Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism
Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entrop...
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| Format: | Article |
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The Royal Society
2021-12-01
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| Series: | Open Biology |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsob.210182 |
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| author | Nehad Noby Husam Sabah Auhim Samuel Winter Harley L. Worthy Amira M. Embaby Hesham Saeed Ahmed Hussein Christopher R. Pudney Pierre J. Rizkallah Stephen A. Wells D. Dafydd Jones |
| author_facet | Nehad Noby Husam Sabah Auhim Samuel Winter Harley L. Worthy Amira M. Embaby Hesham Saeed Ahmed Hussein Christopher R. Pudney Pierre J. Rizkallah Stephen A. Wells D. Dafydd Jones |
| author_sort | Nehad Noby |
| collection | DOAJ |
| description | Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are important for of EstN7's cold adaptation rather than changes in dynamics. |
| first_indexed | 2024-04-09T15:27:58Z |
| format | Article |
| id | doaj.art-742a9bfe43b248879d57a96a80adc331 |
| institution | Directory Open Access Journal |
| issn | 2046-2441 |
| language | English |
| last_indexed | 2024-04-09T15:27:58Z |
| publishDate | 2021-12-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Open Biology |
| spelling | doaj.art-742a9bfe43b248879d57a96a80adc3312023-04-28T11:06:27ZengThe Royal SocietyOpen Biology2046-24412021-12-01111210.1098/rsob.210182Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanismNehad Noby0Husam Sabah Auhim1Samuel Winter2Harley L. Worthy3Amira M. Embaby4Hesham Saeed5Ahmed Hussein6Christopher R. Pudney7Pierre J. Rizkallah8Stephen A. Wells9D. Dafydd Jones10Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, EgyptSchool of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UKDepartment of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UKSchool of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UKDepartment of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, EgyptDepartment of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, EgyptDepartment of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, EgyptDepartment of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UKSchool of Medicine, Cardiff University, Cardiff CF14 4XN, UKDepartment of Physics, University of Bath, Bath BA2 7AYSchool of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UKHere we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are important for of EstN7's cold adaptation rather than changes in dynamics.https://royalsocietypublishing.org/doi/10.1098/rsob.210182serine esterasemolecular dynamicsenzyme structureprotein stabilitystructure–function |
| spellingShingle | Nehad Noby Husam Sabah Auhim Samuel Winter Harley L. Worthy Amira M. Embaby Hesham Saeed Ahmed Hussein Christopher R. Pudney Pierre J. Rizkallah Stephen A. Wells D. Dafydd Jones Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism Open Biology serine esterase molecular dynamics enzyme structure protein stability structure–function |
| title | Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism |
| title_full | Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism |
| title_fullStr | Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism |
| title_full_unstemmed | Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism |
| title_short | Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism |
| title_sort | structure and in silico simulations of a cold active esterase reveals its prime cold adaptation mechanism |
| topic | serine esterase molecular dynamics enzyme structure protein stability structure–function |
| url | https://royalsocietypublishing.org/doi/10.1098/rsob.210182 |
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