From: Axel Kohlmeyer (
Date: Tue Nov 15 2011 - 22:57:45 CST

On Wed, 2011-11-16 at 13:58 +1100, Aaron Oakley wrote:
> Thanks for responses so far.
> Just to clarify, we are working on a protein with a flexible
> region at the C-terminus. Part of the function involves that
> region "reaching out" to interact with another protein.
> I would like to know the maximum extent of this reach in
> order to set up a periodic box of water molecules with enough room.

how about using molfacture (or some other equivalent tool)
to build a single strand of a beta sheet with your N amino
acids to estimate the length you desire?

you still need some safety margin, but unless you manually
stretch the chain, it is very unlikely that it will stretch
to the maximum extent.

> Clearly, the maximum reach will be influenced by how much tension is in
> the peptide, but I would assume an energy minimised conformation at maximum
> extent.

well, this statement is confusing. if you have something
that will stretch out, it won't be "minimized". you will
have to have a special sequence of side chains to make it
want to stretch out, but then it won't want to "flail"


> a++