Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach

Dian Herasari^1,2, Rukman Hertadi¹, Fida M. Warganegara¹ and Akhmaloka^1,3

¹Biochemistry Research Group, Faculty of Mathematics and Natural Science, Institut Teknologi Bandung, Indonesia.

²Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Lampung, Indonesia.

³Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Indonesia.

Corresponding Author E-mail: loka@chem.itb.ac.id

DOI : http://dx.doi.org/10.13005/bbra/2632

ABSTRACT: Manuk lipase (lipMNK) from the thermophilic bacterium Geobacillus sp is a double lid lipase containing short and long lid segments. A few studies demonstrated that catalytic action of lipase involved the movement of lid segments from closed to open conformation upon the substrate binding. One factor that affects conformational dynamics of the lid segments is solvent polarity. The presence of acetonitrile in certain concentration has showed to enhance lipase activity. In this study, the effect of acetonitrile to the stability and activity of lipMNK was studied at the atomic level by molecular dynamics (MD) simulation. MD was carried out by NPT ensemble at 358 K for 100 nano seconds in various ratio of acetonitrile:water solvent mixtures. The results showed that the conformation of lipMNK was stable up to 70%. However, the effect of lid movement was significantly observed since the concentration at 20% acetonitrile. Detailed molecular analysis at this acetonitrile concentration revealed that the two lids moved in different modes upon opening and closing movement. In the opening movement, the two lids appeared to move in almost simultaneously, while during the closing movement, it was observed sequentially, started by short segment followed by long segment lid.

KEYWORDS: lipMNK; lid; Molecular Dynamics

[ HTML Full Text]