Protein simulation in supercritical CO2: The challenge of force field

Abstract

Supercritical CO2 is one of the most important green solvents for biotechnological applications. Due to the high-pressure conditions and gas–liquid properties of the fluid, the structural investigations of the biological macromolecules such as proteins and enzymes in supercritical conditions is problematic. Molecular dynamics simulation has emerged as a good tool to study the molecular-levels phenomena in macromolecule/supercritical CO2 environments. Many unsolved aspects of such systems have been explored by this method in recent years. One of the most important challenges in biomolecular simulations in supercritical CO2 is the applied force field for the bio-macromolecules. Most of simulations in supercritical CO2 have been performed by united-atoms and GROMOS96-based force fields for proteins and enzymes. The reliability of the obtained results should be examined by applying the other protein force fields. There is no comprehensive work about the effect of the force field on a single protein model in supercritical CO2. In this work, I have applied four famous biomolecular force fields including: GROMOS96 (43a1), CHARMM (27), AMBER (03) and OPLS-AA for simulation of chymotrypsin inhibitor 2 as a model protein in supercritical CO2 and also in the aqueous conditions. Different structural properties of protein have been examined using the different force fields. Results show that all of the force fields confirm the structural deviations of the protein structure from its native state in supercritical CO2. GROMOS43a1, similar to the previous simulations, showed the higher flexibility of protein backbone in scCO2 in comparison to the aqueous condition. In contrast, in simulations with all-atom force fields, the protein flexibility was almost identical in two solvents. Simulations by all of the force fields confirm the previously proposed mechanism for protein denaturation in scCO2 which states that the changing of the interaction pattern of protein destabilizes the conformation in supercritical CO2. However, the extent of changes was different among the force fields. While united-atom force field show higher changes and deviations from the native state, all-atom force fields, in agreement with each other, show moderate changes and deviations.