The function of most proteins is strictly connected to their structure, which depends on their sequence and external factors, such as the surrounding environment. Interactions of proteins with lipid bilayers, for example, can significantly affect both systems and strongly depend on the lipid composition. This presentation will focus on demonstrating how external factors can impact protein structure and dynamics, examined through molecular dynamics simulations. I will present examples of several protein systems in bulk water, as well as when interacting or embedded into lipid bilayers of various compositions and how environmental conditions and other factors, such as the presence or absence of disulfide bonds, can influence them.