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Comparative modelling studies of fruit bromelain using molecular dynamics simulation

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Abstract

Fruit bromelain is a cysteine protease accumulated in pineapple fruits. This proteolytic enzyme has received high demand for industrial and therapeutic applications. In this study, fruit bromelain sequences QIM61759, QIM61760 and QIM61761 were retrieved from the National Center for Biotechnology Information (NCBI) Genbank Database. The tertiary structure of fruit bromelain QIM61759, QIM61760 and QIM61761 was generated by using MODELLER. The result revealed that the local stereochemical quality of the generated models was improved by using multiple templates during modelling process. Moreover, by comparing with the available papain model, structural analysis provides an insight on how pro-peptide functions as a scaffold in fruit bromelain folding and contributing to inactivation of mature protein. The structural analysis also disclosed the similarities and differences between these models. Lastly, thermal stability of fruit bromelain was studied. Molecular dynamics simulation of fruit bromelain structures at several selected temperatures demonstrated how fruit bromelain responds to elevation of temperature.

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Abbreviations

Dope:

Discrete optimized protein energy

GROMACS:

GROningen MAchine for Chemical Simulations

LINCS:

Linear Constraint Solver

MD:

Molecular dynamics

NCBI:

National Center for Biotechnology Information

NPT:

Constant number of particles, pressure and temperature

NVT:

Constant number of particles, volume and temperature

PDB ID:

Protein Data Bank identification

PME:

Particle mesh Ewald method

Rg:

Radius of gyration

RMSD:

Root-mean-square deviations.

RMSF:

Root-mean-square fluctuations

SASA:

Solvent accessible surface area

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Funding

This research was supported by the Universiti Malaysia Pahang through research grants RDU180345 and PGRS180362.

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Authors and Affiliations

  1. Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia

    Wei Cheng Pang & Aizi Nor Mazila Ramli

  2. Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia

    Aizi Nor Mazila Ramli

  3. Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia

    Azzmer Azzar Abdul Hamid

  4. Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia

    Azzmer Azzar Abdul Hamid

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  1. Wei Cheng Pang
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  2. Aizi Nor Mazila Ramli
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  3. Azzmer Azzar Abdul Hamid
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Correspondence to Aizi Nor Mazila Ramli.

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Pang, W.C., Ramli, A.N.M. & Hamid, A.A.A. Comparative modelling studies of fruit bromelain using molecular dynamics simulation. J Mol Model 26, 142 (2020). https://doi.org/10.1007/s00894-020-04398-1

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