Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins:- Protein Structure Affects How Ligands Bind
The binding of a ligand to a protein is rarely as simple as the above equations would suggest. The interaction is greatly affected by protein structure and is often ac companied by conformational changes. For example, the specificity with which heme binds its various ligands is altered when the heme is a component of myoglobin. Carbon monoxide binds to free heme molecules more than 20,000 times better than does O2 (that is, the Kd or P50 for CO binding to free heme is more than 20,000 times lower than that for O2), but it binds only about 200 times better when the heme is bound in myoglobin. The difference may be partly explained by steric hindrance. When O2 binds to free heme, the axis of the oxy gen molecule is positioned at an angle to the Fe-O bond (Fig. 5–5a). In contrast, when CO binds to free heme, the Fe, C, and O atoms lie in a straight line (Fig. 5–5b). In both cases, the binding reflects the geometry of hybrid orbitals in each ligand. In myoglobin, His64 (His E7), on the O2-binding side of the heme, is too far away to coordinate with the heme iron, but it does interact with a ligand bound to heme. This residue, called the distal His, does not affect the binding of O2 (Fig. 5–5c) but may preclude the linear binding of CO, providing one explanation for the diminished binding of CO to heme in myoglobin (and hemoglobin). A reduction in CO binding is physiologically important, because CO is a low-level byproduct of cellular metabolism. Other factors, not yet well-defined, also seem to modulate the inter action of heme with CO in these proteins. The binding of O2 to the heme in myoglobin also de pends on molecular motions, or “breathing,” in the protein structure. The heme molecule is deeply buried in the folded polypeptide, with no direct path for oxygen to move from the surrounding solution to the ligand binding site. If the protein were rigid, O2 could not enter or leave the heme pocket at a measurable rate. How ever, rapid molecular flexing of the amino acid side chains produces transient cavities in the protein structure, and O2 evidently makes its way in and out by moving through these cavities. Computer simulations of rapid structural fluctuations in myoglobin suggest that there are many such pathways. One major route is provided by rotation of the side chain of the distal His (His64), which occurs on a nanosecond (10-9 s) time scale. Even subtle conformational changes can be critical for protein activity.
