.83) was used for multiple-sequence alignment.…”

Section: Methodsmentioning

confidence: 99%

Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase

Ma¹,

Gao

Bi³

et al. 2020

Sci Rep

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chitin deacetylase (cDA) can hydrolyse the acetamido group of chitin polymers to produce chitosans, which are used in various fields including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment. cDA represents a more environmentally-friendly and easier to control alternative to the chemical methods currently utilised to produce chitosans from chitin; however, the majority of identified CDAs display activity toward low-molecular-weight oligomers and are essentially inactive toward polymeric chitin or chitosans. therefore, it is important to identify novel cDAs with activity toward polymeric chitin and chitosans. in this study, we isolated the bacterium Rhodococcus equi F6 from a soil sample and showed that it expresses a novel CDA (ReCDA), whose activity toward 4-nitroacetanilide reached 19.20 U/mL/h during fermentation and was able to deacetylate polymeric chitin, colloidal chitin, glycol-chitin, and chitosan. Whole genome sequencing revealed that RecDA is unique to the R. equi F6 genome, while phylogenetic analysis indicated that RecDA is evolutionarily distant from other cDAs. in conclusion, RecDA isolated from the R. equi F6 strain expands the known repertoire of CDAs and could be used to deacetylate polymeric chitosans and chitin in industrial applications.Chitin is the second most abundant biopolymer after cellulose and is mainly obtained as a waste product of the seafood industry at a relatively low cost 1 . The chitin derivative, chitosan, is a linear polysaccharide comprised of β-(1→4)-linked glucosamine and N-acetyl glucosamine units which are randomly arranged within the chitosan polysaccharide chain 2 . Due to its ability to dissolve in dilute acids, chitosan is more useful than its crystalline precursor chitin in various industrial applications 3 , including the biomedical and pharmaceutical industries, food production, agriculture, and water treatment 4 .Chitosan occurs naturally and is mainly found in the cell walls of certain fungi, the exoskeletons of certain insects (such as the abdominal wall of termite queens), and in some yeasts 5,6 . Although chitosan can be extracted from fungal sources 7 , the method is commercially inapplicable as it provides too low a yield at too high a cost. Therefore, chitosan is still obtained by treating marine-derived chitin with thermo-alkaline 8 , a method that is inexpensive and results in high yields but is environmentally unsafe and difficult to control, producing a heterogeneous range of products depending on the degree of deacetylation 9 . The enzymatic production of chitosan using microbial chitin deacetylase (CDA; EC 3.5.1.41), which can hydrolyse the acetamido group in chitin polymers to produce chitosans 10 , is an environmentally-friendly process that is easy to control and results in a high yield of homogeneous end products 11 .CDAs have been identified in marine and soil bacteria, several fungi, a few insects, and at least one virus 12,13 . Fungal CDAs exist mostly as N-glycosylated (20-70%) glycoproteins, w...

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Homology modeling, molecular docking and molecular dynamics studies of the catalytic domain of chitin deacetylase from Cryptococcus laurentii strain RY1

Cited by 24 publications

References 61 publications

Comparative protein profile studies and in silicostructural/functional analysis of HMGR (ApHMGR)in Andrographispaniculata (Burm.f.) Wall. ex Nees

Comparative protein profile studies and in silicostructural/functional analysis of HMGR (ApHMGR)in Andrographispaniculata (Burm.f.) Wall. ex Nees

Neurotoxic Effects of Linalool and β-Pinene on Tribolium castaneum Herbst

Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase

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