Abstract
Brownian dynamics simulation has been applied to analyze the influence of the electrostatic field of a reverse micelle on the enzyme-substrate complex formation inside a micelle. The probability that the enzyme-substrate complex will form from serine protease (trypsin) and the specific hydrophilic cationic substrate Nα-benzoyl-l-arginine ethyl ester has been studied within the framework of the encounter complex formation theory. It has been shown that surfactant charge, dipole moments created by charged surfactant molecules and counterions, and permittivity of the inner core of reverse micelles can all be used as regulatory parameters to alter the substrate orientation near the active site of the enzyme and to change the probability that the enzyme-substrate complex will form.
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Acknowledgments
Authors are very grateful to Dr. S. Northrup for providing us with the MacroDox program. The support of the Russian Academy of Sciences under the programme “Molecular and Cellular Biology” is acknowledged. Calculations were carried out at the Supercomputer Centre of the Kazan Scientific Centre of the Russian Academy of Sciences.
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Ermakova, E.A., Zakhartchenko, N.L. & Zuev, Y.F. Brownian dynamics simulation of substrate motion near active site of enzyme entrapped inside reverse micelle. Eur Biophys J 39, 1335–1341 (2010). https://doi.org/10.1007/s00249-010-0586-y
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DOI: https://doi.org/10.1007/s00249-010-0586-y