BCH210H1 Lecture Notes - Lecture 21: Enzyme Kinetics, Binding Constant, Atp Hydrolysis

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BCH210 Lecture 19 โ€“ Binding kinetics
Characterizing binding interactions
- Biochemical interactions are needed for cellular processes to occur
- Binding affinity and kinetics can be used to characterize and compare the non-covalent
interactions between two molecules
- Binding is saturable meaning that there are limited number of binding sites
o It depends on stoichiometry
o Reversible in non-covalent interactions
- Eg. Ca2+-ATPase is a membrane transporter and enzyme
o It has TM helixes
o Ca2+ transport for muscle contraction
o Lots of conformational changes facilitate calcium diffusion across the membrane
o Hydrolysis of ATP helps with conformational change
Binding interactions
- The way a protein interacts with a molecule can be quantified using equilibrium rates
and association or dissociation constants
- Ka = association constant
- Kd = dissociation constant
๐พ๐‘‘=[๐ด][๐ต]
[๐ด๐ต]=๐‘˜๐‘œ๐‘›
๐‘˜๐‘œ๐‘“๐‘“
= ๐พ๐‘Ž
โˆ’1
- The dissociation constant is either based on:
o The concentration of free molecules or
o The concentration of bound molecules
- Molecules that bind tightly with their binding partner have high Ka values and low Kd
values
Binding affinity example
- Non-covalent interactions such as ionic bonds, hydrogen bonds and van der Waals
interactions between amino acid side chains and moleculeโ€™s functional groups influence
the binding affinity
- The ๏ข2-adrengergic receptor contains a hydrophobic binding pocket that determines the
binding affinity
o The binding pocket interacts with the substrate and aides in tighter binding
o It can bid epinephrine and agonist
o Agonist has a lower Kd meaning that the it binds more tightly to the enzyme
- Adding large side chains may prevent binding from taking place
Thermodynamics of binding
- Binding energy is released when an enzyme and substrate form many weak interactions
- Interactions result in a conformational change to the unstable transition state
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