Cold adaptations study of glycosyl hydrolase enzymes via computational methods

Abstract

Psychrophiles are cold loving organisms that have adapted to live in permanently cold environments. These microorganisms synthesize psychrophilic enzymes with high catalytic efficiencies at cold temperaturesranging from -20°C to +10°C. This research intends to perform an in silico analysis of the cold adaptation of Glycosyl hydrolase enzymes isolated from psychrophilic yeast Glaciozyma antarctica. Two enzyme were selected; ß-mannanase (PMAN) and ß-glucanase (PLAM) from two different glycosyl hydrolase families with different domains. A 3D model was predicted for both genes using a fold recognition method. The proteins were comparatively studied against their mesophilic, thermophilic, and hyperthermophilic counterparts. The study of these enzymes illustrates that they mostly use similar strategies for cold adaptation.The structure of PLAM and PMAN consist of longer loops in three different positions. Their structure also has several amino acids substitution including increased number of alanine, glycine, and polar residues and decreased number of proline, arginine, and hydrophobic residues. The PLAM and PMAN structure showed longer motions around the entrance region to active site. A lower number of salt bridges and H-bonds have been observed in the PLAM and PMAN structure. PLAM consists of 5 salt bridges while its homologous proteins have 9, 7, and 18 salt bridges, respectively. Also, the number of H-bonds per residue is 0.54 where it is 0.62, 0.63, and 0.70 for its homologous counterparts. Furthermore, PMAN includes 5 salt bridges in its structure while its homologous counterparts have 10, 14, and 21 salt bridges, respectively. The number of H-bonds per residue for PMAN is 0.62 while it is 0.71, 0.73 and 0.78 for its homologous counterparts. The PLAM structure has 41% of secondary structure, while its homologous counterparts have 54%, 58%, and 60% of secondary structure. Also, this percentage is 47% for PMAN, and 48%, 50%, and 53% for its homologous proteins. Additionally, they also use different strategies related to the role of salt bridges in their structure. The PLAM structure contains alternative salt bridges connecting inner and outer leaflets, while the PMAN structure includes weakly linked salt bridges between residues located on a loop instead of ß-sheet. In conclusion, in silico analysis of two psychrophilic proteins revealed novel characteristics of these cold adapted enzymes. The analysis showed the adopted strategies by these two proteins in contributing to the general and local flexibility of their structure and increase capability of the enzymes to be active at cold temperatures. The presented findings in this research will assist future attempts in the rational design of enzymes with enhanced enzymatic capabilities.