Structure and dynamics of Candida rugosa lipase: the role of organic solvent |
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Authors: | Bimo Ario Tejo Abu Bakar Salleh Juergen Pleiss |
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Institution: | (1) Department of Biochemistry and Microbiology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia;(2) Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia;(3) Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany |
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Abstract: | 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 (C 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.
Figure Superimposition of open (black, PDB entry 1CRL) and closed (gray, PDB entry 1TRH) conformers of C. rugosa lipase. The mobile lid is indicated This revised version was published online in October 2004 with corrections to the Graphical Abstract. |
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Keywords: | Lipase Lid movement Molecular dynamics simulation Organic solvent |
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