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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

(A) Active site information by CASTp. Green color shows the active site position from 33 to 321 with the beta-sheet in between them. (B) The table shows the area and the volume for different active sites of cysteine protease YopT and the best active site remains in an area of 1677.7 and a volume of 2009.1 amino acid. (C) The 3D structure of best active site.
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f5-dti-8-2014-001: (A) Active site information by CASTp. Green color shows the active site position from 33 to 321 with the beta-sheet in between them. (B) The table shows the area and the volume for different active sites of cysteine protease YopT and the best active site remains in an area of 1677.7 and a volume of 2009.1 amino acid. (C) The 3D structure of best active site.

Mentions: The active site of cysteine protease YopT was predicted using CASTp server. Further, in this study we have also reported the best active site area of the experimental enzyme as well as the number of amino acid involved in it. [Fig. 5] shows the number of pockets, with their area and volume. The best active site is marked with 1677.7 areas and a volume of 2009.1.


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)

(A) Active site information by CASTp. Green color shows the active site position from 33 to 321 with the beta-sheet in between them. (B) The table shows the area and the volume for different active sites of cysteine protease YopT and the best active site remains in an area of 1677.7 and a volume of 2009.1 amino acid. (C) The 3D structure of best active site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5-dti-8-2014-001: (A) Active site information by CASTp. Green color shows the active site position from 33 to 321 with the beta-sheet in between them. (B) The table shows the area and the volume for different active sites of cysteine protease YopT and the best active site remains in an area of 1677.7 and a volume of 2009.1 amino acid. (C) The 3D structure of best active site.
Mentions: The active site of cysteine protease YopT was predicted using CASTp server. Further, in this study we have also reported the best active site area of the experimental enzyme as well as the number of amino acid involved in it. [Fig. 5] shows the number of pockets, with their area and volume. The best active site is marked with 1677.7 areas and a volume of 2009.1.

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