Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure
Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English English |
| Published: |
Multidisciplinary Digital Publishing Institute (MDPI)
2017
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| Subjects: | |
| Online Access: | http://irep.iium.edu.my/59250/ http://irep.iium.edu.my/59250/1/59250_Molecular%20Dynamic%20Simulation.pdf http://irep.iium.edu.my/59250/2/59250_Molecular%20Dynamic%20Simulation_SCOPUS.pdf |
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| author | Ishak, Siti Nor Hasmah Mohamad Aris, Sayangku Nor Ariati Abd Halim, Khairul Bariyyah Mohamad Ali, Mohd Shukuri Thean, Chor Leow Ahmad Kamarudin, Nor Hafizah Masomlan, Malihe Raja Abd Rahman, Raja Noor Zaliha |
| author_facet | Ishak, Siti Nor Hasmah Mohamad Aris, Sayangku Nor Ariati Abd Halim, Khairul Bariyyah Mohamad Ali, Mohd Shukuri Thean, Chor Leow Ahmad Kamarudin, Nor Hafizah Masomlan, Malihe Raja Abd Rahman, Raja Noor Zaliha |
| author_sort | Ishak, Siti Nor Hasmah |
| building | IIUM Repository |
| collection | Online Access |
| description | Less sedimentation and convection in a microgravity environment has become a well-suited
condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium
Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth
conditions. Preliminary study using YASARA molecular modeling structure program for both
structures showed differences in number of hydrogen bond, ionic interaction, and conformation.
The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown
crystal structure. A molecular dynamics simulation study was used to provide insight on the
fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean
square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that
space-grown structure is more stable than the earth-grown structure. Space-structure also showed
more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis
also revealed that the space-grown structure has long-lived interactions, hence it is considered as the
more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure
grown in space and earth condition. |
| first_indexed | 2025-11-14T16:50:33Z |
| format | Article |
| id | iium-59250 |
| institution | International Islamic University Malaysia |
| institution_category | Local University |
| language | English English |
| last_indexed | 2025-11-14T16:50:33Z |
| publishDate | 2017 |
| publisher | Multidisciplinary Digital Publishing Institute (MDPI) |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | iium-592502018-03-09T04:33:20Z http://irep.iium.edu.my/59250/ Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure Ishak, Siti Nor Hasmah Mohamad Aris, Sayangku Nor Ariati Abd Halim, Khairul Bariyyah Mohamad Ali, Mohd Shukuri Thean, Chor Leow Ahmad Kamarudin, Nor Hafizah Masomlan, Malihe Raja Abd Rahman, Raja Noor Zaliha Q Science (General) Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition. Multidisciplinary Digital Publishing Institute (MDPI) 2017-08 Article PeerReviewed application/pdf en http://irep.iium.edu.my/59250/1/59250_Molecular%20Dynamic%20Simulation.pdf application/pdf en http://irep.iium.edu.my/59250/2/59250_Molecular%20Dynamic%20Simulation_SCOPUS.pdf Ishak, Siti Nor Hasmah and Mohamad Aris, Sayangku Nor Ariati and Abd Halim, Khairul Bariyyah and Mohamad Ali, Mohd Shukuri and Thean, Chor Leow and Ahmad Kamarudin, Nor Hafizah and Masomlan, Malihe and Raja Abd Rahman, Raja Noor Zaliha (2017) Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure. Molecules, 22 (10). pp. 1-13. ISSN 1420-3049 http://www.mdpi.com/1420-3049/22/10/1574 10.3390/molecules22101574 |
| spellingShingle | Q Science (General) Ishak, Siti Nor Hasmah Mohamad Aris, Sayangku Nor Ariati Abd Halim, Khairul Bariyyah Mohamad Ali, Mohd Shukuri Thean, Chor Leow Ahmad Kamarudin, Nor Hafizah Masomlan, Malihe Raja Abd Rahman, Raja Noor Zaliha Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title | Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title_full | Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title_fullStr | Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title_full_unstemmed | Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title_short | Molecular dynamic simulation of space and earth-grown crystal structures of thermostable T1 lipase geobacillus zalihae revealed a better structure |
| title_sort | molecular dynamic simulation of space and earth-grown crystal structures of thermostable t1 lipase geobacillus zalihae revealed a better structure |
| topic | Q Science (General) |
| url | http://irep.iium.edu.my/59250/ http://irep.iium.edu.my/59250/ http://irep.iium.edu.my/59250/ http://irep.iium.edu.my/59250/1/59250_Molecular%20Dynamic%20Simulation.pdf http://irep.iium.edu.my/59250/2/59250_Molecular%20Dynamic%20Simulation_SCOPUS.pdf |