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Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis.

Malathi J, Umashankar V, Sathyabaarathi R, Muthukumaran S, Ishwarya M, Madhavan HN - Bioinformation (2011)

Bottom Line: The reported variant was found to be resistant to Ganciclovir (GCV) as per the clinical records.Docking simulation studies of the phosphorylated forms of Ganciclovir (GCV), Cidofovir (CDV) and Foscarnet (PFA) with the reported mutants showed significant variation in terms of binding affinity and inhibitory constant (Ki) in comparison to wild type UL54.The findings of this study revealed that the observed coupled mutation could potentially induce allosteric effects in the binding pockets of UL54 and thereby alter the drug binding affinity.

View Article: PubMed Central - PubMed

ABSTRACT
This study reports the probable impact of the coupled mutations observed in our clinical isolate of HCMV UL54 polymerase, through structural bioinformatics approaches. The reported variant was found to be resistant to Ganciclovir (GCV) as per the clinical records. The presence of Glutamine deletion at 639 (Glu639) and a mis sense mutation of Serine 655 Leucine (Ser655Leu) in UL54 were identified by DNA sequencing and were predicted to lie in the DNA polymerase type-II domain. Docking simulation studies of the phosphorylated forms of Ganciclovir (GCV), Cidofovir (CDV) and Foscarnet (PFA) with the reported mutants showed significant variation in terms of binding affinity and inhibitory constant (Ki) in comparison to wild type UL54. The findings of this study revealed that the observed coupled mutation could potentially induce allosteric effects in the binding pockets of UL54 and thereby alter the drug binding affinity. In specific, it was observed that this coupled mutation could confer changes in the binding affinity of GCV and PFA by altering the binding energies and inhibitory constants to -0.88Kcal/mol and 226.71mM, -5.81Kcal/mol and 54.83µM, respectively, in comparison to Wild Type. On the other hand, CDV showed increased susceptibility for the reported mutant with a binding energy of -6.16Kcal/mol and inhibitory constant of 30.47µM.

No MeSH data available.


(a) Superposition of WT (blue) with MT(red) shows backbone RMSD of 0.2Å. (b) Zoom view of Glu639 deletion. (c) Zoom view of Missense Mutation Ser 655 Leu.
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Figure 4: (a) Superposition of WT (blue) with MT(red) shows backbone RMSD of 0.2Å. (b) Zoom view of Glu639 deletion. (c) Zoom view of Missense Mutation Ser 655 Leu.

Mentions: The structure of MT UL54 with the deletion of Gln at 639th position coupled with the missense mutation, Ser to Leu at 655th position, shared 98% of sequence identity with the generated WT model. Hence, the WT model was chosen as a template to model the 3D structure for MT based on homology modeling approach using MODELLER 9v7. The predicted MT structure was further validated by superposing its backbone using PyMOL with that of WT structure and the Root Mean Square Deviation (RMSD) was found to be 0.2 Å, and was suggestive of fold level similarity and structure plausibility. Furthermore, the backbone conformation of the model generated was validated using PROCHECK. The generated model as found to be highly plausible (Figure 4), since none of the residues spanned the disallowed region of Ramachandran plot.


Functional characterization of novel mutations in UL54 of ganciclovir resistant HCMV strain using structural analysis.

Malathi J, Umashankar V, Sathyabaarathi R, Muthukumaran S, Ishwarya M, Madhavan HN - Bioinformation (2011)

(a) Superposition of WT (blue) with MT(red) shows backbone RMSD of 0.2Å. (b) Zoom view of Glu639 deletion. (c) Zoom view of Missense Mutation Ser 655 Leu.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3044428&req=5

Figure 4: (a) Superposition of WT (blue) with MT(red) shows backbone RMSD of 0.2Å. (b) Zoom view of Glu639 deletion. (c) Zoom view of Missense Mutation Ser 655 Leu.
Mentions: The structure of MT UL54 with the deletion of Gln at 639th position coupled with the missense mutation, Ser to Leu at 655th position, shared 98% of sequence identity with the generated WT model. Hence, the WT model was chosen as a template to model the 3D structure for MT based on homology modeling approach using MODELLER 9v7. The predicted MT structure was further validated by superposing its backbone using PyMOL with that of WT structure and the Root Mean Square Deviation (RMSD) was found to be 0.2 Å, and was suggestive of fold level similarity and structure plausibility. Furthermore, the backbone conformation of the model generated was validated using PROCHECK. The generated model as found to be highly plausible (Figure 4), since none of the residues spanned the disallowed region of Ramachandran plot.

Bottom Line: The reported variant was found to be resistant to Ganciclovir (GCV) as per the clinical records.Docking simulation studies of the phosphorylated forms of Ganciclovir (GCV), Cidofovir (CDV) and Foscarnet (PFA) with the reported mutants showed significant variation in terms of binding affinity and inhibitory constant (Ki) in comparison to wild type UL54.The findings of this study revealed that the observed coupled mutation could potentially induce allosteric effects in the binding pockets of UL54 and thereby alter the drug binding affinity.

View Article: PubMed Central - PubMed

ABSTRACT
This study reports the probable impact of the coupled mutations observed in our clinical isolate of HCMV UL54 polymerase, through structural bioinformatics approaches. The reported variant was found to be resistant to Ganciclovir (GCV) as per the clinical records. The presence of Glutamine deletion at 639 (Glu639) and a mis sense mutation of Serine 655 Leucine (Ser655Leu) in UL54 were identified by DNA sequencing and were predicted to lie in the DNA polymerase type-II domain. Docking simulation studies of the phosphorylated forms of Ganciclovir (GCV), Cidofovir (CDV) and Foscarnet (PFA) with the reported mutants showed significant variation in terms of binding affinity and inhibitory constant (Ki) in comparison to wild type UL54. The findings of this study revealed that the observed coupled mutation could potentially induce allosteric effects in the binding pockets of UL54 and thereby alter the drug binding affinity. In specific, it was observed that this coupled mutation could confer changes in the binding affinity of GCV and PFA by altering the binding energies and inhibitory constants to -0.88Kcal/mol and 226.71mM, -5.81Kcal/mol and 54.83µM, respectively, in comparison to Wild Type. On the other hand, CDV showed increased susceptibility for the reported mutant with a binding energy of -6.16Kcal/mol and inhibitory constant of 30.47µM.

No MeSH data available.