Structural Identification of Spectroscopic Substates in Neuroglobin

The structural origins of infrared absorptions of photodissociated CO in murine neuroglobin (Ngb) are determined by combining Fourier transform infrared (FTIR) spectroscopy and molecular dynamics (MD) simulations. Such an approach allows to identify and characterize both the different conformations of the Ngb active site and the transient ligand docking sites. To capture the influence of the protein environment on the spectroscopy and dynamics, experiments and simulations are carried out for the wild type protein and its F28L and F28W mutants. It is found that a voluminous side chain at position 28 divides site B into two subsites, B’ and B”. At low temperatures, CO in wt Ngb only migrates to site B’ from where it can rebind, and B” is not populated. The spectra of CO in site B’ for wt Ngb from simulations and experiments are very similar in spectral shift and shape. They both show doublets, red-shifted with respect to gas-phase CO and split by≈8 cm−1. The FTIR spectra of the F28L mutant show additional bands which are also found in the simulations and can be attributed to CO located in substate B”. The different bands are mainly related to different orientations of the His64 side chain with respect to the CO ligand. Large red-shifts arise from strong interactions between the Histidine[BOND]NH and the CO oxygen. After dissociation from the heme iron, the CO ligand visits multiple docking sites. The locations of the primary docking site B and a secondary site C, which corresponds to the Mb Xe4 cavity, could be identified unambiguously. Finally, by comparing experiment and simulations it is also possible to identify protonation of its ε position (Hisε64 NgbCO) as the preferred heme-bound conformation in the wild type protein with a signal at 1935 cm−1.