Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure

被引:25
|
作者
Ishak, Siti Nor Hasmah [1 ,6 ]
Aris, Sayangku Nor Ariati Mohamad [1 ,2 ]
Abd Halim, Khairul Bariyyah [3 ]
Ali, Mohd Shukuri Mohamad [1 ,4 ]
Leow, Thean Chor [1 ,2 ,5 ]
Kamarudin, Nor Hafizah Ahmad [1 ,2 ]
Masomian, Malihe [1 ,6 ]
Abd Rahman, Raja Noor Zaliha Raja [1 ,5 ,6 ,7 ]
机构
[1] Univ Putra Malaysia, Fac Biotechnol & Biomol Sci, Enzyme & Microbial Technol Res Ctr, Upm Serdang 43400, Selangor, Malaysia
[2] Univ Putra Malaysia, Fac Biotechnol & Biomol Sci, Dept Cell & Mol Biol, Upm Serdang 43400, Selangor, Malaysia
[3] Int Islamic Univ Malaysia, Kuliyyah Sci, Dept Biotechnol, Kuantan 25200, Pahang, Malaysia
[4] Univ Putra Malaysia, Fac Biotechnol & Biomol Sci, Dept Biochem, Upm Serdang 43400, Selangor, Malaysia
[5] Univ Putra Malaysia, Inst Biosci, Upm Serdang 43400, Selangor, Malaysia
[6] Univ Putra Malaysia, Inst Biosci, Dept Microbiol, Upm Serdang 43400, Selangor, Malaysia
[7] Univ Putra Malaysia, Halal Prod Res Inst, Lab Halal Sci Res, Upm Serdang 43400, Selangor, Malaysia
关键词
T1; lipase; Geobacillus zalihae; microgravity; molecular dynamic simulation; hydrogen bond; ion interaction; SURFACE SALT BRIDGES; PROTEIN STABILITY; ION-PAIRS; THERMAL-STABILITY; FORCE-FIELD; MICROGRAVITY; CRYSTALLIZATION; QUALITY;
D O I
10.3390/molecules22101574
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
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页数:13
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