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In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers.

Ahad A, Ahmad A, Din SU, Rao AQ, Shahid AA, Husnain T - Front Plant Sci (2015)

Bottom Line: Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols.Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK.It will help in color manipulations in different plant species.

View Article: PubMed Central - PubMed

Affiliation: Center of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.

ABSTRACT
Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII), sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157) was tested. Results showed that proline rich region position 12, 26, and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake. Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

No MeSH data available.


Ramachandran plot analysis of Gossypium hirsutum protein model to visualize dihedral angles; φ against ψ. At the bottom of the image the summary of evaluating residues is presented.
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Figure 6: Ramachandran plot analysis of Gossypium hirsutum protein model to visualize dihedral angles; φ against ψ. At the bottom of the image the summary of evaluating residues is presented.

Mentions: Further refinement was achieved by using the ModRefiner tool. The constructed models were subjected to RAMPAGE to create Ramachandran Plot for model evaluation. Figures 5, 6 showed a Ramachandran plot of the Dihydroflavonol 4-Reductase protein's model. Plot displayed the presence of 343 (97.2%) residues in favored region, 8 (2.3%) residues in allowed region while 2 (0.6%) residues in outlier region in case of Gossypium hirsutum DFR (Figure 6) and 338 (94.2%) residues in favored region 17 (4.7%) residues in allowed region plus 4 (1.1%) residues in outlier region in Iris DFR (Figure 5). These computed results validated the models because for a fine model more than 90% residues should be in both favored and allowed region.


In silico study for diversing the molecular pathway of pigment formation: an alternative to manual coloring in cotton fibers.

Ahad A, Ahmad A, Din SU, Rao AQ, Shahid AA, Husnain T - Front Plant Sci (2015)

Ramachandran plot analysis of Gossypium hirsutum protein model to visualize dihedral angles; φ against ψ. At the bottom of the image the summary of evaluating residues is presented.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4584984&req=5

Figure 6: Ramachandran plot analysis of Gossypium hirsutum protein model to visualize dihedral angles; φ against ψ. At the bottom of the image the summary of evaluating residues is presented.
Mentions: Further refinement was achieved by using the ModRefiner tool. The constructed models were subjected to RAMPAGE to create Ramachandran Plot for model evaluation. Figures 5, 6 showed a Ramachandran plot of the Dihydroflavonol 4-Reductase protein's model. Plot displayed the presence of 343 (97.2%) residues in favored region, 8 (2.3%) residues in allowed region while 2 (0.6%) residues in outlier region in case of Gossypium hirsutum DFR (Figure 6) and 338 (94.2%) residues in favored region 17 (4.7%) residues in allowed region plus 4 (1.1%) residues in outlier region in Iris DFR (Figure 5). These computed results validated the models because for a fine model more than 90% residues should be in both favored and allowed region.

Bottom Line: Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols.Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK.It will help in color manipulations in different plant species.

View Article: PubMed Central - PubMed

Affiliation: Center of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.

ABSTRACT
Diversity of colors in flowers and fruits is largely due to anthocyanin pigments. The flavonoid/anthocyanin pathway has been most extensively studied. Dihydroflavonol 4-reductase (DFR) is a vital enzyme of the flavonoid pathway which displays major impact on the formation of anthocyanins, flavan 3-ols and flavonols. The substrate specificity of the DFR was found to play a crucial role in determination of type of anthocyanidins. Altering the flavonoid/anthocyanin pathway through genetic engineering to develop color of our own choice is an exciting subject of future research. In the present study, comparison among four DFR genes (Gossypium hirsutum, Iris × hollandica, Ang. DFRI and DFRII), sequence alignment for homology as well as protein modeling and docking is demonstrated. Estimation of catalytic sites, prediction of substrate preference and protein docking were the key features of this article. For specific substrate uptake, a proline rich region and positions 12 plus 26 along with other positions emphasizing the 26-amino acid residue region (132-157) was tested. Results showed that proline rich region position 12, 26, and 132-157 plays an important role in selective attachment of DFRs with respective substrates. Further, "Expasy ProtParam tool" results showed that Iris × hollandica DFR amino acids (Asn 9: Asp 23) are favorable for reducing DHQ and DHM thus accumulating delphinidin, while Gossypium hirsutum DFR has (Asn 13: Asp 21) hypothesized to consume DHK. Protein docking data showed that amino acid residues in above mentioned positions were just involved in attachment of DFR with substrate and had no role in specific substrate uptake. Advanced bioinformatics analysis has revealed that all above mentioned positions have role in substrate attachment. For substrate specificity, other residues region is involved. It will help in color manipulations in different plant species.

No MeSH data available.