AMBER Archive (2003)

Subject: RE: AMBER: aminoacid mutation

From: Endres, Robert G. (endresrg_at_ornl.gov)
Date: Mon Oct 27 2003 - 21:02:15 CST

Dear Ioana:
you could try likely side-chain conformations from a backbone-dependent rotamer library (like bbdep02.May.sortlib.gz from
http://dunbrack.fccc.edu/bbdep/bbdepdownload.php).

1) measure local backbone dihedral angles (phi and psi) of amino acid with leap
2) remove side chain atoms of amino acid to be mutated with leap
3) rename amino acid with leap
4) look up statistical significant side chain conformations for that particluar amino acid (characterized by dihedral angles of side chain)
5) adjust dihedral angles in topology file accordingly
6) "grow" new side chain with leap
7) pick side chain with lowest total energy of protein

All this could be automated with a script. Good luck.

Robert

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Yong Duan
Sent: Mon 10/27/2003 9:09 PM
To: amber_at_scripps.edu
Cc:
Subject: RE: AMBER: aminoacid mutation

Dear Ioana:

I am interested in that too. So, let me know if you, or anybody else,
know a way or a program to do this automatically.

LEU -> ALA mutation is simple. But ALA -> LEU can be a bit tricky if it
has to potential to bump into other neighboring atoms.

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Ioana Cozmuta
Sent: Monday, October 27, 2003 7:46 PM
To: Amber List
Subject: AMBER: aminoacid mutation

Hi amber users,

Is there a way to "automatically" mutate an aminoacid from a protein
structure into another one. Say I want to replace an ALA aminoacid with
a
LEU aminoacid. Is it possible just to select the ALA aminoacid I want to
mutate and turn it into LEU? Is there some software out there that
could do this on a more automatic basis?
The way I thought doing it was to edit the pdb file myself and try to
edit
the coordinates of the atoms in the new aminoacid such that the bond
lengths are preserved and then equilibrate the new positions. But then
my
boss told me to try "not to lose time with this" and find a software
that
does it automatically :)

Any suggestions are welcomed!
Thanks,
Ioana

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