Although there are many interests to use proteins in supercritical CO2, protein destabilization in this solvent is the major drawback. This is because of the non-natural CO2 environment which imposes essential instability on the protein structure. Due to the limitations of the experimental techniques to obtain in situ molecular levels information about protein microstructure at high pressures of the supercritical state, the molecular level reasons of the protein destabilization remains controversial and relatively unknown in supercritical CO2. While there is a consensus about the probable roles of surface lysine residues in destabilization of proteins in supercritical CO2, no clear mechanism is presented about the way that these amino acids impose instabilities on the protein conformation. Here, using molecular dynamics simulations, we extensively examined the structural behavior of the surface lysine residues of chymotrypsin inhibitor 2 as a model protein in supercritical CO2. In this way, a new molecular mechanism is proposed which states that the inappropriate interactions of polar side chain of lysine residues with the non-polar nature of supercritical CO2 enforce these exposed residues to return from the solvent bulk to the protein exterior and also to form new non-native hydrogen bonds with the acidic residues such as glutamic acid. This induces some surface regions to be very labile and dynamics. These regions are the starting sequence in the process of protein denaturation in supercritical CO2. Denaturation is extended by collapsing the structure due to the formation of multiple non-native interactions between different residues. To evaluate the proposed mechanism, surface exposed lysine residues were replaced to leucine amino acids with the hydrophobic side chains. Interestingly, the protein remains intact by this replacement even at 200 bar in supercritical CO2. However, replacing of lysine residues by negatively charged glutamic acid and also by glycine residues cannot prevent protein denaturation process. These molecular levels explorations not only address some unknown aspects of protein denaturation mechanism in supercritical CO2, but it also can essentially help to design new CO2-tolerant proteins which can be used in popular processes such as biocatalysis in supercritical CO2.