Structure and dynamics of Candida rugosa lipase: the role of organic solvent
The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the...
| Huvudupphovsmän: | , , |
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| Materialtyp: | Artikel |
| Språk: | English English |
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Springer
2004
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| Ämnen: | |
| Länkar: | http://psasir.upm.edu.my/id/eprint/18401/1/Structure%20and%20dynamics%20of%20Candida%20rugosa%20lipase.pdf |
| _version_ | 1825946185194536960 |
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| author | Tejo, Bimo Ario Salleh, Abu Bakar Pleiss, Juergen |
| author_facet | Tejo, Bimo Ario Salleh, Abu Bakar Pleiss, Juergen |
| author_sort | Tejo, Bimo Ario |
| collection | UPM |
| description | The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (Cα rms deviation 1-1.3 Å). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 Å, organic solvent reduced flexibility to 0.9 Å. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. © Springer-Verlag 2004. |
| first_indexed | 2024-03-06T07:43:06Z |
| format | Article |
| id | upm.eprints-18401 |
| institution | Universiti Putra Malaysia |
| language | English English |
| last_indexed | 2024-03-06T07:43:06Z |
| publishDate | 2004 |
| publisher | Springer |
| record_format | dspace |
| spelling | upm.eprints-184012016-01-21T03:48:00Z http://psasir.upm.edu.my/id/eprint/18401/ Structure and dynamics of Candida rugosa lipase: the role of organic solvent Tejo, Bimo Ario Salleh, Abu Bakar Pleiss, Juergen The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (Cα rms deviation 1-1.3 Å). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 Å, organic solvent reduced flexibility to 0.9 Å. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. © Springer-Verlag 2004. Springer 2004-12 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/18401/1/Structure%20and%20dynamics%20of%20Candida%20rugosa%20lipase.pdf Tejo, Bimo Ario and Salleh, Abu Bakar and Pleiss, Juergen (2004) Structure and dynamics of Candida rugosa lipase: the role of organic solvent. Journal of Molecular Modeling, 10 (5-6). pp. 358-366. ISSN 1610-2940 http://dx.doi.org/10.1007/s00894-004-0203-z Candida rugosa Lipase - chemistry Organic solvents doi:10.1007/s00894-004-0203-z English |
| spellingShingle | Candida rugosa Lipase - chemistry Organic solvents Tejo, Bimo Ario Salleh, Abu Bakar Pleiss, Juergen Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title | Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title_full | Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title_fullStr | Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title_full_unstemmed | Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title_short | Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
| title_sort | structure and dynamics of candida rugosa lipase the role of organic solvent |
| topic | Candida rugosa Lipase - chemistry Organic solvents |
| url | http://psasir.upm.edu.my/id/eprint/18401/1/Structure%20and%20dynamics%20of%20Candida%20rugosa%20lipase.pdf |
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