Molecular dynamic study of subtilisin Carlsberg in aqueous and nonaqueous solvents

• Published in: Molecular simulation Vol. 35; no. 3; pp. 205 - 212
• Main Authors: Cruz, Anthony, Ramirez, Eunice, Santana, Alberto, Barletta, Gabriel, López, Gustavo E.
• Format: Journal Article
• Language: English
• Published: Taylor & Francis Group 01-03-2009
• Subjects: enzyme catalysis; enzyme stability; essential waters
• ISSN: 0892-7022; 1029-0435
• DOI: 10.1080/08927020802415670

Using molecular dynamics simulations, we have obtained an important insight into the structural and dynamical changes exerted by a nonaqueous solvent on the serine protease subtilisin Carlsberg. Our findings show that the structural properties of the subtilisin-acetonitrile (MeCN) system were sensitive to the amount of water present at the protein surface. A decrease or lack of water promoted the enzyme-MeCN interaction, which increased structural changes of the enzyme primarily at the surface loops. This effect caused variations on the secondary and tertiary structure of the protein and induced the opening of a pathway for the solvent to the protein core. Also, disturbance of the oxyanion hole was observed due to changes in the orientation in the Asn-155 side chain. The disruption of the oxyanion hole and the changes of the tertiary structure should affect the optimal activity of the enzyme.