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

Abstract

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 Geobacilluszalihae 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.

Keywords: Geobacillus zalihae; T1 lipase; hydrogen bond; ion interaction; microgravity; molecular dynamic simulation.

Figure 1

The conformation of residues Asp175, Arg179, and Val174 in T1 lipase crystal structures: (a) earth-grown T1 lipase crystal structure; (b) Space-grown T1 lipase crystal structure.

Figure 2

Analysis of molecular dynamic simulation of earth-grown (red) and space-grown (blue) crystal structures in water at 70 °C: (a) The Root Mean Square Deviation (RMSD) of earth-grown and space-grown T1 lipase crystal structures; (b) Radius of gyration of earth-grown and space-grown T1 lipase crystal structures; (c) Root Mean Square Fluctuation (RMSF) of earth-grown and space-grown T1 lipase crystal structure.

Figure 3

Superimposed T1 lipase structures before and after 20 ns of simulation: (a) Earth-grown structure at 0 ns (color in elements) and after 20 ns of simulation (color in magenta); (b) Space-grown crystal structure at 0 ns (color in elements) and after 20 ns of simulation (color in magenta). The arrows showed the region with a high flexible value in the earth-grown structure compared with the space-grown structure.

Figure 4

Changes in secondary structure of earth-grown T1 lipase crystal structure before and after 20 ns of simulation: (a) Crystal strcuture of earth-grown T1 lipase before simulation; (b) Earth-grown T1 lipase after 20 ns of simulation.

Figure 5

The secondary structure analysis for the earth-grown and space-grown structures: (a) Earth-grown structure; (b) Space-grown structure.

Figure 6

Hydrogen bond interaction in the earth-grown and space-grown T1 lipase structures: (a) Hydrogen bond numbers between amino acid Thr306 and Asn304 in the space-grown (blue) and earth-grown (red) structures during 20 ns of simulation; (b) Number of hydrogen bonds in the space-grown (blue) and earth-grown (red) structures during 20 ns of simulation.

Figure 7

Interaction in earth-grown and space-grown T1 lipase structures: (a) Number of interaction between residue Arg230 and Glu226 in the space-grown (blue) and earth-grown (red) structures during 20 ns of simulation; (b) Number of interaction between residue Lys229 and Asp178 in the space-grown (blue) and earth-grown (red) structures during 20 ns of simulation.

Figure 8

Ion pair interaction in earth-grown and space-grown T1 lipase structures: (a) Superpose of earth-grown T1 lipase crystal structure (color in elements) and structure at 20 ns (color in yellow); (b) Superpose of space-grown T1 lipase crystal structure (color in elements) and structure after 20 ns of trajectory (color in green). Ion pair interaction is indicated using dotted lines in magenta.