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Mechanism of hydrogen cyanide binding to myoglobin
Y Dou1, J S Olson, A J Wilkinson
1Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-4970, USA.
Insights
Cyanide binds slowly to myoglobin due to distal pocket constraints, not ligand entry. Water displacement and internal acidity, not direct histidine interactions, primarily control cyanide affinity.
Area of Science:
- Biochemistry
- Protein Dynamics
- Ligand Binding Kinetics
Background:
- Myoglobin (Mb) is a crucial oxygen-binding protein.
- Cyanide (CN-) binding to Mb is notably slower than other ligands.
- The distal pocket's role in ligand kinetics is under investigation.
Purpose of the Study:
- To elucidate the rate-limiting steps in cyanide binding to myoglobin.
- To investigate the influence of distal pocket mutations on ligand kinetics.
- To identify key factors governing cyanide affinity in myoglobin.
Main Methods:
- Site-directed mutagenesis of key distal pocket residues (His64, Phe46) in myoglobin.
- Kinetic analysis of cyanide and azide binding/dissociation rate constants.
- Characterization of metmyoglobin variants.
Main Results:
- Mutations affecting solvent access or distal histidine mobility minimally impacted cyanide association rates.
- These mutations significantly increased azide binding rates, indicating diffusion limitation for azide.
- Cyanide dissociation rates were insensitive to mutations at position 64, unlike azide.
- Water displacement, internal acidity (K*a), and pocket polarity were key determinants of cyanide affinity.
Conclusions:
- Cyanide binding to myoglobin is limited by bond formation/disruption, not ligand diffusion.
- Distal pocket polarity and internal acidity (K*a) are critical for cyanide affinity.
- Direct hydrogen bonding by distal histidine is not a major factor for cyanide stabilization.
Abstract:
Cyanide binding to myoglobin is much slower than that of other ferric and ferrous ligands, suggesting rate limitation by bond formation and disruption within the distal pocket. This interpretation is supported by two key experimental observations. First, His64(E7) to Gly and Ala mutations, which open a direct channel from the solvent to the iron atom, and Phe46(CD4) to Leu, Ile, and Val mutations, which increase the mobility of the distal histidine, have little effect on the association rate constant for cyanide binding. In contrast, these mutations cause 100-1000-fold increases in the rate constant for azide binding, showing convincingly that the binding of this ligand is limited by the rate of its movement into the protein. Second, the rate constant for cyanide dissociation is unaffected by changing the size of the residue at position 64(E7) in the series Gly, Val, Leu, Ile, Phe, whereas there is a 2000-fold decrease in the rate of azide dissociation in going from Gly64 to Phe64 metmyoglobin. The major determinants of the cyanide affinity are the ease of water displacement from the ferric iron atom in metmyoglobin, the acid dissociation constant of HCN inside the protein (K*a), and steric hindrance and electrostatic interactions at the sixth coordination position. Direct hydrogen bonding to the distal histidine does not appear to play an important role in stabilizing bound cyanide. Instead, the general polarity of the distal pocket and its effect on K*a are the key factors regulating cyanide affinity under physiological conditions.