Herasari, Dian and Ilim, Ilim and Pandiangan, Kamisah Delilawati and Aspita, Laila and Satria, Heri (2018) Effect of Mutation on the Dynamics of Lid lipMNK by Molecular Dynamics Approach. In: The 2nd International Conference on Applied Sciences Mathematics and Informatics, 9-11 Agustus 2018, Hotel Horison, Bandar Lampung, Indonesia. (Unpublished)
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Abstract
Manuk Lipase (lipMNK) is a double lid lipase from thermophilic microorganism, Geobacillus uzenencis, isolated from Manuk Crater, Garut, West Java, Indonesia. Several studies have demonstrated that the catalytic action of lipase involved the dynamics movement of lid segments from closed to open states upon the substrate binding. The lipMNK conformational dynamics also result in changes in ionic interactions involving residues in lid segment. In this study, the effect of mutation to dynamics of lid lipMNK. was studied at the atomic level by molecular dynamics (MD) simulation. In-silico mutation was performed on the lipMNK primary structure using Pymol software. Next, mutant structure solvated in 20% acetonitrile. MD is done by using AMBER software, force field ff03.r1. temperature 358K for 100 ns simulation. The results showed that dynamics conformation of lid lipMNK involving 3 pairs of salt bridges, Asp178 - Ly2229, Asp182 - Arg179, and Glu189 - Lys185. Mutations in Lys229Gln, Arg179Gln and Lys185Gln, can accelerate the lid opening movement, as can be seen from differences in lid movement distance compared to wild type. Visualization of MD mutant yield structure and distance changes of some reference residues suggest that mutations in these three residues cause unfolding in other segments of lipMNK. This suggests that a salt bridge involving all three residues has an important role in maintaining the stability of lipMNK structure. These results indicate that lid integrity is not only important for the stability of the lid but is also important for the overall stability of lipMNK structure.
| Item Type: | Conference or Workshop Item (Poster) |
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| Subjects: | Q Science > QD Chemistry |
| Divisions: | Fakultas Matematika dan Ilmu Pengetahuan Alam (FMIPA) > Prodi Kimia |
| Depositing User: | DR DIAN HERASARI |
| Date Deposited: | 02 Nov 2018 01:52 |
| Last Modified: | 02 Nov 2018 01:52 |
| URI: | http://repository.lppm.unila.ac.id/id/eprint/9161 |
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