Molecular dynamics studies of an endoglucanase from fusarium oxysporum
Abstract: Use of computational methods to model and design new enzymes with enhanced functionalities is an emerging technology. In this work endoglucanase obtained from Fusarium oxysporum is modeled using homology modeling, and the dynamics of this enzyme in vacuum and water medium is examined to...
| Main Authors: | , , |
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| Format: | Proceeding Paper |
| Language: | English |
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2010
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| Online Access: | http://irep.iium.edu.my/2388/1/MD_studies_of_Endoglucanase_proceedings.pdf |
| _version_ | 1825644307773652992 |
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| author | Noorbatcha, Ibrahim Ali Waesoho, Shukree Mohd. Salleh, Hamzah |
| author_facet | Noorbatcha, Ibrahim Ali Waesoho, Shukree Mohd. Salleh, Hamzah |
| author_sort | Noorbatcha, Ibrahim Ali |
| collection | IIUM |
| description | Abstract: Use of computational methods to model and design new enzymes with enhanced functionalities is an emerging technology. In this work endoglucanase obtained from Fusarium oxysporum is modeled using homology modeling, and the dynamics of this enzyme in vacuum and water medium is examined to analyze the effect of the environment on the structural and dynamical factors during the simulation. It is shown that the presence of water as the solvent medium has significant effects on the dynamics of the enzyme. The structural compactness of the enzyme increases, and the fluctuations of the backbone and the enzyme as a whole entity, becomes smooth in water. These effects are attributed to the presence of electrostatic network of interactions including hydrogen bonds in the water as the solvent medium. This study shows the importance of including appropriate solvent models in molecular dynamics simulations.
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| first_indexed | 2024-03-05T22:30:56Z |
| format | Proceeding Paper |
| id | oai:generic.eprints.org:2388 |
| institution | International Islamic University Malaysia |
| language | English |
| last_indexed | 2024-03-05T22:30:56Z |
| publishDate | 2010 |
| record_format | dspace |
| spelling | oai:generic.eprints.org:23882021-06-23T03:25:38Z http://irep.iium.edu.my/2388/ Molecular dynamics studies of an endoglucanase from fusarium oxysporum Noorbatcha, Ibrahim Ali Waesoho, Shukree Mohd. Salleh, Hamzah TP248.13 Biotechnology Abstract: Use of computational methods to model and design new enzymes with enhanced functionalities is an emerging technology. In this work endoglucanase obtained from Fusarium oxysporum is modeled using homology modeling, and the dynamics of this enzyme in vacuum and water medium is examined to analyze the effect of the environment on the structural and dynamical factors during the simulation. It is shown that the presence of water as the solvent medium has significant effects on the dynamics of the enzyme. The structural compactness of the enzyme increases, and the fluctuations of the backbone and the enzyme as a whole entity, becomes smooth in water. These effects are attributed to the presence of electrostatic network of interactions including hydrogen bonds in the water as the solvent medium. This study shows the importance of including appropriate solvent models in molecular dynamics simulations. 2010-08-04 Proceeding Paper PeerReviewed application/pdf en http://irep.iium.edu.my/2388/1/MD_studies_of_Endoglucanase_proceedings.pdf Noorbatcha, Ibrahim Ali and Waesoho, Shukree and Mohd. Salleh, Hamzah (2010) Molecular dynamics studies of an endoglucanase from fusarium oxysporum. In: 1st International Conference on Computation for Science and Technology (ICSST-1), 4-6 August 2010, Chiang Mai, Thailand. http://www.iccst2010.fa.itb.ac.id/ |
| spellingShingle | TP248.13 Biotechnology Noorbatcha, Ibrahim Ali Waesoho, Shukree Mohd. Salleh, Hamzah Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title | Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title_full | Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title_fullStr | Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title_full_unstemmed | Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title_short | Molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| title_sort | molecular dynamics studies of an endoglucanase from fusarium oxysporum |
| topic | TP248.13 Biotechnology |
| url | http://irep.iium.edu.my/2388/1/MD_studies_of_Endoglucanase_proceedings.pdf |
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