[AMBER] on salt bridge affinity by AMBER

From: Acoot Brett <acootbrett.yahoo.com>
Date: Fri, 12 Oct 2012 20:28:31 -0700 (PDT)

Dear All,

A protein contain 2 chains. Chain A is ----FKY-----, Chain B is -----E----. Chain A and B are binding by the salt affinity between K in chain A and E in chain B.

Another protein is the mutation form of the first protein. Chain A is ----AKA-----, Chain B is -----E----. A and E still forms salt bridge.

As I know, AMBER has the same force field (can we regard it as homogeneous force field?) for the first protein and the second protein.

But there is another explanation, even maybe from the text book. It says for the first protein, the F and Y hydrophobic environment makes the binding affinity between K in Chain A and E in chain B much higher. I think this explanation contradicts the homogeneous force field for the 2 proteins used by AMBER.

What is your explanation?

I am looking forward to getting your reply.



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Received on Fri Oct 12 2012 - 20:30:03 PDT
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