Molecular Dynamic and Docking Interaction Study of Heterodera glycines Serine Proteinase with Vigna mungo Proteinase Inhibitor

Prasad, C. V. S. Siva; Gupta, Saurabh; Gaponenko, A. K.; Tiwari, Murlidhar

doi:10.1007/s12010-013-0342-8

Cited by 11 publications

(5 citation statements)

References 47 publications

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“…This docking interaction analysis also confirmed the substrate binding groove of cHSP70. Such substrate binding groove in HSP70 and other proteins were reported earlier in other species [ 53 , 54 ]. Moreover, to confirm the presence of the above said active sites in other animal HSP70 protein expressed by HSPA1A gene, we performed MSA of 17 selected sequences ( S4 Fig ).…”

Section: Resultssupporting

confidence: 79%

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

et al. 2015

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Heat shock protein 70 (HSP70) is an important chaperone, involved in protein folding, refolding, translocation and complex remodeling reactions under normal as well as stress conditions. However, expression of HSPA1A gene in heat and cold stress conditions associates with other chaperons and perform its function. Experimental structure for Camel HSP70 protein (cHSP70) has not been reported so far. Hence, we constructed 3D models of cHSP70 through multi- template comparative modeling with HSP110 protein of S. cerevisiae (open state) and with HSP70 protein of E. coli 70kDa DnaK (close state) and relaxed them for 100 nanoseconds (ns) using all-atom Molecular Dynamics (MD) Simulation. Two stable conformations of cHSP70 with Substrate Binding Domain (SBD) in open and close states were obtained. The collective mode analysis of different transitions of open state to close state and vice versa was examined via Principal Component Analysis (PCA) and Minimum Distance Matrix (MDM). The results provide mechanistic representation of the communication between Nucleotide Binding Domain (NBD) and SBD to identify the role of sub domains in conformational change mechanism, which leads the chaperone cycle of cHSP70. Further, residues present in the chaperon functioning site were also identified through protein-peptide docking. This study provides an overall insight into the inter domain communication mechanism and identification of the chaperon binding cavity, which explains the underlying mechanism involved during heat and cold stress conditions in camel.

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Section: Resultssupporting

confidence: 79%

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

et al. 2015

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“…Evaluation with VERIFY 3D indicated a reasonably good sequence-to-structure agreement as in crystal structure (Prasad, Gupta, Gaponenko, & Dhar, 2012). Similar validation study was also observed by Prasad et al, (Prasad, Gupta, Gaponenko & Tiwari, 2013). Moreover, a detailed secondary structural investigation of PfPP5 shows that structure folds into 13 Alfa-helices, 3 sheets, 14…”

Section: Generation Of Pfpp5 Modelsupporting

confidence: 82%

Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 ofPlasmodium falciparum: a docking and simulation study

Gupta

Jadaun

Kumar

et al. 2015

Journal of Biomolecular Structure and Dynamics

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Protein phosphorylation is an important mechanism that implicates in physiology of any organism including parasitic protozoa. Metallic protein Ser/Thr protein phosphatase 5 (PP5) controls various cellular signaling pathways of Plasmodium falciparum. The structure and inhibitory mechanism of PP5 in P. falciparum is not known. In fact, no experimental structural data are available for P. falciparum Ser/Thr protein phosphatase 5 (PfPP5) till date. Hence, we have proposed computer-generated model of catalytic subunit of PfPP5 and its inhibitory mechanism was analyzed. A set of 42 known natural inhibitors of protein phosphate family were docked against metal-binding catalytic site of PfPP5 and we found that cantharidin and its derivatives shows better binding energy among them. Similarity search was performed by taking these compounds as lead compounds against PubChem and ChemBank. The search result provides 3703 similar compounds; out of which 2245 qualified the Lipinski rule of five. Further, virtual screening of these compounds was performed and selected top 25 were selected on the basis of binding energy. In continuation, rigid and flexible docking of these screened compounds was performed to get the insight of interactions. Finally, top 5 compounds were verified for ADMET properties, and then, all are subjected to MD simulations for 25 ns in order to validate their stability. Compounds CBI: 3554182, CID: 23561913, and CID: 21168680 showed most stable binding, although some of hydrogen bonds pairing varied throughout simulation. These finding would be helpful to the medicinal chemists for the development of antimalarial drugs to combat this deadly disease.

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“…Moreover, PA works as a metabolite and play protective as other defensive roles in response to stress (Liu et al, 2015). Three transcripts encode nonspecific serine/threonine protein kinase enzyme (EC 2.7.11.1) which belongs to the family of transferases (Prasad et al, 2013; Gupta et al, 2015b). Generally, these enzymes are involved in plant response to abiotic stresses and abscisic acid (ABA)-dependent plant development through phosphorylation process (Kulik et al, 2011).…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

et al. 2017

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Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.

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Molecular Dynamic and Docking Interaction Study of Heterodera glycines Serine Proteinase with Vigna mungo Proteinase Inhibitor

Cited by 11 publications

References 47 publications

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study

Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 ofPlasmodium falciparum: a docking and simulation study

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

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