title: Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin.
abstract: 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 MbNO2coordination states to resolve the most important motions in the protein at 298K. 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 pH6.0 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.
authors.affiliation: Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
authors.forename: Androulla
authors.initials: A
authors.lastname: Ioannou
authors.affiliation: Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Lambrou
authors.affiliation: Department of Environmental Science and Technology, Cyprus University of Technology, 3603 Lemessos, Cyprus. Electronic address: evangelos.daskalakis@cut.ac.cy.
authors.forename: Vangelis
authors.initials: V
authors.lastname: Daskalakis
authors.affiliation: Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus. Electronic address: effiep@ucy.ac.cy.
authors.forename: Eftychia
authors.initials: E
authors.lastname: Pinakoulaki
mesh_terms: D000818:Animals; D001665:Binding Sites; D006418:Heme / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D009573:Nitrites / Q000737:chemistry*; D025341:Principal Component Analysis; D017433:Protein Structure, Secondary; D013059:Spectrum Analysis, Raman
chemical_list: D009211:Myoglobin; D009573:Nitrites; D006418:Heme
keywords: Heme proteins; Molecular Dynamics; Nitrite; Raman spectroscopy