Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin

•Molecular Dynamics (MD) simulations for the Mb-nitrite complexes•Formation of the 2-nitrovinyl species in Mb is associated with motion of helix F.•Coordination of NO2− to heme iron is mainly associated with the motion of helix E.

Myoglobin (Mb) is known to react slowly with nitirite to form the green pigment by NO2− cordination to the heme Fe in the O-binding nitrito (O1NO2) mode and to the heme 2-vinyl position. Nitrite is a powerful oxidizing agent and a biological reservoir for NO that has been implicated in a variety of aerobic biological systems. Accordingly, it is important to elucidate the nature and variety of NO2− reaction mechanisms with Mb. We have performed principal component analysis (PCA, or essential dynamics) on Molecular Dynamics trajectories of all MbNO2 coordination states to resolve the most important motions in the protein at 298 K. We show that the coordination or removal of NO2− to/from the heme iron is associated mainly with a motion of helix E and the coordination of NO2− to the 2-vinyl is associated with a motion of helix F and a correlated motion of helices E-F. This latter correlated motion can be attributed to the interaction of Val68 and Ile107 with the 2-nitrovinyl moiety. The resonance Raman results show that coordination of NO2− to the 2-vinyl is increased at pH 6.0 demonstrating that the amide protons in the F helix are not protected from access of solvent water and the helix F motion allows solvent access to the 2-vinyl group, without affecting the coordination to the heme Fe.

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