Molybdenum disulfide (MoS2) has recently emerged as a promising nanomaterial in a wide range of applications due to its unique and impressive properties. For example, MoS2 has gained attention in the biomedical field because of its ability to act as an antibacterial and anticancer agent. However, the potential influence of this exciting nanomaterial on biomolecules is yet to be extensively studied. Molecular dynamics (MD) simulations are invaluable tools in the examination of protein interactions with nanomaterials such as MoS2. Previous protein MD studies have employed MoS2 force field parameters which were developed to accurately model bulk crystal structures and thermal heat transport but may not necessarily be amendable to its properties at the interface with biomolecules. By adopting a newly developed MoS2 force field, which was designed to better capture its interaction with water and proteins, we have examined the changes in protein structures between the original and refitted MoS2 force field parameters of three representative proteins, polyalanine (α-helix), YAP65 WW-domains (β-sheet), and HP35 (globular protein) when adsorbed onto MoS2 nanomaterials. We find that the original force field, with much larger van der Waals (vdW) contributions, resulted in more dramatic protein structural damage than the refitted parameters. Importantly, some denaturation of the protein tertiary structure and the local secondary structure persisted with the refitted force field albeit overall less severe MoS2 denaturation capacity was found. This work suggests that the denaturation ability of MoS2 to the protein structure is not as dire as previously reported and provides noteworthy findings on the dynamic interactions of proteins with this emergent material.