After the reaction, the products must leave the protein. The substrate, an oxygen molecule, and the catalyzed products are transferred via different pathways. Thus, the pathways for substrate access and product export play a significant role in the catalysis of P450. Although the mechanism of channel opening is not completely clear at present, multiple active site access channels have been identified in the P450 proteins of different species with different functional states. The movement of two secondary structure elements, the B-C and F-G loops are essential for channel opening, which border a few channels and act as hinged lids on the conformations of channels. Recent studies have suggested that electron transfer partner protein binding influences the global motion of P450 by changing the motion in the F-G loop region. In addition, increasing the flexibility or variation of length of the B-C loop also affects the opening of relative channels. However, the detailed regulation mechanism of the F-G and B-C loops is unclear. The enzymes CYP82E4 and CYP82E3, which have high sequence identity but different activities, provide a good example for studying the mediation mechanism of complex channel systems. Thus, four distinct homology models for CYP82E4, CYP82E3, and their cys–trp mutants were constructed to gain a structural insight into their functional mechanism. Six separate molecular dynamics simulations were performed on CYP82E4, CYP82E3, and their mutants at 300 K, as well as on the wild-type and the mutant for CYP82E4 at 330 K, which improves the reliability of the study. The conformational behaviors of these proteins in both the active and inactive state are analyzed. The transfer channels of CYP82E4 and CYP82E3 are detected in two distinct states. Interestingly, analysis of the MD simulation results BAY-60-7550 suggests that helix I may mediate the flexibility of the F-G and B-C loops. This study provides new insight into understanding the functional mechanism of P450 proteins. Overall, this suggests that the monooxygenase reaction of P450 requires that the pathways for substrate access, product egress, and water egress to be open coordinately, which is consistent with the P450 mechanism mentioned in the introduction. It also shows that the mutation affects the channel openingclosing movement by altering the motion of the F-G and B-C loops. However, a question arises regarding how the mutation site affects the motion of the F-G and B-C loops. TRAPPC4, the human ortholog of yeast Trs23p, also known as synbindin.