Molecular dynamics simulation of nitric oxide in myoglobin
Journal of Physical Chemistry
By: Myung Won Lee and Markus Meuwly
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Abstract
The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm–1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm–1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is ΔGB→C = 1.7–2.0 kcal/mol. The reverse barrier is ΔGB←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.
Suggested Citation
Lee, M.W., and Meuwly, M., 2012, Molecular dynamics simulation of nitric oxide in myoglobin: Journal of Physical Chemistry, v. 116, no. 14, p. 4154-4162, https://doi.org/10.1021/jp212112f.
| Publication type | Article |
|---|---|
| Publication Subtype | Journal Article |
| Title | Molecular dynamics simulation of nitric oxide in myoglobin |
| Series title | Journal of Physical Chemistry |
| DOI | 10.1021/jp212112f |
| Volume | 116 |
| Issue | 14 |
| Publication Date | March 28, 2012 |
| Year Published | 2012 |
| Language | English |
| Publisher | American Chemical Society |
| Publisher location | Easton, PA |
| Description | 9 p. |
| Larger Work Type | Article |
| Larger Work Subtype | Journal Article |
| Larger Work Title | Journal of Physical Chemistry |
| First page | 4154 |
| Last page | 4162 |