Ligand Dynamics in Myoglobin: Calculation of Infrared Spectra for Photodissociated NO

Abstract

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Hyperconjugation

“…As early as 1937, it was found that a linear relationship exists between H‐bond strength and the shift in the IR H–X stretching frequency, termed the Badger–Bauer rule (Figure ) . The qualitative correlation between H‐bond strengths and stretching frequencies has been observed in many chemical systems . Although a single linear relationship does not hold throughout the many diverse types of H‐bonding, satisfactory linear correlations between enthalpy of H‐bond formation, the IR stretching frequency shift, and the X–H bond elongation were found for structurally related compounds …”

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

“…FPCs have proved to be useful to describe the electron density as a molecule undergoes conformational changes 34 and to reproduce up to the quadrupole moment in diatomic molecules. 29,49,50 The nuclear charges are a function of the coordinate of interest, which is the CF bond length in the present case. From the electronic structure calculations for the CF-Morse potential described above, nuclear charges are fitted to the electrostatic field.…”

Coupled protein–ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks

“…The CHARMM22 forcefield [12] is used for the protein while the NO and O 2 parametrizations are those from previous work [13,14]. The TIP3P model is used for water [15].…”