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Suggested HW Ch. 5. 1 – 9 (Chapter 5.1, 5.2) Note: Protein Explorer (originally due Friday) delayed. K d. What is the definition of K d ?

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suggested hw ch 5
Suggested HW Ch. 5
  • 1 – 9 (Chapter 5.1, 5.2)
  • Note: Protein Explorer (originally due Friday) delayed
slide2
Kd
  • What is the definition of Kd?
  • Protein X interacts with Mg2+ with a Kd of 0.5mM. You have a solution of 0.1 mM Protein X. How much Mg2+ should you add so that the equilibrium concentration of complex (X•Mg2+) is 0.08 mM?
  • You do an experiment to measure the interaction between proteins Y and Z. When a solution of 0.15 pM Y and 0.56 nM Z reaches equilibrium, you determine that the concentration of Y•Z is 0.021 pM. What is the Kd describing the interaction?
case study oxygen binding in myoglobin and hemoglobin
Case study: oxygen binding in myoglobin and hemoglobin
  • Oxygen is poorly soluble in water (blood)
  • Iron (Fe2+)/O2 complex is soluble
    • But free iron is toxic
  • Use proteins containing an iron cofactor
    • Myoglobin
    • Hemoglobin
iron is part of a heme prosthetic group permanent association with protein
Iron is part of a heme prosthetic group: permanent association with protein

“Porphyrin” ring

iron has six coordination sites
Iron has six coordination sites

Four bind heme nitrogens

One binds protein histidine

“proximal” histidine

His93/HisF8

One can bind O2

structure of myoglobin
Structure of myoglobin
  • Extremely compact
  • “Globin” family
  • ~75% a helix (no b structure)
    • Eight helical segments
      • A-H
    • Four terminate in proline
  • Interior: hydrophobic except for two histidines
slide8

Proximal His coordinates

Iron

Distal His binds oxygen

-increases affinity

-decreases affinity

for carbon monoxide

CO still preferred over O2

-rotation (breathing)

allows O2 exit &

entry

Distal His

His64

His E7

Proximal His

His93

His F8

globin fold
“Globin” fold

Six helices:

“Three-over-three a-helical sandwich”

Oxygen-carrying molecules

Hemoglobins, myoglobins, cytoglobins, etc

Heme-utilizing enzymes

dehaloperoxidase

Mammals

Worms

Fish

Plants

Bacteria

o 2 binding by myoglobin
O2 binding by myoglobin
  • Reversible

Myoglobin•O2 ↔ Myoglobin + O2

  • O2 is a gas: use partial pressures (pO2) instead of molarity
    • Gas concentration proportional to pressure
slide11

Myoglobin:

Hyperbolic dependence of O2 binding on pO2

protein flexibility in myoglobin
Protein flexibility in myoglobin
  • Structural ‘breathing’ to allow O2 entry
  • Deoxymyoglobin vs. oxymyoglobin
    • Change in porphyrin ring, position of iron
why hemoglobin ie why not just myoglobin
Why hemoglobin (ie. why not just myoglobin)?
  • This is where the binding calculations get interesting
  • Oxygen carrier needs to ‘pick up’ O2 in oxygen-rich (pO2 > 10 kPa) blood surrounding lungs, & ‘drop off’ O2 in oxygen-poor tissues (pO2 ~ 4)
  • Hyperbolic binding of myoglobin: too insensitive to these types of Ds
hemoglobin cooperative binding
Hemoglobin: cooperative binding

Much better

O2 release