Suggested hw ch 5
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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

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Suggested HW Ch. 5

  • 1 – 9 (Chapter 5.1, 5.2)

  • Note: Protein Explorer (originally due Friday) delayed


  • 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

  • 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

“Porphyrin” ring

Iron has six coordination sites

Four bind heme nitrogens

One binds protein histidine

“proximal” histidine


One can bind O2

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

Proximal His coordinates


Distal His binds oxygen

-increases affinity

-decreases affinity

for carbon monoxide

CO still preferred over O2

-rotation (breathing)

allows O2 exit &


Distal His


His E7

Proximal His


His F8

“Globin” fold

Six helices:

“Three-over-three a-helical sandwich”

Oxygen-carrying molecules

Hemoglobins, myoglobins, cytoglobins, etc

Heme-utilizing enzymes







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


Hyperbolic dependence of O2 binding on pO2

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)?

  • 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

Myoglobin: good at “picking up” O2, but won’t let go



Little O2

“Dropped Off”

Hemoglobin: cooperative binding

Much better

O2 release

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