Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method
The thermoalkalophilic lipase from B. stearothermophilus L1 (L1 lipase) is one of the well characterized lipase. The mature form of L1 lipase, which consists of 388 amino acids (43 kDa) is highly thermostable and has the unfolding temperature of 74 °C. In addition to the thermostability, L1 lipase e...
| Main Authors: | , , , , |
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| Format: | Conference or Workshop Item |
| Language: | English |
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2007
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| Online Access: | http://psasir.upm.edu.my/id/eprint/8775/1/ID%208775.pdf |
| _version_ | 1796967597858619392 |
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| author | Abdul Rahman, Mohd Basyaruddin Abedikargiban, Roghayeh Basri, Mahiran Raja Abdul Rahman, Raja Noor Zaliha Salleh, Abu Bakar |
| author_facet | Abdul Rahman, Mohd Basyaruddin Abedikargiban, Roghayeh Basri, Mahiran Raja Abdul Rahman, Raja Noor Zaliha Salleh, Abu Bakar |
| author_sort | Abdul Rahman, Mohd Basyaruddin |
| collection | UPM |
| description | The thermoalkalophilic lipase from B. stearothermophilus L1 (L1 lipase) is one of the well characterized lipase. The mature form of L1 lipase, which consists of 388 amino acids (43 kDa) is highly thermostable and has the unfolding temperature of 74 °C. In addition to the thermostability, L1 lipase exhibits a unique thermoactivity, by which the enzyme is most active at 68 °C for the hydrolysis of olive oil. The thermostability and thermoactivity of L1 lipase are critically important for many industrial applications because the industrial lipase reactions often require high temperatures (50–80 °C) due to the high melting points of some lipids (Jeong et al., 2002). Here, the thermal behavior of L1 lipase was probed using all-atom molecular dynamics simulations. The crystal structure of L1 lipase in the closed conformation (entry code 1ku0), was taken from Protein Data Bank which resolved to 2.0 Å and Chain A of the crystal structure was selected as the starting structure. We have traditionally relied on extremely elevated temperatures (500 K) to investigate the unfolding process of this structure within the timescale available to molecular dynamics simulations with explicit solvent. We performed three independent but continuous molecular dynamics simulations of L1 lipase in water at 300 K (1 ns as a control), 400 K (4 ns), and 500 K (4 ns). Later on, we probed the unfolding pathway of L1 lipase at elevated temperature by calculating the evolution of structural properties over time. The structural properties that we looked at were Cα-root-mean-square deviation (RMSd), Cα-root-mean-square fluctuation (RMSf), hydrophobic solvent accessible surface area (SASA), and tertiary interaction (contact map analysis). These properties on their own tell us relatively little about the unfolding pathway; however, when considering against each other, they become powerful tools for dissecting L1 lipase’s unfolding mechanism.
Root meant square deviation (RMSd) from the starting structure and root mean square fluctuation (RMSf) per residue number at 400 K and 500 K was computed and the results were plotted in Figure 1(a) and (b). The average Cα-RMSd at 400 K and 500 K was 2.25 Å (± 0.29) and 4.02 Å (± 0.97), respectively. The average RMSf was 1.24 Å (± 0.57) at 400 K and 2.47 Å (± 1.41) at 500 K. The RMSf average value indicated that there was a noticeable flexibility at 500 K. Dynamics at 500 K reveal a heterogeneous distribution of structural flexibilities in comparison with 400 K. |
| first_indexed | 2024-03-06T07:16:13Z |
| format | Conference or Workshop Item |
| id | upm.eprints-8775 |
| institution | Universiti Putra Malaysia |
| language | English |
| last_indexed | 2024-03-06T07:16:13Z |
| publishDate | 2007 |
| record_format | dspace |
| spelling | upm.eprints-87752016-09-27T07:35:17Z http://psasir.upm.edu.my/id/eprint/8775/ Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method Abdul Rahman, Mohd Basyaruddin Abedikargiban, Roghayeh Basri, Mahiran Raja Abdul Rahman, Raja Noor Zaliha Salleh, Abu Bakar The thermoalkalophilic lipase from B. stearothermophilus L1 (L1 lipase) is one of the well characterized lipase. The mature form of L1 lipase, which consists of 388 amino acids (43 kDa) is highly thermostable and has the unfolding temperature of 74 °C. In addition to the thermostability, L1 lipase exhibits a unique thermoactivity, by which the enzyme is most active at 68 °C for the hydrolysis of olive oil. The thermostability and thermoactivity of L1 lipase are critically important for many industrial applications because the industrial lipase reactions often require high temperatures (50–80 °C) due to the high melting points of some lipids (Jeong et al., 2002). Here, the thermal behavior of L1 lipase was probed using all-atom molecular dynamics simulations. The crystal structure of L1 lipase in the closed conformation (entry code 1ku0), was taken from Protein Data Bank which resolved to 2.0 Å and Chain A of the crystal structure was selected as the starting structure. We have traditionally relied on extremely elevated temperatures (500 K) to investigate the unfolding process of this structure within the timescale available to molecular dynamics simulations with explicit solvent. We performed three independent but continuous molecular dynamics simulations of L1 lipase in water at 300 K (1 ns as a control), 400 K (4 ns), and 500 K (4 ns). Later on, we probed the unfolding pathway of L1 lipase at elevated temperature by calculating the evolution of structural properties over time. The structural properties that we looked at were Cα-root-mean-square deviation (RMSd), Cα-root-mean-square fluctuation (RMSf), hydrophobic solvent accessible surface area (SASA), and tertiary interaction (contact map analysis). These properties on their own tell us relatively little about the unfolding pathway; however, when considering against each other, they become powerful tools for dissecting L1 lipase’s unfolding mechanism. Root meant square deviation (RMSd) from the starting structure and root mean square fluctuation (RMSf) per residue number at 400 K and 500 K was computed and the results were plotted in Figure 1(a) and (b). The average Cα-RMSd at 400 K and 500 K was 2.25 Å (± 0.29) and 4.02 Å (± 0.97), respectively. The average RMSf was 1.24 Å (± 0.57) at 400 K and 2.47 Å (± 1.41) at 500 K. The RMSf average value indicated that there was a noticeable flexibility at 500 K. Dynamics at 500 K reveal a heterogeneous distribution of structural flexibilities in comparison with 400 K. 2007-08-05 Conference or Workshop Item NonPeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/8775/1/ID%208775.pdf Abdul Rahman, Mohd Basyaruddin and Abedikargiban, Roghayeh and Basri, Mahiran and Raja Abdul Rahman, Raja Noor Zaliha and Salleh, Abu Bakar (2007) Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method. In: 41st IUPAC World Chemistry Congress, 5-10 Aug. 2007, Torino, Italy. (pp. 1-2). Lipase Molecular dynamics |
| spellingShingle | Lipase Molecular dynamics Abdul Rahman, Mohd Basyaruddin Abedikargiban, Roghayeh Basri, Mahiran Raja Abdul Rahman, Raja Noor Zaliha Salleh, Abu Bakar Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title | Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title_full | Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title_fullStr | Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title_full_unstemmed | Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title_short | Thermal behavioral analysis of bacillus stearothermophilus L1 lipase at elevated temperature by molecular dynamics simulation method |
| title_sort | thermal behavioral analysis of bacillus stearothermophilus l1 lipase at elevated temperature by molecular dynamics simulation method |
| topic | Lipase Molecular dynamics |
| url | http://psasir.upm.edu.my/id/eprint/8775/1/ID%208775.pdf |
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