| Chem 431 |
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Fall 2008 |
| Lecture Notes: 29 September |
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| PREVIOUS |
Myoglobin and Hemoglobin as Example Proteins
Myoglobin
Myoglobin is a 153 residue globular protein in the globin family. Eight alpha helices form its single domain (myoglobin fold) tertiary structure; about 80% alpha helix (high for globular proteins). (text Figure 5-3) Interior almost exclusively hydrophobic residues, with water excluded from interior. Surface has mix of hydrophobic and hydrophilic residues, with ionizable groups on surface.
Myoglobin functions to store and facilitate the diffusion of oxygen in muscle. Oxygen binds to a heme {Fe (II)-protoporphyrin IX} prosthetic grp (text Figure 5-1). Four of iron's six ligands are to heme nitrogens, with a fifth to a histidine nitrogen. The final ligand bond goes to oxygen. (text Figure 5-2) Breathing motions (see below) are necessary to allow the exchange of oxygen, since the heme is in a closed pocket. [overhead 8-9, 8-10, V&V]
Protein Dynamics
"Breathing" motions:
- Atomic fluctuations (10-15- 10-11 sec; 0.001 - 0.1 nanometer) Myoglobin example [overhead v&v 8.9, 8.10]
- Collective motions of covalently linked atoms, from aa R-groups to domains (10-12 - 10-3 sec; 0.001 - >0.5 nanometer)
- Triggered conformational changes: in response to ligand binding, covalent modification etc.
- How do we know about the mobility of protein structures?
- X-ray diffraction studies of proteins with and without ligand bound
- NMR (phe, his ring protons/carbons show up on edges of signal envelope)
- H-exchange
- Antibody binding: make antibodies to normally interior aa residues, over time protein ppt forms as interior groups momentarily exposed.
Let's look at binding in terms of saturation, Y, where if Y = 1 every site of every Myoglobin is occupied by an oxygen molecule (thus if Y = 0.5, then 50% of the myoglobin are binding oxygen and 50% are "empty"). Mb/Hb binding curve (text Figure 5-4b):
Reviewing the curve in terms of saturation, Y, if Y = 1 then every site of every Myoglobin is occupied by an oxygen molecule (thus if Y = 0.5, then 50% of the myoglobin are binding oxygen and 50% are "empty").
Can describe binding as dissociation equilibrium,then:
MbO2
Mb + O2 ; 
& 
for saturation. Substituting, 
, the equation of a hyperbola. If expressed as pressures, then 
where P50 = pO2 @ 50% saturation. Note that the binding curve for Mb is indeed hyperbolic in shape.
Hemoglobin is an alpha-alpha-beta-beta oligomeric protein: its quaternary structure consists of a tetramer of myoglobin like subunits. (text Figure 5-6) The two types of chain are slightly shorter than myoglobin chains (alpha= 141 aa residues, beta= 146 aa residues). There are extensive contacts between an alpha and a beta subunit to give a dimer. The dimers have additional contacts to give the tetramer. Oxygen binding results in a change of conformation in Hb. (text Figure 5-10) The change of conformation affects the binding of oxygen (text Figure 5-11) {oxygen binding is reduced in the "blue" form due to steric hindrance between the oxygen and the heme}.
What about Hb oxygen binding? Obviously more complex. The sigmoid shape (s-shape) of the curve indicates cooperativity (text Figure 5-12, or see below). That is, if one site binds, another is more likely to as well (it cooperates with the first site).
 Pathway Diagrams |
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Last modified 30 September 2008
