8885ac05_157-1898/12/038:55 AM Page162mac78mac78:385 162 Part I Structure and Catalysis 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 Fe Is greatly affected by protein structure and is often ac- (a) 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 Pso 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 hin- Phe cD1 drance. When Oe binds to free heme, the axis of the oxy- gen molecule is positioned at an angle to the Fe-0 bond val ell( (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 hy brid orbitals in each ligand In myoglobin, His(His E7 on the Oo-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 His F 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 bind- ing is physiologically important, because Co is a lot level byproduct of cellular metabolism. Other factors not yet well-defined, also seem to modulate the inter- FIGURE 5-5 Steric effects on the binding of ligands to the heme of action of heme with CO in these proteins myoglobin. (a) Oxygen binds to heme with the O2 axis at an angle, The binding of O2 to the heme in myoglobin also de- a binding conformation readily accommodated by myoglobin. (b)Car- pends on molecular motions, or "breathing, "in the pro- bon monoxide binds to free heme with the CO axis perpendicular tein structure. The heme molecule is deeply buried in the plane of the porphyrin ring. When binding to the heme in myo- the folded polypeptide, with no direct path for oxyge globin, CO is forced to adopt a slight angle because the perpendicu to move from the surrounding solution to the ligand lar arrangement is sterically blocked by His E7, the distal His. This ef- binding site. If the protein were rigid, O, could not en- fect weakens the binding of co to myoglobin. (c) Another view ter or leave the heme pocket at a measurable rate How- ever, rapid molecular flexing of the amino acid side acid residues around the heme of myoglobin. The bound Oz is hy chains produces transient cavities in the protein struc- drogen-bonded to the distal His, His E7(His), further facilitating the ture, and Oe evidently makes its way in and out by mov- ing through these cavities. Computer simulations of rapid structural fluctuations in myoglobin suggest that there are many such pathways. One major route is pro- the maturation process, the stem cell produces daugh- vided by rotation of the side chain of the distal His ter cells that form large amounts of hemoglobin and then (His), which occurs on a nanosecond (10s) time lose their intracellular organelles--nucleus, mitochon- scale. Even subtle conformational changes can be criti dria, and endoplasmic reticulum Erythrocytes are thus cal for protein activity incomplete, vestigial cells, unable to reproduce and, in humans, destined to survive for only about 120 days. Oxygen Is Transported in Blood by Hemoglobin Their main function is to carry hemoglobin, which is dis solved in the cytosol at a very high concentration (-34% 9 Oxygen-Binding Proteins-Hemoglobin: Oxygen Transport by weight) Nearly all the oxygen carried by whole blood in animals In arterial blood passing from the lungs through the is bound and transported by hemoglobin in erythrocytes heart to the peripheral tissues, hemoglobin is about 96% (red blood cells). Normal human erythrocytes are small saturated with oxygen. In the venous blood returning to (6 to 9 um in diameter), biconcave disks. They are formed the heart, hemoglobin is only about 64% saturated. Thus from precursor stem cells called hemocytoblasts. In each 100 mL of blood passing through a tissue releasesProtein 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 hin￾drance. When O2 binds to free heme, the axis of the oxy￾gen molecule is positioned at an angle to the FeOO 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 hy￾brid 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 bind￾ing 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 pro￾tein 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 en￾ter 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 struc￾ture, and O2 evidently makes its way in and out by mov￾ing through these cavities. Computer simulations of rapid structural fluctuations in myoglobin suggest that there are many such pathways. One major route is pro￾vided by rotation of the side chain of the distal His (His64), which occurs on a nanosecond (109 s) time scale. Even subtle conformational changes can be criti￾cal for protein activity. Oxygen Is Transported in Blood by Hemoglobin Oxygen-Binding Proteins—Hemoglobin: Oxygen Transport Nearly all the oxygen carried by whole blood in animals is bound and transported by hemoglobin in erythrocytes (red blood cells). Normal human erythrocytes are small (6 to 9 m in diameter), biconcave disks. They are formed from precursor stem cells called hemocytoblasts. In the maturation process, the stem cell produces daugh￾ter cells that form large amounts of hemoglobin and then lose their intracellular organelles—nucleus, mitochon￾dria, and endoplasmic reticulum. Erythrocytes are thus incomplete, vestigial cells, unable to reproduce and, in humans, destined to survive for only about 120 days. Their main function is to carry hemoglobin, which is dis￾solved in the cytosol at a very high concentration (~34% by weight). In arterial blood passing from the lungs through the heart to the peripheral tissues, hemoglobin is about 96% saturated with oxygen. In the venous blood returning to the heart, hemoglobin is only about 64% saturated. Thus, each 100 mL of blood passing through a tissue releases 162 Part I Structure and Catalysis FIGURE 5–5 Steric effects on the binding of ligands to the heme of myoglobin. (a) Oxygen binds to heme with the O2 axis at an angle, a binding conformation readily accommodated by myoglobin. (b) Car￾bon monoxide binds to free heme with the CO axis perpendicular to the plane of the porphyrin ring. When binding to the heme in myo￾globin, CO is forced to adopt a slight angle because the perpendicu￾lar arrangement is sterically blocked by His E7, the distal His. This ef￾fect weakens the binding of CO to myoglobin. (c) Another view (derived from PDB ID 1MBO), showing the arrangement of key amino acid residues around the heme of myoglobin. The bound O2 is hy￾drogen-bonded to the distal His, His E7 (His64), further facilitating the binding of O2. Phe CD1 His E7 His F8 (c) Fe H O2 Val E11 (a) O X A O O Fe A O J (b) O X A O O Fe A c C 8885d_c05_157-189 8/12/03 8:55 AM Page 162 mac78 mac78:385_REB: