Free energy profiles were calculated for the reduction of the four disulfide bridges in lysozyme by tris(2-carboxyethyl)phosphine (TCEP). The computational method combines high-precision density functional theory (DFT) calculations performed on the core of the reactant system with classical mechanical free energy evaluations based on the sampling of the configuration space of reaction environment. The predicted reaction energy barriers are in satisfactory agreement with experimental data, proving that the present method provides a reliable description of the mechanism of reaction. The role of the protein environment in this mechanism is further emphasized by analyzing the different contributions to the free energy profiles. It is shown that the protein environment affects the reaction by three factors: polarizability, steric hindrance of the reactant site, and S-S bridge distortion due to structural constraints. The corresponding effects are quantitatively evaluated, and the results are discussed in connection with the current two-step reaction model for the reduction of S-S bridges in proteins.