First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO

Abstract

Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.

Spin‐inversion mechanisms in O2 binding to a model heme complex revisited by density function theory calculations

“…Many theoretical studies have investigated atomic‐level spin‐inversion mechanisms in O 2 binding with a simplified model heme, namely, a Fe(II)‐porphyrin complex with a proximal imidazole or a related ligand . These theoretical studies have shown that the electronic ground state of the Fe(II)‐porphyrin complex with a d 6 configuration is a quintet spin state and that the second lowest spin state is a triplet state, although the energy difference between these spin states is very small .…”

Gas Sensing by Bacterial H-NOX Proteins: An MD Study

“…A wide variety of experimental techniques (e.g., site-directed mutagenesis, EPR and Xe-binding X-ray diffraction) have been exploited to describe gas migration in the protein matrix [ 20 , 24 , 25 , 26 ]. Theoretical approaches, such as molecular dynamics (MD) simulations can provide complementary information on the dynamics of gas permeation through the protein matrix to obtain a full molecular-scale understanding of ligand transport [ 21 , 22 , 26 , 27 ]. First, we aimed at identifying those regions of the proteins that are most sensitive to gas ligand permeation.…”

“…We recently developed and validated against experimental results a three-state kinetic model for the study of ligand diffusion [ 22 ] that is much simpler than the complex Markov model used by Blumberger et al [ 30 , 31 , 32 ]. The model groups the instantaneous position of the ligands into three different categories: in the solvent phase, protein matrix or distal pocket ( Figure 3 ).…”

“…Depending on the relative values of k 1 , k −1 , k 2 and k −2 , the bottleneck of the reactions can be determined. For example, in the case of myoglobin, we showed that diffusion is rate-limiting in the case of NO binding, while for CO binding both processes are partially rate-limiting and influence the overall value of k on [ 22 ]. In contrast to binding, bond scission is the rate-limiting step of ligand release in all cases, as a consequence, no agreement between k −1 and k off can be expected.…”

“…We recently developed a multiscale model for the theoretical description of the CO and NO ligand-binding events of myoglobin, another histidine-ligated Fe(II)-heme protein and obtained very good agreement between calculated and measured rate constants [ 22 ]. A meaningful characterization of the overall process can be obtained by using a classical approach for the study of ligand diffusion and, in a separate step, quantum mechanical approach for bond formation between the ligand and the iron(II) center, which is a significant factor for the stabilization of the ligand in the distal pocket ( Figure 1 ).…”