Molecular Docking of Bacillus pumilus Xylanase and Xylan Substrate Using Computer Modeling

Lin, Jinxia; Zhang, Liaoyuan; Zhang, Guangya; Fang, Baishan

doi:10.1016/s1872-2075(07)60047-8

Cited by 4 publications

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References 6 publications

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“…Three-dimensional (3D) protein structure of GH-11 xylanase from Bacillus firmus K-1 were docked with various oligos such as xylobiose, xylotriose, xylotetrose, xylopentose, xylohexose xyloheptaose by the Jommuengbout et al [10] and free energy binding reveals that xylobiose and xylotiose acted as the end product inhibitors. The xylanase from Bacillus pumilus has been sequenced and tertiary structure of protein has been docked to observe catalytic interactions by Lin et al [11]. The information collected from molecular docking were analyzed and found involvement of various amino acid residues towards its vital role in catalytic reaction which instructs to incorporate a further modification in xylanase for site directed evolution of xylanase [11].…”

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confidence: 99%

“…The xylanase from Bacillus pumilus has been sequenced and tertiary structure of protein has been docked to observe catalytic interactions by Lin et al [11]. The information collected from molecular docking were analyzed and found involvement of various amino acid residues towards its vital role in catalytic reaction which instructs to incorporate a further modification in xylanase for site directed evolution of xylanase [11].…”

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confidence: 99%

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Thermostability and Substrate Specificity of GH-11 Xylanase from Thermomyces lanuginosus VAPS24

2018

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The three dimensional structure (3D structure) of GH-11 xylanase from was obtained through homology modeling. To study the enzyme interaction with an end product of enzyme catalysis, the xylanase two sugar molecules xylose and xylobiose has been docked into the active site of GH-11 xylanase through molecular docking. Based on the free binding energy and Inhibition constant, concluded xylose makes more stable complex than xylobiose. Further, the molecular dynamic simulation studies were carried out at different temperature, i.e. 323, 333, 343 and 353 K (i.e. 50, 60, 70 and 80 °C). It has been observed that there was minor structural modification in 3D-structure of xylanase at 323, 333, and 343 K. But the helix and sheets moved out of the initial structure when simulation carried out at during 353 K (80 °C).

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confidence: 99%

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confidence: 99%