The molecular dynamics simulation approach has been effectively employed to determine suitable activity conditions of chymotrypsin (α-CT) within a range of nano-pools. Results from eleven molecular dynamics simulations were presented, which were performed in ten water-AOT-isooctane reverse micelles and a bulk aqueous solution. Half of the RMs are empty, and the other half are loaded with α-CT in their water pools. Each batch of five RMs is studied in five different compositions of 3, 5, 10, 15 and 20 water-to-surfactant concentration ratios (W0) at ambient temperature and pressure. The simulation is not started from generally predefined geometric structures. Our simulations all started from random molecular configurations and then allowed sufficient simulation time for the system to reach equilibrium. The general shapes of RMs without protein cores are elongated ellipsoids at low W0 values and quasi-spherical at higher W0 values, while the overall shapes of RMs with protein cores are quasi-spherical and almost independent of W0 values. Previously published experimental data strongly support the results of our predicted simulated structures and analyzed dynamics. In both the simulated RM and the experimentally well-studied α-CT protein within RM at W0 15, the dynamics and structure closely mirror those of the actual bulk water environment. The shift in behavior was identified that led to the alteration of the protein structure’s activity during the increase in water content of reverse micelles between W0 15 and 20. Overall, the rise in surface area interaction between the protein and nonpolar iso-Octane can be attributed to the reduction in surfactant coverage, causing the transition from W0 15 to 20.

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