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The interaction pattern between a homology model of 40S ribosomal S9 protein of Rhizoctonia solani and 1-hydroxyphenaize by docking study.

Dharni S - Biomed Res Int (2014)

Bottom Line: 1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani.In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein.Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

View Article: PubMed Central - PubMed

Affiliation: Agronomy and Soil Science Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India.

ABSTRACT
1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani. In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein. Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

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Ramachandran map of 40S ribosomal ligand moleS9 protein of Rhizoctonia solani.
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fig6: Ramachandran map of 40S ribosomal ligand moleS9 protein of Rhizoctonia solani.

Mentions: 40S ribosomal S9 protein is an important target responsible for fungal growth [32]. To predict the structure of this protein, homology modeling approach was performed. The query sequence of target protein was found homologous to the known structure of protein of the same family of Thermomyces lanuginosus. After BLAST search the high resolution crystal structure of homologous protein having PDB id 3JYV was considered as template for comparative modeling. The query and template sequences showed 78% identity and 6e − 87 Evalue in sequence alignment and were taken as template for homology modeling (Figure 3). The structure was modeled on automated mode of SWISS-MODEL workspace, http://swissmodel.expasy.org/, with its default parameters. The residues ranging between 6 and 163 participated in homology modeling. The total energy −5238.173 KJ/mol of the model was converted to −7587.487 KJ/mol after minimizing the energy through SWISS PDB Viewer. The final predicted 3D structure of the protein was represented through Pymol viewer, http://www.pymol.org/, (Figure 4). Alpha helices are shown in green color and antiparallel beta sheet in red color in the structure (Figure 5). There are many loop structures that help in connecting the secondary structures together. The model was submitted to the PMDB database and it can be downloaded using id “PM0078917.” The modeled structure of protein was evaluated with ramachandran plot generated by Rampage server, http://mordred.bioc.cam.ac.uk/~rapper/rampage.php, and fulfilled the criterion of proper distribution of residues in different regions (Figure 6) [21]. 82.1% and 11.5% of the residues were present in favored and allowed regions, respectively.


The interaction pattern between a homology model of 40S ribosomal S9 protein of Rhizoctonia solani and 1-hydroxyphenaize by docking study.

Dharni S - Biomed Res Int (2014)

Ramachandran map of 40S ribosomal ligand moleS9 protein of Rhizoctonia solani.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016899&req=5

fig6: Ramachandran map of 40S ribosomal ligand moleS9 protein of Rhizoctonia solani.
Mentions: 40S ribosomal S9 protein is an important target responsible for fungal growth [32]. To predict the structure of this protein, homology modeling approach was performed. The query sequence of target protein was found homologous to the known structure of protein of the same family of Thermomyces lanuginosus. After BLAST search the high resolution crystal structure of homologous protein having PDB id 3JYV was considered as template for comparative modeling. The query and template sequences showed 78% identity and 6e − 87 Evalue in sequence alignment and were taken as template for homology modeling (Figure 3). The structure was modeled on automated mode of SWISS-MODEL workspace, http://swissmodel.expasy.org/, with its default parameters. The residues ranging between 6 and 163 participated in homology modeling. The total energy −5238.173 KJ/mol of the model was converted to −7587.487 KJ/mol after minimizing the energy through SWISS PDB Viewer. The final predicted 3D structure of the protein was represented through Pymol viewer, http://www.pymol.org/, (Figure 4). Alpha helices are shown in green color and antiparallel beta sheet in red color in the structure (Figure 5). There are many loop structures that help in connecting the secondary structures together. The model was submitted to the PMDB database and it can be downloaded using id “PM0078917.” The modeled structure of protein was evaluated with ramachandran plot generated by Rampage server, http://mordred.bioc.cam.ac.uk/~rapper/rampage.php, and fulfilled the criterion of proper distribution of residues in different regions (Figure 6) [21]. 82.1% and 11.5% of the residues were present in favored and allowed regions, respectively.

Bottom Line: 1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani.In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein.Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

View Article: PubMed Central - PubMed

Affiliation: Agronomy and Soil Science Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India.

ABSTRACT
1-Hydroxyphenazine (1-OH-PHZ), a natural product from Pseudomonas aeruginosa strain SD12, was earlier reported to have potent antifungal activity against Rhizoctonia solani. In the present work, the antifungal activity of 1-OH-PHZ on 40S ribosomal S9 protein was validated by molecular docking approach. 1-OH-PHZ showed interaction with two polar contacts with residues, Arg69 and Phe19, which inhibits the synthesis of fungal protein. Our study reveals that 1-OH-PHZ can be a potent inhibitor of 40S ribosomal S9 protein of R. solani that may be a promising approach for the management of fungal diseases.

Show MeSH
Related in: MedlinePlus