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In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification.

Hasan MA, Alauddin SM, Al Amin M, Nur SM, Mannan A - Drug Target Insights (2014)

Bottom Line: Interacting partners and active sites were also determined.The verify 3D value of 0.78 indicates that the environmental profile of the model is good.SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh.

ABSTRACT
Plague is a major health concern and Yersinia pestis plays the central causal role in this disease. Yersinia pestis has developed resistance against the commonly available drugs. So, it is now a key concern to find a new drug target. Cysteine protease YopT enzyme is an important factor used by Yersinia pestis for pathogenesis in its host and it has the anti-phagocytic function of removal of C-termini lipid modification. The 3D structure of cysteine protease YopT of Yersinia pestis was determined by means of homology modeling through multiple alignments followed by intensive optimization and validation. The modeling was done by Phyre 2 and refined by ModRefiner. The obtained model was verified with structure validation programs such as PROCHECK, verify 3D and ERRAT for reliability. Interacting partners and active sites were also determined. PROCHECK analysis showed that 93% of the residues are in the most favored region, 5.9% are in the additional allowed region and 1.1% are in the generously allowed region of the Ramachandran plot. The verify 3D value of 0.78 indicates that the environmental profile of the model is good. SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT. Active site determination through CASTp proposes that this protein can be utilized as a potential drug target. However, these findings should further be confirmed by wet lab studies for a targeted therapeutic agent design against Yersinia pestis.

No MeSH data available.


Related in: MedlinePlus

Final model of cysteine protease YopT from Yersinia pestis.
© Copyright Policy - open-access
Related In: Results  -  Collection


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f4-dti-8-2014-001: Final model of cysteine protease YopT from Yersinia pestis.

Mentions: For validation of the predicted structure. Ramachandran plot analysis was done by PROCHECK server. The results of this analysis are depicted in Figure 3 and Table 3. The selected model was then verified by using ERRAT, Verify 3D, and 3D match from Softberry. Validated 3D structure of cysteine protease YopT was determined by SWISS-PDB (see Fig. 4).


In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification.

Hasan MA, Alauddin SM, Al Amin M, Nur SM, Mannan A - Drug Target Insights (2014)

Final model of cysteine protease YopT from Yersinia pestis.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3921076&req=5

f4-dti-8-2014-001: Final model of cysteine protease YopT from Yersinia pestis.
Mentions: For validation of the predicted structure. Ramachandran plot analysis was done by PROCHECK server. The results of this analysis are depicted in Figure 3 and Table 3. The selected model was then verified by using ERRAT, Verify 3D, and 3D match from Softberry. Validated 3D structure of cysteine protease YopT was determined by SWISS-PDB (see Fig. 4).

Bottom Line: Interacting partners and active sites were also determined.The verify 3D value of 0.78 indicates that the environmental profile of the model is good.SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh.

ABSTRACT
Plague is a major health concern and Yersinia pestis plays the central causal role in this disease. Yersinia pestis has developed resistance against the commonly available drugs. So, it is now a key concern to find a new drug target. Cysteine protease YopT enzyme is an important factor used by Yersinia pestis for pathogenesis in its host and it has the anti-phagocytic function of removal of C-termini lipid modification. The 3D structure of cysteine protease YopT of Yersinia pestis was determined by means of homology modeling through multiple alignments followed by intensive optimization and validation. The modeling was done by Phyre 2 and refined by ModRefiner. The obtained model was verified with structure validation programs such as PROCHECK, verify 3D and ERRAT for reliability. Interacting partners and active sites were also determined. PROCHECK analysis showed that 93% of the residues are in the most favored region, 5.9% are in the additional allowed region and 1.1% are in the generously allowed region of the Ramachandran plot. The verify 3D value of 0.78 indicates that the environmental profile of the model is good. SOPMA is employed for calculation of the secondary structural features of cysteine protease YopT. Active site determination through CASTp proposes that this protein can be utilized as a potential drug target. However, these findings should further be confirmed by wet lab studies for a targeted therapeutic agent design against Yersinia pestis.

No MeSH data available.


Related in: MedlinePlus