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

Sikiru Akinyeye Ahmed; Nizakat Ali; Urooj Qureshi; Ruqaiya Khalil; Zaheer-Ul Haq Qasmi

doi:doi:10.11648/j.ijctc.20200801.13

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

Sikiru Akinyeye Ahmed, Nizakat Ali, Urooj Qureshi, Ruqaiya Khalil, Zaheer-Ul Haq Qasmi

Published in International Journal of Computational and Theoretical Chemistry (Volume 8, Issue 1)

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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APA Style

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
AU  - Urooj Qureshi
AU  - Ruqaiya Khalil
AU  - Zaheer-Ul Haq Qasmi
Y1  - 2020/02/28
PY  - 2020
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

Sikiru Akinyeye Ahmed

Department of Chemistry, Kwara State University, Malete, Ilorin, Nigeria
Nizakat Ali

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

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

International Centre for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
Zaheer-Ul Haq Qasmi

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

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APA Style

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}
}

Copy | Download

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
AU  - Urooj Qureshi
AU  - Ruqaiya Khalil
AU  - Zaheer-Ul Haq Qasmi
Y1  - 2020/02/28
PY  - 2020
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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