Making Up an Enzyme

[MrSandman]

Ok, I have a project to construct my own enzyme. here is the criteria for the model.

 

1. 100-500 peptides long

 

2. Must have 2 disulfide links and 1 salt bridge.

 

3. Must make since in the environment you specify.

 

4. Must provide (a) protein sequence (b) DNA sequence

 

5. Must be able to specify and explain DNA change that yeilds a protein change that knocks out your protein.

 

Part (b) of 4 and 5 I don't want to bring up right now.

 

I putting down the criteria, because I'll be refering to it.

 

Note: I don't want you guys to do my project for me, but I think this post will help all understand the Primary, Secondary, and Tertiary Structure of an Enzyme. I'll end my post here and make posts after it for questions I have.

 

Ok, lets talk primary here. The disulfide bond will just be between two cystein proteins I know that, and it will have to be inside the protein, just because of how it is, or can be outside too?

 

Now, the salt bridge will also be hydrophobic (inside), because it would break apart if it was outside, right?

[DrDNA]

 

Ok, lets talk primary here. The disulfide bond will just be between two cystein proteins I know that, and it will have to be inside the protein, just because of how it is, or can be outside too?

 

 

It's your protein and it doesn't seem like you have too many limits, but one way to answer that question is to ask yourself, what useful purpose might a disulfide bond serve on the outside?

[MrSandman]

Well I'm trying to figure out the likelyhood of it occuring on the outside. Also salt bridges will prefer to be hydrophilic and not phobic I made a mistake.

 

The use of it being on the outside would be to make stop hydrophilic substance from entering a hydrophobic area. That is very small used for a holder maybe for a different hydrophobic substance.

And since has a side of the bond outside another enzyme can easily access the bond and alter it to get the hydrophobic substance. It would be like a carrier. If you have it on the inside you would have to break through the amino acide sequence and the disulfide bond. Does that make since. Thanx for the question it expanded my thinking on it.

 

The likelyhood however says that the bond would be nonpolar making it hydrophobic, or does that not matter?

[DrDNA]

Hint:

Look up the function of disulfide bonds in antibodies (for example) and what happens after you reduce the disulfides into thiols to make Fab fragements and such.

 

Why would you want to stop things from going in to hydrophobic areas? You could look up where active sites reside, what they look like, what residues are generally found in there, in the binding pocket, and the cleft........