AMBER: Distorted ring...

From: Waqas Nasir <>
Date: Thu, 11 Dec 2008 03:48:45 -0800 (PST)


Hope you are doing fine.

Well, I have a situation here in my md run. The system that I have contains a big sugar in the complex with protein. The sugar is proved in vitro that it does not bind with the protein in question. The system is built using the lowest free energy conformations for sugars complexed with the reported conformation of protein. The charge on sugar is -1 whereas on proteins its +8. When the md run starts the conformation of the sugar complexed in protein is like that it resides on one ring sitting strongly (with a network of non bonded interactions) in the binding pocket, this ring is then connected to another Nac ring which then connects the whole chain of sugar molecule. The point to note here is that in the initial conformation the whole sugar chain (3 saccharides) is sticking out of the protein with minimal possible interactions except the ring which is in the binding pocket.

When the md run is at about 20ps, the Nac ring that connects the whole chain with the ring in the binding pocket gets distorted. It has happened at least 3 to 4 times making sure that its not by chance or just a bad luck. My perception after watching the trajectory files is that as long as the Nac ring is in the proper shape the sugar chain is unable to bind and sticks somewhat out of the protein binding pocket, but due to the opposite charges on the two molecules and the decoration of binding pocket with proton donors and acceptors, the chain tends to fall back but it does so on the expense of the Nac ring distortion, which can not hold the whole chain's energy to fall back and gets distorted.

Do you think that it might be a possible explanation of the rings getting distorted or the rings should never distort what ever the reason be. I mean to say if there is any room for logical explanation as written above when the rings continuously get distorted, or there is something TECHNICALLY wrong with the system always when we come across such distortions?

The force fields that I am using are ff99SB and Glycam06 with latest parameters from Glycam website. The system runs under AMBER version 8.

Thanks for reading,

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Received on Fri Dec 12 2008 - 01:16:03 PST
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