Three-Point Binding Model

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Three-Point Binding Model

• First proposed by Ogsten (1948) to explain
  biological enantioselection/enantiospecificity
• Serves as a model for chromatographic chiral
  stationary phases

• Preferential binding occurs via intramolecular
  non-covalent forces
• H-bonding
• salt bridge
• Ionic
• Dipole-dipole
• Van der Waals

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Enantioselection by an Enzyme
CH2OH moieties are different because of
non-equivalent binding sites in the enzyme
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Three-Point Binding Model - Enantiospecificity

• Only one enantiomer binds to enzyme is involved
  in reaction

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With the other enantiomer
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• ? we get enantiospecificity (substrate
  biomolecule are chiral)
• To do this efficiently, we need a large
  biomolecule to align three binding sites to give
  high specificity
• One problem with model
• Model is a static representation ? lock key

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Binding

• The cost of binding
• Km (Michaelis constant) small value indicates
  high affinity for substrate
• ? Kbinding ( 1/Km)
• Strong binding ? K gt 1
• ?G -RT ln K
• ?G must be ve

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• ?Gbinding ?Hbinding- T?Sbinding
• For 2 molecules in, 1 out ?S is ve
• ? (-T?S) term is ve
• Entropy disfavors binding of substrate to enzyme
• To get good binding, need ve ?H (i.e. bond
  formation)
• Each non-covalent interaction is small (H-bond
  5 kcal/mol), but still gives a ve ?H
• Enzymes use many FGs to sum up many weak
  non-covalent interactions (i.e. 3 points)

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• Back to tyrosyl-tRNA synthase

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Tyrosyl-tRNA synthase

• Use binding to orient CO2- nucleophile adjacent
  to P? specifically as electrophile ? specificity
• Many non-covalent interactions overcome entropy
  of binding H-bonds

Can isolate this complex in the absence of tRNA
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Tyrosyl-tRNA Synthase.tyr-adenylate
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Bind ATP
Binding AAs

3 point binding enantiospecificity
ATP, not dATP
Tyr specificity


Main chain contacts
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Orient ? PO4 towards CO2-

Increase P?


Main chain contacts