Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3

In the cytochrome P450BM-3, the flavin mononucleotide (FMN) binding domain is an intermediate electron donor between the flavin adenine dinucleotide (FAD) binding domain and the HEME domain. Experimental evidence has shown that different redox states of FMN cofactor were found to induce conformational changes in the FMN domain. Herein, molecular dynamics (MD) simulation is used to gain insight into the latter phenomenon at the atomistic level. We have studied the effect of FMN cofactor and its redox states (oxidized and reduced) on the structure and dynamics of the FMN domain. The results of our study show significant differences in the atomic fluctuation amplitude of the FMN domain in both holo- and apoprotein. The change in the protonation state of FMN cofactor mostly affects its binding in holo-protein. In particular, the loops involved in the binding of the isoalloxazine ring (Lβ4) and ribityl side chain (Lβ1) adopt different conformations in both reduced and oxidized states. In addition, the reduced FMN cofactor mainly induces a conformational change in Trp574 residue (Lβ4) that is essential for controlling electron transfer (ET) within P450BM-3 domains. The structure of the apoprotein in solution remains mostly unchanged with respect to the crystal structure of the holo-protein. However, FMN binding loops were more flexible in apoprotein that might favor the rebinding of FMN cofactor. In the holo-protein simulation, the largest conformational changes in FMN cofactor are caused by the ribityl side chain. The isoalloxazine ring of FMN cofactor remains almost planar (∼177°) in the oxidized state and bends along the N5-N10 axis at an angle of ∼160° in the reduced state. The collective modes of the isoalloxazine ring were identical in both protonation states of FMN cofactor except the first eigenvector. In the reduced state, the isoalloxazine ring attains the butterfly motion as a dominant collective motion in the first eigenvector due to the bending along the N5-N10 axis.