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Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes

Received: 25 January 2020     Accepted: 17 February 2020     Published: 28 February 2020
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Abstract

Although the structure of Human Pancreatic Lipase has been documented through the X-ray crystallography, the knowledge about the molecular rearrangement and dynamic equilibrium in the structure (particularly in the catalytic triad and lid domains) is very scanty. The structural fluctuations and conformational changes undergo by Human Pancreatic Lipase (HPL) with and without colipase were computationally investigated through molecular dynamics simulation technique using GROMACS 2018.4, MOE 2016.0801 and VMD softwares in order to gain insight into the complex transitions at different domains. The structural stability was revealed vis-a-vis Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) plots. The levels of compactness/folding and conformational changes of the protein were determined using Radius of gyration and secondary analysis respectively. Salt bridge analysis gives more ionic pairs interactions than experimentally determined results. Results show that though both proteins are stable, lipase-colipase complex is more deviated and flexible than lipase. Also, additional information regarding the conformational transitions, interactions and dynamics that govern stability of lipase-colipase complex which were ‘hidden’ to experimental techniques were revealed.

Published in International Journal of Computational and Theoretical Chemistry (Volume 8, Issue 1)
DOI 10.11648/j.ijctc.20200801.13
Page(s) 19-26
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), 2020. Published by Science Publishing Group

Keywords

Human Pancreatic Lipase, Conformational Change, RMSD, Radius of Gyration

References
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    Sikiru Akinyeye Ahmed, Nizakat Ali, Urooj Qureshi, Ruqaiya Khalil, Zaheer-Ul Haq Qasmi. (2020). Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes. International Journal of Computational and Theoretical Chemistry, 8(1), 19-26. https://doi.org/10.11648/j.ijctc.20200801.13

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    ACS Style

    Sikiru Akinyeye Ahmed; Nizakat Ali; Urooj Qureshi; Ruqaiya Khalil; Zaheer-Ul Haq Qasmi. Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes. Int. J. Comput. Theor. Chem. 2020, 8(1), 19-26. doi: 10.11648/j.ijctc.20200801.13

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    AMA Style

    Sikiru Akinyeye Ahmed, Nizakat Ali, Urooj Qureshi, Ruqaiya Khalil, Zaheer-Ul Haq Qasmi. Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes. Int J Comput Theor Chem. 2020;8(1):19-26. doi: 10.11648/j.ijctc.20200801.13

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  • @article{10.11648/j.ijctc.20200801.13,
      author = {Sikiru Akinyeye Ahmed and Nizakat Ali and Urooj Qureshi and Ruqaiya Khalil and Zaheer-Ul Haq Qasmi},
      title = {Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes},
      journal = {International Journal of Computational and Theoretical Chemistry},
      volume = {8},
      number = {1},
      pages = {19-26},
      doi = {10.11648/j.ijctc.20200801.13},
      url = {https://doi.org/10.11648/j.ijctc.20200801.13},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20200801.13},
      abstract = {Although the structure of Human Pancreatic Lipase has been documented through the X-ray crystallography, the knowledge about the molecular rearrangement and dynamic equilibrium in the structure (particularly in the catalytic triad and lid domains) is very scanty. The structural fluctuations and conformational changes undergo by Human Pancreatic Lipase (HPL) with and without colipase were computationally investigated through molecular dynamics simulation technique using GROMACS 2018.4, MOE 2016.0801 and VMD softwares in order to gain insight into the complex transitions at different domains. The structural stability was revealed vis-a-vis Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) plots. The levels of compactness/folding and conformational changes of the protein were determined using Radius of gyration and secondary analysis respectively. Salt bridge analysis gives more ionic pairs interactions than experimentally determined results. Results show that though both proteins are stable, lipase-colipase complex is more deviated and flexible than lipase. Also, additional information regarding the conformational transitions, interactions and dynamics that govern stability of lipase-colipase complex which were ‘hidden’ to experimental techniques were revealed.},
     year = {2020}
    }
    

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  • TY  - JOUR
    T1  - Molecular Dynamics Simulation of Human Pancreatic Lipase and Lipase-colipase Complex: Insight into the Structural Fluctuations and Conformational Changes
    AU  - Sikiru Akinyeye Ahmed
    AU  - Nizakat Ali
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    AU  - Zaheer-Ul Haq Qasmi
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    N1  - https://doi.org/10.11648/j.ijctc.20200801.13
    DO  - 10.11648/j.ijctc.20200801.13
    T2  - International Journal of Computational and Theoretical Chemistry
    JF  - International Journal of Computational and Theoretical Chemistry
    JO  - International Journal of Computational and Theoretical Chemistry
    SP  - 19
    EP  - 26
    PB  - Science Publishing Group
    SN  - 2376-7308
    UR  - https://doi.org/10.11648/j.ijctc.20200801.13
    AB  - Although the structure of Human Pancreatic Lipase has been documented through the X-ray crystallography, the knowledge about the molecular rearrangement and dynamic equilibrium in the structure (particularly in the catalytic triad and lid domains) is very scanty. The structural fluctuations and conformational changes undergo by Human Pancreatic Lipase (HPL) with and without colipase were computationally investigated through molecular dynamics simulation technique using GROMACS 2018.4, MOE 2016.0801 and VMD softwares in order to gain insight into the complex transitions at different domains. The structural stability was revealed vis-a-vis Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) plots. The levels of compactness/folding and conformational changes of the protein were determined using Radius of gyration and secondary analysis respectively. Salt bridge analysis gives more ionic pairs interactions than experimentally determined results. Results show that though both proteins are stable, lipase-colipase complex is more deviated and flexible than lipase. Also, additional information regarding the conformational transitions, interactions and dynamics that govern stability of lipase-colipase complex which were ‘hidden’ to experimental techniques were revealed.
    VL  - 8
    IS  - 1
    ER  - 

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Author Information
  • Department of Chemistry, Kwara State University, Malete, Ilorin, Nigeria

  • International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan

  • International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan

  • International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan

  • International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan

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