Ferric and Ferrous Iron in Nitroso‐Myoglobin: Computer Simulations of Stable and Metastable States and Their Infrared Spectra

Abstract

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O(2), which only bind to ferrous (Fe(II)) iron, NO binds to both ferrous and ferric (Fe(III)) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ab initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta(1)-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe(II)-NO, which exhibits only two minima (the eta(2) coordination mode for Fe(II) is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe(III) than for Fe(II). We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.

Atomistic simulations of reactive processes in the gas- and condensed-phase

“…For rapid rebinding, p(d) has a broad maximum between 0.2 and 0.3 Å whereas for slower rebinding the maximum in p(d) shifts to 0.33 Å which agrees quite well with results from X-ray crystallography [166]. Apart from the previously considered relative orientation of the NO ligand to the heme-iron [150,152,153,158,167,168], the iron-out-of-plane (doming) coordinate will be explicitly considered. Recent time-resolved resonance Raman experiments suggested that the photodissociated ligand can rebind to the domed, Fe-out-of-plane conformation of the heme unit [156].…”

“…The Fe-ON minimum determined on the d ¼ À 0.2 Å surface located % 21.5 kcal/mol above the global Fe-NO minimum, is, however, shifted toward smaller values of (%120 ), with a geometry resembling more the metastable Fe-NO described previously [153]. Fe-NO transition is %3 kcal/mol.…”

“…Interactions of myoglobin and its mutants with NO have been studied experimentally and theoretically for almost four decades now [15,16,126,[144][145][146][147][148][149][150][151][152][153][154][155][156][157][158]. Experiment [147,159] has shown that the rebinding of NO to Mb features non-exponential kinetics at all temperatures.…”

“…Fe-NO transition is %3 kcal/mol. Classical MD simulations were performed using CHARMM [170] with the CHARMM22 force field [171] supplemented with parameters described earlier [153]. The Fe-ON minimum determined on the d ¼ À 0.2 Å surface located % 21.5 kcal/mol above the global Fe-NO minimum, is, however, shifted toward smaller values of (%120 ), with a geometry resembling more the metastable Fe-NO described previously [153].…”

The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase

“…39 This engenders interactions between the NO and the distal histidine in myoglobin that occur through a lone pair donation mechanism rather than a hydrogen bond leading to an upshift of the frequency. 45 In the case of substrate-free HRP, although a distal histidine residue is present in the active site, it has been shown to be more distant from the haem than would be required for direct interaction.…”