Proteins and enzymes, Section 4, relating structure to function (Dr. Taylorson) Flashcards
What is induced fit ?
The induced-fit theory states that the binding of a substrate or some other molecule to an enzyme causes a change in the shape of the enzyme so as to enhance or inhibit its activity.
What does molecular recognition depend on ?
complementarity of shape and charge distribution between the ligand and the protein.
What shapes can the binding sites have ?
For macromolecules, binding sites can be concave, convex, flat of maybe grooves.
For smaller molecules, they can be clefts, pockets or cavities.
Where are catalytic sites often situated in quaternary structure ?
At the interface between subunits or domains in the protein.
What types of residues usually make up binding sites ?
A higher than average amount of hydrophobic AAs.
How is the NRG for driving binding events usually provided ?
By the displacement of water molecules from the ligand binding site.
What is Kd ?
What does it express ?
Kd is the dissociation constant
Kd = [L]*[P] / [P.L]
It represents the affinity of the ligand for the protein.
A low Kd means a tight binding and a high Kd means a weak binding.
What is the Kd of the Biotin ligand for avidin protein ?
Of Ca2+ for calmodulin ?
- 10E-15 M
1. 10E-5 M
How is O2 transported in the bloodstream ?
It is bound to proteins, haemoglobin and myoglobin, because it is v poorly soluble in the bloodstream.
What is the structure of myoglobin ?
Predominantly helical (80%), compact single polypeptide of 153 AAs. Helices A to F. It contains a ham group comprising protoporphyrin IX w/ a bound iron in the ferrous state. The iron has 6 coordination bonds, 4 to the flat porphyrin ring system and two perpendicular to it. One is associated w/ the proximal histidine on the F-helix and the other is free to bind oxygen. In deoxymyoglobin, the interaction of the iron with the proximal histidine induces a puckering of the porphyrin ring system.
Describe the binding of O2 to hemoglobin.
O2 binds to the iron in the haem. This pulls the iron into the plane of the ring of the porphyrin and moves the F-helix.
The binding results in a transfer of an e- from the ferrous ion to O2 creating a superoxide ion. This ion is stabilized by a H-bond donated by the distal histidine on the E-helix.
The H-bond pulls the O2 into the plane of the porphyrin ring and the whole structure changes shape slightly via mvnt of the H-helix to tighten up around the bound O2 molecule.
What are the relative affinities of myoglobin and haemoglobin for O2 ?
Myoglobin has a v high affinity for oxygen and is described by a hyperbolic curve.
Haemoglobin has a lower affinity for oxygen and is described by a sigmoidal curve.
What are the subunits of haemoglobin ?
Haemoglobin has two alpha and to beta subunits. Each subunit has a bound harm containing an iron in the ferrous state.
Whilst sequentially dissimilar, each subunit is structurally v similar to myoglobin.
Key residues, likes the proximal and distal histidine chains, as well as the haem binding pocket interactions, are conserved.
What did the studies of Max Perutz in the 1960s-70s show concerning haemoglobin ?
That O2 can bind haemoglobin in 2 possible state: T and R. O2 has a much higher affinity for the R state and stabilizes the R state.
Haemoglobin is predominantly in the T state.
Upon binding O2 in the T state, it switches to the R state. This causes the subunits to change relative to one another.
What is the overall effect of O2 binding to one of the haemoglobin subunits ?
It causes the bound subunit to rotate relative to the other subunits in the structure and the overall shape of the molecule changes from T to R.