Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures
Thermostability is an important requirement for protein function, and one goal of protein engineering is improvement of activity of the enzymes at higher temperatures, particularly for industrial applications. Computational approaches to investigate factors influencing thermostability of proteins ar...
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iium-641492019-01-24T07:49:26Z http://irep.iium.edu.my/64149/ Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures Ahmad, Abdul Aziz Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah TP248.13 Biotechnology Thermostability is an important requirement for protein function, and one goal of protein engineering is improvement of activity of the enzymes at higher temperatures, particularly for industrial applications. Computational approaches to investigate factors influencing thermostability of proteins are becoming researchers’ choice. This study investigates the influence of substrate binding on the protein dynamics by comparing the molecular dynamics simulations of substrate-enzyme complex against un-bound enzyme, using endoglucanase I from Fusarium oxysporum. Endoglucanase-substrate complex was prepared by docking and molecular dynamics simulations were carried out at three different temperatures, 313 K, 333 K and 353 K. Our finding shows that the secondary structures for substrate-enzyme complex show more fluctuations relative to un-complexed structure. The same trend was observed for solvent accessible surface area and radius of gyration. At the highest temperature studied (353 K), the substrate-enzyme complex form showed the highest fluctuations. The fluctuations around the active site regions reach a minimum at the optimum temperature, compared to the other structural regions and other temperatures. Kestabilan (ketahanan) terhadap haba merupakan keperluan yang penting untuk fungsi protin, salah satu matlamat kejuruteraan protin adalah penambahbaikan aktiviti enzim pada suhu yang tinggi khususnya untuk aplikasi industri. Kini para penyelidik memilih kaedah komputasi, bagi mengkaji faktor yang mempengaruhi kestabilan terhadap haba. Kajian ini menyelidik pengaruh ikatan substrat pada protin dengan membandingkan simulasi molekular dinamik diantara substrat-enzim kompleks dan enzim sahaja, menggunakan endoglucanase I dari Fusarium oxysporum. Kompleks endoglucanase-substrat disediakan melalui kaedah docking dan simulasi molekular dinamik dilakukan pada suhu 313 K, 333 K dan 353 K. Kajian kami menunjukkan struktur sekunder bagi substrat-enzim kompleks kurang stabil berbanding enzim sahaja. Pola yang sama bagi luas permukaan boleh dicapai pelarut (SASA) dan jejari gyrasi. Pada suhu tertinggi dikaji (353 K), substrat-enzim kompleks paling tidak stabil. Pada suhu optimum, kadar ubah-ubah sekitar amino asid aktif adalah minimum berbanding struktur dan suhu lain. Kulliyyah of Engineering, International Islamic University Malaysia 2018-06 Article PeerReviewed application/pdf en http://irep.iium.edu.my/64149/13/64149%20%20Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics.pdf application/pdf en http://irep.iium.edu.my/64149/19/64149_Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics_SCOPUS.pdf application/pdf en http://irep.iium.edu.my/64149/25/64149%20Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics%20of%20an%20endoglucanase%20from%20Fusarium%20Oxysporum%20At%20Different%20temperatures_wos.pdf Ahmad, Abdul Aziz and Noorbatcha, Ibrahim Ali and Mohd. Salleh, Hamzah (2018) Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures. IIUM Engineering Journal, 19 (1). pp. 307-314. ISSN 1511-788X E-ISSN 2289-7860 http://journals.iium.edu.my/ejournal/index.php/iiumej/article/view/894/651 10.31436/iiumej.v19i1.894 |
| repository_type |
Digital Repository |
| institution_category |
Local University |
| institution |
International Islamic University Malaysia |
| building |
IIUM Repository |
| collection |
Online Access |
| language |
English English English |
| topic |
TP248.13 Biotechnology |
| spellingShingle |
TP248.13 Biotechnology Ahmad, Abdul Aziz Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| description |
Thermostability is an important requirement for protein function, and one goal of protein engineering is improvement of activity of the enzymes at higher temperatures, particularly for industrial applications. Computational approaches to investigate factors influencing thermostability of proteins are becoming researchers’ choice. This study investigates the influence of substrate binding on the protein dynamics by comparing the molecular dynamics simulations of substrate-enzyme complex against un-bound enzyme, using endoglucanase I from Fusarium oxysporum. Endoglucanase-substrate complex was prepared by docking and molecular dynamics simulations were carried out at three different temperatures, 313 K, 333 K and 353 K. Our finding shows that the secondary structures for substrate-enzyme complex show more fluctuations relative to un-complexed structure. The same trend was observed for solvent accessible surface area and radius of gyration. At the highest temperature studied (353 K), the substrate-enzyme complex form showed the highest fluctuations. The fluctuations around the active site regions reach a minimum at the optimum temperature, compared to the other structural regions and other temperatures.
Kestabilan (ketahanan) terhadap haba merupakan keperluan yang penting
untuk fungsi protin, salah satu matlamat kejuruteraan protin adalah penambahbaikan
aktiviti enzim pada suhu yang tinggi khususnya untuk aplikasi industri. Kini para
penyelidik memilih kaedah komputasi, bagi mengkaji faktor yang mempengaruhi
kestabilan terhadap haba. Kajian ini menyelidik pengaruh ikatan substrat pada protin
dengan membandingkan simulasi molekular dinamik diantara substrat-enzim kompleks
dan enzim sahaja, menggunakan endoglucanase I dari Fusarium oxysporum. Kompleks
endoglucanase-substrat disediakan melalui kaedah docking dan simulasi molekular
dinamik dilakukan pada suhu 313 K, 333 K dan 353 K. Kajian kami menunjukkan
struktur sekunder bagi substrat-enzim kompleks kurang stabil berbanding enzim sahaja.
Pola yang sama bagi luas permukaan boleh dicapai pelarut (SASA) dan jejari gyrasi.
Pada suhu tertinggi dikaji (353 K), substrat-enzim kompleks paling tidak stabil. Pada
suhu optimum, kadar ubah-ubah sekitar amino asid aktif adalah minimum berbanding
struktur dan suhu lain. |
| format |
Article |
| author |
Ahmad, Abdul Aziz Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah |
| author_facet |
Ahmad, Abdul Aziz Noorbatcha, Ibrahim Ali Mohd. Salleh, Hamzah |
| author_sort |
Ahmad, Abdul Aziz |
| title |
Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| title_short |
Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| title_full |
Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| title_fullStr |
Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| title_full_unstemmed |
Role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| title_sort |
role of substrate binding on the protein dynamics of an endoglucanase from fusarium oxysporum at different temperatures |
| publisher |
Kulliyyah of Engineering, International Islamic University Malaysia |
| publishDate |
2018 |
| url |
http://irep.iium.edu.my/64149/ http://irep.iium.edu.my/64149/ http://irep.iium.edu.my/64149/ http://irep.iium.edu.my/64149/13/64149%20%20Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics.pdf http://irep.iium.edu.my/64149/19/64149_Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics_SCOPUS.pdf http://irep.iium.edu.my/64149/25/64149%20Role%20of%20substrate%20binding%20on%20the%20protein%20dynamics%20of%20an%20endoglucanase%20from%20Fusarium%20Oxysporum%20At%20Different%20temperatures_wos.pdf |
| first_indexed |
2023-09-18T21:30:58Z |
| last_indexed |
2023-09-18T21:30:58Z |
| _version_ |
1777412508361949184 |