Comparative modelling studies of fruit bromelain using molecular dynamics simulation
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ORIGINAL PAPER
Comparative modelling studies of fruit bromelain using molecular dynamics simulation Wei Cheng Pang 1 & Aizi Nor Mazila Ramli 1,2 & Azzmer Azzar Abdul Hamid 3,4 Received: 15 October 2019 / Accepted: 28 April 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords Cysteine protease . Fruit bromelain . Comparative modelling . Thermostability . MD simulation
Abbreviations Dope Discrete optimized protein energy GROMACS G R O n i n g e n M A c h i n e f o r C h e m i c a l Simulations LINCS Linear Constraint Solver
MD NCBI NPT NVT
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00894-020-04398-1) contains supplementary material, which is available to authorized users. * Aizi Nor Mazila Ramli [email protected] 1
Faculty of Industrial Science & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
2
Bio Aromatic Research Centre of Excellence, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang Darul Makmur, Malaysia
3
Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
4
Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia (IIUM), Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
PDB ID PME Rg RMSD RMSF SASA
Molecular dynamics National Center for Biotechnology Information Constant number of particles, pressure and temperature Constant number of particles, volume and temperature Protein Data Bank identification Particle mesh Ewald method Radius of gyration Root-mean-square deviations. Root-mean-square fluctuations Solvent accessible surface area
Introduction Proteases are degradative enzymes that catalyse the hydrolysis of peptide bonds of prote
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