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I'm a little confused on binding sites in general, since we never went into that much detail in elementary biochem. I have watched all the KA videos and done the EK review but am still a bit hazy.
Do hydrophobic binding sites on enzymes mean that they will interact preferably with hydrophobic amino acids? What about with hydrophilic AA's?
For example, if given the binding site of 3 enzymes A,B and C, where:
The binding site of enzyme A is Glutamic acid
The binding site of enzyme B is Valine
The binding site of enzyme C is Lysine
Which enzyme would prefer to interact with an Arg/ Ala/Asp/ residue from the substrate and what is the method of reasoning behind it? Normally I think that pos charged AA's prefer to interact w/ neg charged AA's but this doesn't always seem to be the case when dealing with enzymes and their substrates.
Do hydrophobic binding sites on enzymes mean that they will interact preferably with hydrophobic amino acids? What about with hydrophilic AA's?
For example, if given the binding site of 3 enzymes A,B and C, where:
The binding site of enzyme A is Glutamic acid
The binding site of enzyme B is Valine
The binding site of enzyme C is Lysine
Which enzyme would prefer to interact with an Arg/ Ala/Asp/ residue from the substrate and what is the method of reasoning behind it? Normally I think that pos charged AA's prefer to interact w/ neg charged AA's but this doesn't always seem to be the case when dealing with enzymes and their substrates.