Fig. 7: The results of normal mode analysis (NMA).
From: Key role of quinone in the mechanism of respiratory complex I
Both lowest-frequency modes, mode 7 a and mode 8 b, bending and rotation respectively, are observed experimentally. The overlap analysis c shows that transitions to CXIDQ conformation involve a large contribution of rotational motions (mostly mode 8 plus some additional modes), which is not the case for transitions between unliganded conformations, the CXIINT → CXIMN and CXIMN → CXIMJ. The CXIINT → CXIMJ transition features no bending motion (mode 7) at all, but residual, localized rotational motions of higher frequency. The results of deformation analysis d identify the most flexible parts of complex I: the long loop of the Nqo7 subunit at the junction between PA and MD, as well as part of Nqo12 traverse helix HL, both involved in almost all of the first 20 motions (modes), which characterize the essential dynamics of complex I. The inset shows the view from PA.
