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CHAPTER 5 (Picture) - David L Nelson and Michael M Cox...

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Lehninger Principles of Biochemistry Fourth Edition Chapter 5: Protein Function Copyright  ©  2004 by W. H. Freeman & Company David L. Nelson and Michael M. Cox
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Reversible binding of a protein to a ligand: Oxygen-binding proteins Oxygen can be bound to a heme prosthetic group Protoporphyrin Porphyrin ring Myoglobin has a single binding site for oxygen
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6 Protein - Ligand Definitions. Ligand – A molecule bound reversibly to. by a protein. Bind site –site on a protein that ligand binds Induced fit – structural adaptation that occur between protein and ligand. Substrate – molecule acted upon by enzymes Catalytic site or active site –substrate binding site on an enzyme. i. Protein – ligand interactions Consider reversible bind of a protein (P) to a ligand (L) at equilibrium is P + L = PL Ka = [PL]/[P][L], Ka = association constant Rearrangement Ka[L] = [PL]/[P] If [L] >>> L-binding site the L remains constant. θ = fraction of ligand-binding site (PL) on the protein that are occupied θ =(binding site)/(total binding area) = [PL]/[PL] + [P], substitute Ka[L][P] for [PL] θ = Ka[L][P]/Ka[L][P] +[P] = Ka[L]/Ka[L] +1 = [L]/[L] +1/Ka Ka can be obtained by plotting θ vs [L] ( Fig 5-4a ) - The fraction of the ligand-binding sites occupied approaches saturation asymptotically as [L] increases . - The [L] at which half of the available ligand-binding site are occupied ( θ = 0.5) correspond to 1/Ka or Kd.
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7 Protein - Ligand Kd = [P][L]/[PL] [PL] = [P][L]/Kd θ = [L]/[L] + Kd When [L] = Kd, one-half of the ligand-binding sites are occupied. Note : Tighter binders require low [L] and hence lower Kd value ( TABLE 5-1 ). Binding Oxygen: θ = [O 2 ]/[O 2 ] + Kd If Kd = [O 2 ] 0.5 . Then, θ = [O 2 ]/[O 2 ] + [O 2 ] 0.5 . Concentration of volatile substance in solution is proportional to its partial pressure of the gas phase above. θ = PO 2 /PO 2 + P 50
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ii. Protein structure and ligand binding Binding of the ligand to protein depend on the protein structure and the accompanied conformational change . For example : CO binds to free heme molecules 20,000 times better than O 2 does, but binds only 200 times better when heme is bound to myoglobin. WHY? Steric hindrance (Geometry of hydride orbitals) ( Fig 5-5a, 5-5b ). Free oxygen is positioned at an angle and CO is straight. In Myoglobin, oxygen interacts with HisE7 while CO cannot ( Fig 5-5c ). Breathing effect Rapid molecular flexing of amino acid R groups produce transient cavities in protein structure to allow oxygen but not CO.
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11 Protein - Ligand iii. Hemoglobin and oxygen transport (Fig. 5-6) Hemoglobin transport oxygen throughout the body. Myoglobin being insensitive to small changes in concentration of dissolved oxygen – function mostly for storage . Hemoglobin is a tetrameric protein containing four heme prosthetic. In adults hemoglobin contains Two α -chain (141 residues each) Two β -chains (146 residues each) The alpha and beta chains are structurally identical and are similar in structure to Myoglobin ( Fig. 5-6 ).
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