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Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4.

Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S - Bioinformation (2013)

Bottom Line: The best conformation for each domain was selected using standard procedure.Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding.Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan.

ABSTRACT
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

No MeSH data available.


: Domain wise docking analyses of the CBP50: The CBP50 domains are represented in green color while substrate is represented in sticks model. On the basis of lowest RMSD and minimum energy, the best docking was selected for each domain: A) N-terminal domain-substrate interaction, four amino acid residues of N-terminal domain, Glu-71, Ser-74, Glu-76 and Gln-90 have shown interaction with the substrate; B) The amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 from the Fn-III like domain have shown interaction with chitin hexamer; C) The residues Glu-15, Ala-17, Ser-18 and Leu-35 have shown H-bonding with the substrate.
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Figure 3: : Domain wise docking analyses of the CBP50: The CBP50 domains are represented in green color while substrate is represented in sticks model. On the basis of lowest RMSD and minimum energy, the best docking was selected for each domain: A) N-terminal domain-substrate interaction, four amino acid residues of N-terminal domain, Glu-71, Ser-74, Glu-76 and Gln-90 have shown interaction with the substrate; B) The amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 from the Fn-III like domain have shown interaction with chitin hexamer; C) The residues Glu-15, Ala-17, Ser-18 and Leu-35 have shown H-bonding with the substrate.

Mentions: For the verification of the best selected model of each domain and of whole CBP50, the model and the template were superimposed on the selected templates (Figure 2). Superimposition was done by CHIMERA's structure comparison command; the RMSD value validates the model for each domain. The RMSD between 165 atom pairs of superposed N-Terminal domain was 0.274 Å. While the structure alignment had 167 equivalent positions with an RMSD of 0.32, without twist according to FATCAT server. Both the Fn-III domains were superimposed with their template 1K85. For this superimposition, RMSD was 0.257 Å between 85 atom pairs, whereas according to FATCAT the structure alignment had 85 equivalent positions with an RMSD of 0.26, without twists. For second Fn-III like domain, the RMSD was 0.441 Å between 62 atom pairs and FATCAT server shown structure alignment of 72 equivalent positions with an RMSD of 0.58, without twists. The C-Terminal domain was superimposed with its template 1ED7 and showed RMSD 0.705 Å between 33 atom pairs whereas the structure alignment had 43 equivalent positions with an RMSD of 1.08, without twists shown (Figure 3).


Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4.

Sehar U, Mehmood MA, Hussain K, Nawaz S, Nadeem S, Siddique MH, Nadeem H, Gull M, Ahmad N, Sohail I, Gill SS, Majeed S - Bioinformation (2013)

: Domain wise docking analyses of the CBP50: The CBP50 domains are represented in green color while substrate is represented in sticks model. On the basis of lowest RMSD and minimum energy, the best docking was selected for each domain: A) N-terminal domain-substrate interaction, four amino acid residues of N-terminal domain, Glu-71, Ser-74, Glu-76 and Gln-90 have shown interaction with the substrate; B) The amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 from the Fn-III like domain have shown interaction with chitin hexamer; C) The residues Glu-15, Ala-17, Ser-18 and Leu-35 have shown H-bonding with the substrate.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3842575&req=5

Figure 3: : Domain wise docking analyses of the CBP50: The CBP50 domains are represented in green color while substrate is represented in sticks model. On the basis of lowest RMSD and minimum energy, the best docking was selected for each domain: A) N-terminal domain-substrate interaction, four amino acid residues of N-terminal domain, Glu-71, Ser-74, Glu-76 and Gln-90 have shown interaction with the substrate; B) The amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 from the Fn-III like domain have shown interaction with chitin hexamer; C) The residues Glu-15, Ala-17, Ser-18 and Leu-35 have shown H-bonding with the substrate.
Mentions: For the verification of the best selected model of each domain and of whole CBP50, the model and the template were superimposed on the selected templates (Figure 2). Superimposition was done by CHIMERA's structure comparison command; the RMSD value validates the model for each domain. The RMSD between 165 atom pairs of superposed N-Terminal domain was 0.274 Å. While the structure alignment had 167 equivalent positions with an RMSD of 0.32, without twist according to FATCAT server. Both the Fn-III domains were superimposed with their template 1K85. For this superimposition, RMSD was 0.257 Å between 85 atom pairs, whereas according to FATCAT the structure alignment had 85 equivalent positions with an RMSD of 0.26, without twists. For second Fn-III like domain, the RMSD was 0.441 Å between 62 atom pairs and FATCAT server shown structure alignment of 72 equivalent positions with an RMSD of 0.58, without twists. The C-Terminal domain was superimposed with its template 1ED7 and showed RMSD 0.705 Å between 33 atom pairs whereas the structure alignment had 43 equivalent positions with an RMSD of 1.08, without twists shown (Figure 3).

Bottom Line: The best conformation for each domain was selected using standard procedure.Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding.Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioinformatics and Biotechnology, Faculty of Science & Technology, Government College University Faisalabad, Faisalabad, Pakistan.

ABSTRACT
This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

No MeSH data available.