Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family
Abstract Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely co...
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crwiley:10.1002/prot.20773 2024-06-23T07:47:06+00:00 Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family Adekoya, Olayiwola A. Helland, Ronny Willassen, Nils‐Peder Sylte, Ingebrigt 2005 http://dx.doi.org/10.1002/prot.20773 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.20773 https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.20773 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Proteins: Structure, Function, and Bioinformatics volume 62, issue 2, page 435-449 ISSN 0887-3585 1097-0134 journal-article 2005 crwiley https://doi.org/10.1002/prot.20773 2024-06-11T04:51:07Z Abstract Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence‐structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold‐adapted enzymes have a more flexible three‐dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation–π electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate. Proteins 2006. © 2005 Wiley‐Liss, Inc. Article in Journal/Newspaper Antarc* Antarctic Wiley Online Library Antarctic Proteins: Structure, Function, and Bioinformatics 62 2 435 449 |
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English |
description |
Abstract Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence‐structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold‐adapted enzymes have a more flexible three‐dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation–π electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate. Proteins 2006. © 2005 Wiley‐Liss, Inc. |
format |
Article in Journal/Newspaper |
author |
Adekoya, Olayiwola A. Helland, Ronny Willassen, Nils‐Peder Sylte, Ingebrigt |
spellingShingle |
Adekoya, Olayiwola A. Helland, Ronny Willassen, Nils‐Peder Sylte, Ingebrigt Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
author_facet |
Adekoya, Olayiwola A. Helland, Ronny Willassen, Nils‐Peder Sylte, Ingebrigt |
author_sort |
Adekoya, Olayiwola A. |
title |
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
title_short |
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
title_full |
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
title_fullStr |
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
title_full_unstemmed |
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
title_sort |
comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family |
publisher |
Wiley |
publishDate |
2005 |
url |
http://dx.doi.org/10.1002/prot.20773 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.20773 https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.20773 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Proteins: Structure, Function, and Bioinformatics volume 62, issue 2, page 435-449 ISSN 0887-3585 1097-0134 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/prot.20773 |
container_title |
Proteins: Structure, Function, and Bioinformatics |
container_volume |
62 |
container_issue |
2 |
container_start_page |
435 |
op_container_end_page |
449 |
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1802650882556297216 |