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Md. Anayet Hasan,Md. Habibul Hasan Mazumder,Md. Arif Khan,Mohammad Uzzal Hossain,A. S. M. Homaun Kabir Chowdhury 한국유전체학회 2014 Genomics & informatics Vol.12 No.4
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire’s disease. The increasingdevelopment of drug resistance against legionellosis has led to explore new novel drug targets. It has been found thatphosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the mostprobable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugarand nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this,the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means ofhomology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structurevalidation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondarystructural features were determined through self-optimized prediction method with alignment (SOPMA) and interactingnetworks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showedthat 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in thegenerously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 forERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorablebinding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensiveinvestigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
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Hasan, Md. Anayet,Mazumder, Md. Habibul Hasan,Khan, Md. Arif,Hossain, Mohammad Uzzal,Chowdhury, A.S.M. Homaun Kabir Korea Genome Organization 2014 Genomics & informatics Vol.12 No.4
The harshness of legionellosis differs from mild Pontiac fever to potentially fatal Legionnaire's disease. The increasing development of drug resistance against legionellosis has led to explore new novel drug targets. It has been found that phosphoglucosamine mutase, phosphomannomutase, and phosphoglyceromutase enzymes can be used as the most probable therapeutic drug targets through extensive data mining. Phosphoglucosamine mutase is involved in amino sugar and nucleotide sugar metabolism. The purpose of this study was to predict the potential target of that specific drug. For this, the 3D structure of phosphoglucosamine mutase of Legionella pneumophila (strain Paris) was determined by means of homology modeling through Phyre2 and refined by ModRefiner. Then, the designed model was evaluated with a structure validation program, for instance, PROCHECK, ERRAT, Verify3D, and QMEAN, for further structural analysis. Secondary structural features were determined through self-optimized prediction method with alignment (SOPMA) and interacting networks by STRING. Consequently, we performed molecular docking studies. The analytical result of PROCHECK showed that 95.0% of the residues are in the most favored region, 4.50% are in the additional allowed region and 0.50% are in the generously allowed region of the Ramachandran plot. Verify3D graph value indicates a score of 0.71 and 89.791, 1.11 for ERRAT and QMEAN respectively. Arg419, Thr414, Ser412, and Thr9 were found to dock the substrate for the most favorable binding of S-mercaptocysteine. However, these findings from this current study will pave the way for further extensive investigation of this enzyme in wet lab experiments and in that way assist drug design against legionellosis.
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In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139
Islam, Md. Saiful,Shahik, Shah Md.,Sohel, Md.,Patwary, Noman I.A.,Hasan, Md. Anayet Korea Genome Organization 2015 Genomics & informatics Vol.13 No.2
In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.
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In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139
Md. Saiful Islam,Shah Md. Shahik,Md. Sohel,Noman I. A. Patwary,Md. Anayet Hasan 한국유전체학회 2015 Genomics & informatics Vol.13 No.2
In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.
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