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Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures

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Abstract

Molecular Dynamics (MD) simulations have been used to understand how protein structure, dynamics, and flexibility are affected by adaptation to high temperature for several years. We report here the results of the high temperature MD simulations of Bacillus stearothermophilus L1 (L1 lipase). We found that the N-terminal moiety of the enzyme showed a high flexibility and dynamics during high temperature simulations which preceded and followed by clear structural changes in two specific regions; the small domain and the main catalytic domain or core domain of the enzyme. These two domains interact with each other through a Zn2+-binding coordination with Asp-61 and Asp-238 from the core domain and His-81 and His-87 from the small domain. Interestingly, the His-81 and His-87 were among the highly fluctuated and mobile residues at high temperatures. The results appear to suggest that tight interactions of Zn2+-binding coordination with specified residues became weak at high temperature which suggests the contribution of this region to the thermostability of the enzyme.

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Abbreviations

3D:

Three-dimensional

Cα-RMSd:

Backbone root mean square deviation

LGA:

Local-global alignment

MD:

Molecular dynamics

NPT:

Isobaric-isothermal ensemble

PDB:

Protein data bank

PME:

Particle mesh Ewald

Rg :

Radius of gyration

RMSf:

Root mean square fluctuation

SASA:

Solvent accessible surface area

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Acknowledgments

The authors gratefully acknowledge financial support from GRF UPM for RA and Malaysia Ministry of High Education (FRGS 5523138) for research grant.

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Authors and Affiliations

  1. Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia

    Roghayeh Abedi Karjiban, Mohd Basyaruddin Abdul Rahman & Mahiran Basri

  2. Laboratory of Industrial Biotechnology, Institute of Biosciences, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia

    Abu Bakar Salleh

  3. Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, NC, USA

    Donald Jacobs

  4. School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia

    Habibah Abdul Wahab

Authors
  1. Roghayeh Abedi Karjiban
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  2. Mohd Basyaruddin Abdul Rahman
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  3. Mahiran Basri
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  4. Abu Bakar Salleh
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  5. Donald Jacobs
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  6. Habibah Abdul Wahab
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Corresponding author

Correspondence to Mohd Basyaruddin Abdul Rahman.

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Abedi Karjiban, R., Abdul Rahman, M.B., Basri, M. et al. Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures. Protein J 28, 14–23 (2009). https://doi.org/10.1007/s10930-008-9159-7

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  • DOI: https://doi.org/10.1007/s10930-008-9159-7

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