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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


  • 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 association with protein

Four bind heme nitrogens

One binds protein histidine

“proximal” histidine


One can bind O2

Structure of myoglobin
Structure of myoglobin association with protein

  • 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 association with protein


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
“Globin” fold association with protein

Six helices:

“Three-over-three a-helical sandwich”

Oxygen-carrying molecules

Hemoglobins, myoglobins, cytoglobins, etc

Heme-utilizing enzymes







O 2 binding by myoglobin
O association with protein2 binding by myoglobin

  • Reversible

    Myoglobin•O2 ↔ Myoglobin + O2

  • O2 is a gas: use partial pressures (pO2) instead of molarity

    • Gas concentration proportional to pressure

Myoglobin: association with protein

Hyperbolic dependence of O2 binding on pO2

Protein flexibility in myoglobin
Protein flexibility in myoglobin association with protein

  • 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)? association with protein

  • 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” O association with protein2, but won’t let go



Little O2

“Dropped Off”

Hemoglobin cooperative binding
Hemoglobin: cooperative binding association with protein

Much better

O2 release