Staff View: Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study

Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study

Fluorescent protein has been applied in various diagnostic and biotechnology application. However, in these applications, the temperature conditions are simulated at higher temperatures of 289K and 300K compared to natural sea anemone Cribrinopsis japonica fluorescent protein. This study evaluates t...

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Main Authors:	Asraf, Muhammad Hariz, Mohamed Zulkifli, Razauden, Ahmad, Nor Azlina, Rusli, Rusna Shakira, Ahmad Shaari, Hilzaiti, Omar, Mohd. Shahir Shamsir, A. Rohman, Siti Noor Aishah
Format:	Article
Language:	English
Published:	Penerbit UTM Press 2022
Subjects:	Q Science (General)
Online Access:	http://eprints.utm.my/id/eprint/102701/1/RazaudenMohamedZulkifli2022_InsightintotheThermostabilityofNovelFluorescent.pdf http://eprints.utm.my/id/eprint/102701/ http://dx.doi.org/10.11113/jurnalteknologi.v84.16492
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spelling	my.utm.1027012023-09-18T04:07:03Z http://eprints.utm.my/id/eprint/102701/ Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study Asraf, Muhammad Hariz Mohamed Zulkifli, Razauden Ahmad, Nor Azlina Rusli, Rusna Shakira Ahmad Shaari, Hilzaiti Omar, Mohd. Shahir Shamsir A. Rohman, Siti Noor Aishah Q Science (General) Fluorescent protein has been applied in various diagnostic and biotechnology application. However, in these applications, the temperature conditions are simulated at higher temperatures of 289K and 300K compared to natural sea anemone Cribrinopsis japonica fluorescent protein. This study evaluates the predictive structure and the molecular dynamic interaction of the protein with its target in different external temperature using ab initio similarity modeling and GROMACS/VMD respectively. Three-dimensional structure of the protein, named cjFP510 were predicted and analysed based on the highest similarity template model of Anemonia sulcata (2c9i) at 66.97%. The predicted model shows alternating α and β helices with longer loops and extra α-helix. cjFP510 was programmed with molecular dynamic simulation with template protein 2c9i as a reference to study its comparative adaptability in two different temperatures of 289K and 300K. cjFP510 was found to be more stable at both temperatures compared to 2c9i. Further simulation was conducted on the gyration radius to evaluate the compactness of the protein folding. Lower gyration radius of cjFP510 denotes more stable protein at 289K simulated environment than 29ci. This may be due to the presence of an extra α-helix based on the predicted model and few amino acid residues such as glycine, lysine, and arginine which contributed to the protein flexibility and thermal stability Conclusively, cjFP510 is more thermostable in the two conditional temperatures tested. Penerbit UTM Press 2022-05 Article PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/102701/1/RazaudenMohamedZulkifli2022_InsightintotheThermostabilityofNovelFluorescent.pdf Asraf, Muhammad Hariz and Mohamed Zulkifli, Razauden and Ahmad, Nor Azlina and Rusli, Rusna Shakira and Ahmad Shaari, Hilzaiti and Omar, Mohd. Shahir Shamsir and A. Rohman, Siti Noor Aishah (2022) Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study. Jurnal Teknologi, 84 (3). pp. 163-171. ISSN 0127-9696 http://dx.doi.org/10.11113/jurnalteknologi.v84.16492 DOI:10.11113/jurnalteknologi.v84.16492
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
language	English
topic	Q Science (General)
spellingShingle	Q Science (General) Asraf, Muhammad Hariz Mohamed Zulkifli, Razauden Ahmad, Nor Azlina Rusli, Rusna Shakira Ahmad Shaari, Hilzaiti Omar, Mohd. Shahir Shamsir A. Rohman, Siti Noor Aishah Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
description	Fluorescent protein has been applied in various diagnostic and biotechnology application. However, in these applications, the temperature conditions are simulated at higher temperatures of 289K and 300K compared to natural sea anemone Cribrinopsis japonica fluorescent protein. This study evaluates the predictive structure and the molecular dynamic interaction of the protein with its target in different external temperature using ab initio similarity modeling and GROMACS/VMD respectively. Three-dimensional structure of the protein, named cjFP510 were predicted and analysed based on the highest similarity template model of Anemonia sulcata (2c9i) at 66.97%. The predicted model shows alternating α and β helices with longer loops and extra α-helix. cjFP510 was programmed with molecular dynamic simulation with template protein 2c9i as a reference to study its comparative adaptability in two different temperatures of 289K and 300K. cjFP510 was found to be more stable at both temperatures compared to 2c9i. Further simulation was conducted on the gyration radius to evaluate the compactness of the protein folding. Lower gyration radius of cjFP510 denotes more stable protein at 289K simulated environment than 29ci. This may be due to the presence of an extra α-helix based on the predicted model and few amino acid residues such as glycine, lysine, and arginine which contributed to the protein flexibility and thermal stability Conclusively, cjFP510 is more thermostable in the two conditional temperatures tested.
format	Article
author	Asraf, Muhammad Hariz Mohamed Zulkifli, Razauden Ahmad, Nor Azlina Rusli, Rusna Shakira Ahmad Shaari, Hilzaiti Omar, Mohd. Shahir Shamsir A. Rohman, Siti Noor Aishah
author_facet	Asraf, Muhammad Hariz Mohamed Zulkifli, Razauden Ahmad, Nor Azlina Rusli, Rusna Shakira Ahmad Shaari, Hilzaiti Omar, Mohd. Shahir Shamsir A. Rohman, Siti Noor Aishah
author_sort	Asraf, Muhammad Hariz
title	Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
title_short	Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
title_full	Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
title_fullStr	Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
title_full_unstemmed	Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
title_sort	insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study
publisher	Penerbit UTM Press
publishDate	2022
url	http://eprints.utm.my/id/eprint/102701/1/RazaudenMohamedZulkifli2022_InsightintotheThermostabilityofNovelFluorescent.pdf http://eprints.utm.my/id/eprint/102701/ http://dx.doi.org/10.11113/jurnalteknologi.v84.16492
_version_	1778160768980615168
score	13.211869

Insight into the thermostability of novel fluorescent protein isolated from sea anemone cribrinopsis japonica: in silico study

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