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Biochemistry : Purification, Characterization, and Biochemical Properties of α-Amylase from Potato
Goutam Kumar Sarker,Sohel Hasan,Farjana Nikkon,Ashik Mosaddik,Niranjan Kumar Sana,Habibur Rahman,Sang Gyu Park,Dong Sun Lee,So Mi Kim Cho 한국응용생명화학회 2010 Journal of Applied Biological Chemistry (J. Appl. Vol.53 No.1
Purification, Characterization, and Biochemical Properties of α-Amylase from Potato
( Goutam Kumar Sarker ),( Sohel Hasan ),( Farjana Nikkon ),( Ashik Mosaddik ),( Niranjan Kumar Sana ),( Habibur Rahman ),( Sang Gyu Park ),( Dong Sun Lee ),( Somi Kim Cho ) 한국응용생명화학회 2010 Applied Biological Chemistry (Appl Biol Chem) Vol.53 No.1
Purification, characterization and biochemical properties of α-amylase from post harvest Bangladeshi Potato (Solanum tuberosum L.) were investigated. The α-amylase was purified by successive chromatography on DEAE and CM-cellulose columns with a yield of 24.24%. SDS-PAGE showed a molecular weight of 44 kDa for the enzyme that contain 2.8% sugar. The enzyme lost total activity in the presence of the chelating agent EDTA, confirming it was an α-type amylase. The enzyme displayed optimum activity at pH 7.2 and 37˚C, with an apparent Km value of 0.26% using starch as its substrate. The enzyme was strongly inhibited by Cu2+, Fe2+ and Zn2+; moderately by Li+, Hg+ and Cd2+; and slightly by Ag+, K+, Mn2+ and Mg2+. Conversely, Fe3+ and Na+ appreciably enhanced activity, while adding calcium ion nearly doubled enzyme activity. In addition, the activity of α-amylase gradually decreased with increasing concentrations of urea. Thus, potato α-amylase is an attractive target for study to better understand the structure-function relationships of α-amylases.
Purification, Characterization, and Biochemical Properties of $\alpha$-Amylase from Potato
Sarker, Goutam Kumar,Hasan, Sohel,Nikkon, Farjana,Mosaddik, Ashik,Sana, Niranjan Kumar,Rahman, Habibur,Park, Sang-Gyu,Lee, Dong-Sun,Cho, So-Mi Kim The Korean Society for Applied Biological Chemistr 2010 Applied Biological Chemistry (Appl Biol Chem) Vol.53 No.1
Purification, characterization and biochemical properties of $\alpha$-amylase from post harvest Bangladeshi Potato (Solanum tuberosum L.) were investigated. The $\alpha$-amylase was purified by successive chromatography on DEAE and CM-cellulose columns with a yield of 24.24%. SDSPAGE showed a molecular weight of 44 kDa for the enzyme that contain 2.8% sugar. The enzyme lost total activity in the presence of the chelating agent EDTA, confirming it was an $\alpha$-type amylase. The enzyme displayed optimum activity at pH 7.2 and $37^{\circ}C$, with an apparent Km value of 0.26% using starch as its substrate. The enzyme was strongly inhibited by $Cu^{2+},\;Fe^{2+}$ and $Zn^{2+}$; moderately by $Li^+,\;Hg^+$ and $Cd^{2+}$; and slightly by $Ag^+,\;K^+,\;Mn^{2+}$ and $Mg^{2+}$. Conversely, $Fe%{3+}$ and $Na^+$ appreciably enhanced activity, while adding calcium ion nearly doubled enzyme activity. In addition, the activity of $\alpha$-amylase gradually decreased with increasing concentrations of urea. Thus, potato $\alpha$-amylase is an attractive target for study to better understand the structure-function relationships of $\alpha$-amylases.
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.
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.
Abdul Musaweer Habib,Md. Saiful Islam,Md. Sohel,Md. Habibul Hasan Mazumder,Mohd. Omar Faruk Sikder,Shah Md. Shahik 한국유전체학회 2016 Genomics & informatics Vol.14 No.4
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog’s in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
Habib, Abdul Musaweer,Islam, Md. Saiful,Sohel, Md.,Mazumder, Md. Habibul Hasan,Sikder, Mohd. Omar Faruk,Shahik, Shah Md. Korea Genome Organization 2016 Genomics & informatics Vol.14 No.4
The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.
In vitro anti-oxidant activity of the leaves of Dillenia indica
Saha, Moni Rani,Alam, Ashraful,Hasan, Raquibul,Akter, Raushanara,Hossain, Mokarram,Mazumder, Ehsanul Hoque,Rana, Sohel Kyung Hee Oriental Medicine Research Center 2009 Oriental pharmacy and experimental medicine Vol.9 No.4
The methanol extract of Dillenia indica was tested for antioxidant activity as determined by free radical scavenging of DPPH radical scavenging assay, reducing power, total antioxidant capacity measured by phosphomolybdenum method, total phenolic content and total flavonoids content determination assays. The extract showed significant activities in all antioxidant assays compared to the standard antioxidant in a dose dependent manner. In DPPH radical scavenging assay the $IC_{50}$ value of the extract was found to be 100.53${\mu}g/ml$ while ascorbic acid has the $IC_{50}$ value 58.92${\mu}g/ml$. Dillenia indica extract showed strong reducing power and total antioxidant capacity. Moreover, methanol extracts also possess high amount of phenolics and flavovonoids and expressed as gallic acid and rutin equivalent respectively. The remarkable activities exhibited in reactive oxygen species scavenging may attributed to the high amount of hydrophilic phenolics present in Dillenia indica.
In vitro anti-oxidant activity of the leaves of Dillenia indica
Moni Rani Saha,Md Ashraful Alam,SM Raquibul Hasan,Raushanara Akter,Md Mokarram Hossain,Ehsanul Hoque Mazumder,Md Sohel Rana 경희대학교 융합한의과학연구소 2009 Oriental Pharmacy and Experimental Medicine Vol.9 No.4
The methanol extract of Dillenia indica was tested for antioxidant activity as determined by free radical scavenging of DPPH radical scavenging assay, reducing power, total antioxidant capacity measured by phosphomolybdenum method, total phenolic content and total flavonoids content determination assays. The extract showed significant activities in all antioxidant assays compared to the standard antioxidant in a dose dependent manner. In DPPH radical scavenging assay the IC50 value of the extract was found to be 100.53 μg/ml while ascorbic acid has the IC50 value 58.92 μg/ml. Dillenia indica extract showed strong reducing power and total antioxidant capacity. Moreover, methanol extracts also possess high amount of phenolics and flavovonoids and expressed as gallic acid and rutin equivalent respectively. The remarkable activities exhibited in reactive oxygen species scavenging may attributed to the high amount of hydrophilic phenolics present in Dillenia indica. The methanol extract of Dillenia indica was tested for antioxidant activity as determined by free radical scavenging of DPPH radical scavenging assay, reducing power, total antioxidant capacity measured by phosphomolybdenum method, total phenolic content and total flavonoids content determination assays. The extract showed significant activities in all antioxidant assays compared to the standard antioxidant in a dose dependent manner. In DPPH radical scavenging assay the IC50 value of the extract was found to be 100.53 μg/ml while ascorbic acid has the IC50 value 58.92 μg/ml. Dillenia indica extract showed strong reducing power and total antioxidant capacity. Moreover, methanol extracts also possess high amount of phenolics and flavovonoids and expressed as gallic acid and rutin equivalent respectively. The remarkable activities exhibited in reactive oxygen species scavenging may attributed to the high amount of hydrophilic phenolics present in Dillenia indica.