Cold adaptations study of glycosyl hydrolase enzymes via computational methods

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 co...

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Main Author: Parvizpour, Sepideh
Format: Thesis
Language:English
Published: 2015
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Online Access:http://eprints.utm.my/id/eprint/54731/1/SepidehParvizpourPFBME2015.pdf
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spelling my-utm-ep.547312020-11-04T08:22:56Z Cold adaptations study of glycosyl hydrolase enzymes via computational methods 2015-09 Parvizpour, Sepideh QA75 Electronic computers. Computer science 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. 2015-09 Thesis http://eprints.utm.my/id/eprint/54731/ http://eprints.utm.my/id/eprint/54731/1/SepidehParvizpourPFBME2015.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:94629 phd doctoral Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering Faculty of Biosciences and Medical Engineering
institution Universiti Teknologi Malaysia
collection UTM Institutional Repository
language English
topic QA75 Electronic computers
Computer science
spellingShingle QA75 Electronic computers
Computer science
Parvizpour, Sepideh
Cold adaptations study of glycosyl hydrolase enzymes via computational methods
description 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.
format Thesis
qualification_name Doctor of Philosophy (PhD.)
qualification_level Doctorate
author Parvizpour, Sepideh
author_facet Parvizpour, Sepideh
author_sort Parvizpour, Sepideh
title Cold adaptations study of glycosyl hydrolase enzymes via computational methods
title_short Cold adaptations study of glycosyl hydrolase enzymes via computational methods
title_full Cold adaptations study of glycosyl hydrolase enzymes via computational methods
title_fullStr Cold adaptations study of glycosyl hydrolase enzymes via computational methods
title_full_unstemmed Cold adaptations study of glycosyl hydrolase enzymes via computational methods
title_sort cold adaptations study of glycosyl hydrolase enzymes via computational methods
granting_institution Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering
granting_department Faculty of Biosciences and Medical Engineering
publishDate 2015
url http://eprints.utm.my/id/eprint/54731/1/SepidehParvizpourPFBME2015.pdf
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