chapter 5 students - From Protein Structure to Function 1....

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From Protein Structure to Function emoglobin and myoglobin: Principles of 1. Hemoglobin and myoglobin: Principles of reversible ligand binding 2. (Antibodies: Principles of specific, high . (p f p f , g affinity ligand binding) 3. Myosin and actin: Protein activity modulated by ATP 4. Enzymes 1 MCDB310 – Chapter 5: Protein Function
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Ligand Binding • usually transient and reversible interaction with others molecule (= ligands) such as metals, hormones • often involves “ molecular breathing ” of the protein, i.e. bility to undergo small conformational changes ability to undergo small conformational changes • often induces molecular rearrangements in the protein • ligand binding sites are - highly conserved - complementary in size, shape, and charge 2 MCDB310 – Chapter 5: Protein Function
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Myoglobin (Mb) & Hemoglobin (Hb) • model proteins to study reversible ligand binding • Mb: First protein whose structure was solved (1958) ery important for xygen binding muscle (Mb) and very important for oxygen binding in muscle (Mb) and oxygen transport in blood (Hb) metal ions (Fe, Co) are good oxygen binders, but free metal ions are very reactive O 2 binding component in Mb and Hb is heme - protoporphyrine ring with a central Fe 2+ , which reversibly inds oxygen binds oxygen 3 MCDB310 – Chapter 5: Protein Function
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Heme prosthetic group of Mb and Hb corporated into Hb and incorporated into Hb and Mb during folding esponsible for reversible • responsible for reversible O 2 binding • responsible for red color of blood and muscles 4 MCDB310 – Chapter 5: Protein Function
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Heme – Basic Structure 4 pyrrole rings linked by methene bridges protoporphyrine) (= protoporphyrine) pyrrole ring py g X: additional functional groups methene bridge 5 MCDB310 – Chapter 5: Protein Function
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Heme – Structure central Fe 2+ 4 methyl groups 2 vinyl groups (buried in protein) 2 propionate groups (exposed) 6 MCDB310 – Chapter 5: Protein Function
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Heme – Iron Coordination e + as coordination sites • Fe 2 has 6 coordination sites (4 with N of pyrrole rings, and 2 perpendicular to ring system) Fe + •Hb : 5 th coordination site is occupied with proximal His + •6 th coordination site: O 2 oxyhemoglobin none deoxyhemoglobin CO carboxyhemoglobin 7 MCDB310 – Chapter 5: Protein Function
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Heme – Binding of CO vs. O 2 • free heme binds C0 10 5 times etter than O better than O 2 • kinked binding topology in Mb avors O 0fold favors O 2 100fold 8 MCDB310 – Chapter 5: Protein Function
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Myoglobin (Mb) • primarily found in muscle (highly abundant in arine mammals such as whales) marine mammals such as whales) • single polypeptide (153 aa) with one bound heme • very simple oxygen binder: Binds oxygen at high pO 2 , releases it at low pO 2 Mb + O 2 MbO 2 • typical globin fold 9 MCDB310 – Chapter 5: Protein Function
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The Globin Fold helices (A ) and loops in between 8 helices (A-H) and loops in between 10 MCDB310 – Chapter 5: Protein Function
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Binding/Association Constant K a Quantitatively describes the affinity of a protein P for its ligand L P + L PL [L]
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chapter 5 students - From Protein Structure to Function 1....

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