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Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction

Received: 14 April 2016     Accepted: 25 April 2016     Published: 10 May 2016
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Abstract

Allitol is an alcohol monosaccharide, is a reduction of D-psicose. It is functions as a cross linking of D- and L-hexoses. It existed in too small quantities in commercial sugars and is difficult to synthesize by using chemical methods. It has a hypoglycemic function, and can use as Laxative in treating of constipation, which can exploit in production of diabetes drugs. The present report investigates about the production of allitol by ribitol dehydrogenase (RDH), its action of the enzyme through homology and molecular docking studies. We have investigated ribitol dehydrogenase (RDH) from providencia alcalifaciens RIMD 1656011. The protein sequence of RDH was conducted for homology modeling through Swiss model. 3D structure revealed was docked with NAD+ and D-psicose using AutoDock Vina software version 5.6. The results of homology modeling and docking studies revealed that the conserved residues of RDH were Tyr 153, Tyr 92, Ser 17 and Lys157 with NAD+, while conserved residues with D-psicose were GLN67 and ASP61. NAD+ has good interaction with RDH showing grid score of -49.84, which is a good score for binding.

Published in American Journal of Bioscience and Bioengineering (Volume 4, Issue 3)
DOI 10.11648/j.bio.20160403.11
Page(s) 34-40
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2016. Published by Science Publishing Group

Keywords

Homology Modeling, Docking, AutoDock Vina, Ribitol Dehydrogenase

References
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  • APA Style

    Hinawi A. M. Hassanin, Wanmeng Mu, Marwa Y. F. Koko, Tao Zhang, Ammar Alfarga, et al. (2016). Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction. American Journal of Bioscience and Bioengineering, 4(3), 34-40. https://doi.org/10.11648/j.bio.20160403.11

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    ACS Style

    Hinawi A. M. Hassanin; Wanmeng Mu; Marwa Y. F. Koko; Tao Zhang; Ammar Alfarga, et al. Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction. Am. J. BioSci. Bioeng. 2016, 4(3), 34-40. doi: 10.11648/j.bio.20160403.11

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    AMA Style

    Hinawi A. M. Hassanin, Wanmeng Mu, Marwa Y. F. Koko, Tao Zhang, Ammar Alfarga, et al. Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction. Am J BioSci Bioeng. 2016;4(3):34-40. doi: 10.11648/j.bio.20160403.11

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  • @article{10.11648/j.bio.20160403.11,
      author = {Hinawi A. M. Hassanin and Wanmeng Mu and Marwa Y. F. Koko and Tao Zhang and Ammar Alfarga and Mandour H. Abdelhai and Bo Jiang},
      title = {Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction},
      journal = {American Journal of Bioscience and Bioengineering},
      volume = {4},
      number = {3},
      pages = {34-40},
      doi = {10.11648/j.bio.20160403.11},
      url = {https://doi.org/10.11648/j.bio.20160403.11},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.bio.20160403.11},
      abstract = {Allitol is an alcohol monosaccharide, is a reduction of D-psicose. It is functions as a cross linking of D- and L-hexoses. It existed in too small quantities in commercial sugars and is difficult to synthesize by using chemical methods. It has a hypoglycemic function, and can use as Laxative in treating of constipation, which can exploit in production of diabetes drugs. The present report investigates about the production of allitol by ribitol dehydrogenase (RDH), its action of the enzyme through homology and molecular docking studies. We have investigated ribitol dehydrogenase (RDH) from providencia alcalifaciens RIMD 1656011. The protein sequence of RDH was conducted for homology modeling through Swiss model. 3D structure revealed was docked with NAD+ and D-psicose using AutoDock Vina software version 5.6. The results of homology modeling and docking studies revealed that the conserved residues of RDH were Tyr 153, Tyr 92, Ser 17 and Lys157 with NAD+, while conserved residues with D-psicose were GLN67 and ASP61. NAD+ has good interaction with RDH showing grid score of -49.84, which is a good score for binding.},
     year = {2016}
    }
    

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  • TY  - JOUR
    T1  - Molecular Modeling and Docking of Ribitol Dehydrogenase Exploring Enzyme NAD+ and D-psicose Interaction
    AU  - Hinawi A. M. Hassanin
    AU  - Wanmeng Mu
    AU  - Marwa Y. F. Koko
    AU  - Tao Zhang
    AU  - Ammar Alfarga
    AU  - Mandour H. Abdelhai
    AU  - Bo Jiang
    Y1  - 2016/05/10
    PY  - 2016
    N1  - https://doi.org/10.11648/j.bio.20160403.11
    DO  - 10.11648/j.bio.20160403.11
    T2  - American Journal of Bioscience and Bioengineering
    JF  - American Journal of Bioscience and Bioengineering
    JO  - American Journal of Bioscience and Bioengineering
    SP  - 34
    EP  - 40
    PB  - Science Publishing Group
    SN  - 2328-5893
    UR  - https://doi.org/10.11648/j.bio.20160403.11
    AB  - Allitol is an alcohol monosaccharide, is a reduction of D-psicose. It is functions as a cross linking of D- and L-hexoses. It existed in too small quantities in commercial sugars and is difficult to synthesize by using chemical methods. It has a hypoglycemic function, and can use as Laxative in treating of constipation, which can exploit in production of diabetes drugs. The present report investigates about the production of allitol by ribitol dehydrogenase (RDH), its action of the enzyme through homology and molecular docking studies. We have investigated ribitol dehydrogenase (RDH) from providencia alcalifaciens RIMD 1656011. The protein sequence of RDH was conducted for homology modeling through Swiss model. 3D structure revealed was docked with NAD+ and D-psicose using AutoDock Vina software version 5.6. The results of homology modeling and docking studies revealed that the conserved residues of RDH were Tyr 153, Tyr 92, Ser 17 and Lys157 with NAD+, while conserved residues with D-psicose were GLN67 and ASP61. NAD+ has good interaction with RDH showing grid score of -49.84, which is a good score for binding.
    VL  - 4
    IS  - 3
    ER  - 

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Author Information
  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

  • State Key Laboratory of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China

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