BiochemistryNote4

BiochemistryNote4 - Binding - intro Protein + Ligand...

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12/9/09 Binding - intro Protein + Ligand Protein-Ligand Complex Binding sites are complementary in - size - shape - charge - hydrophobicity - hydrophilicity Binding is specific - discriminate between molecules
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12/9/09 Binding - Kd Protein + Ligand Protein-Ligand Complex Dissociation constant = Kd K d = [ P ][ L ] [ PL ] K a = [ PL ] [ P ][ L ] Association constant = Ka - the smaller the Kd, the tighter the binding (don’t confuse with the acid dissociation constant Ka (e.g. pKa))
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12/9/09 Binding - Kd Protein + Ligand Protein-Ligand Complex Occupancy = θ θ= binding _ sites _ occupied binding _ sites _ total = [ PL ] [ PL ]+[ P ] = [ L ] [ L ]+ K d Hyperbolic curve
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12/9/09 Binding - hemes Problem: solubility of oxygen in water (blood) is low (0.1 mM). Solution: proteins with special prosthetic groups: the hemes (they provide a protected environment for iron)
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12/9/09 Problem – Heme group in solution is unstable. Fe+2 + O2 Fe+3 Solution – bind heme group to a protein. Proteins can stabilize things that are unstable. Binding Stabilization Myoglobin (in muscle cells) Hemoglobin (in red blood cells)
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12/9/09 Myoglobin Single subunit Binding O2 causes spectral change Denaturing gel filtration – release 1 heme group Hemoglobin Two subunits, around 16,000 Da each Mr = 64,500 Da Binding O2 causes spectral change Denaturing gel filtration – release 4 heme groups
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12/9/09 Binding of O2 to heme. Hemes bind oxygen. Iron in 2+ oxidation state
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12/9/09 Myoglobin Heme is not covalently attached Myoglobin, a simple relative of hemoglobin. All alpha-helical.
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12/9/09 Binding - myoglobin binds oxygen reversibly (because O2 is a gas, use partial pressure of O2 above the solution instead of the actual concentration)
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12/9/09 Myoglobin binds oxygen preferentially CO binds 200 times tighter to myoglobin than O2 1. H-bonds to O2 2. Minimizes binding of linear CO - O2 is buried in protein - protein “breathes”
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12/9/09 Myoglobin vs. hemoglobin (storage ) (transport
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12/9/09 Binding - hemoglobin tetramer (strong interactions between unlike
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12/9/09 Binding - cooperativity pseudoglobin = 0.79 - 0.54 = 0.25 myoglobin = 0.97 - 0.91 = 0.06 hemoglobin = 0.95 - 0.55 = 0.4
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12/9/09 Binding - cooperativity Protein + n Ligand Protein - nLigand Complex n = Hill slope - “the number of ligand binding site” - the amount of cooperativity between them - leads to sigmoidal binding curves - if n = 1, then non-cooperativity - if n > 1, then positive cooperativity - if n < 1, then negative cooperativity - if n = # of ligands, then infinite cooperativity (all or nothing binding) - n number of binding sites (always) θ= [ L ] n [ L ] n + K d
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θ= [ L ] n [ L ] n + K d K IS NOT the microscopic KD for O2
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This note was uploaded on 12/09/2009 for the course CHEM 4711 at Colorado.

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BiochemistryNote4 - Binding - intro Protein + Ligand...

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