AMBER Archive (2009)

Subject: [AMBER] building quadruplex with NAB

From: Peter Varnai (p.varnai_at_sussex.ac.uk)
Date: Sun May 10 2009 - 18:27:38 CDT

Dear NAB-users,

I am trying to build a quadruplex with NAB and I would need some help
from an experienced user: what is an effective strategy?

1) Use a sequence and create structures with distance geometry. This
seems logical as apart from the information for the guanine core using
Hoogsteen pairing from template gg.VIa.pdb, I have additional
distances for the loops from NMR. I try to get a tetrad of residues
(2,6,14,18) using this approach:

[...]
useboundsfrom(b, m,"1:2,6:",getpdb("gg.VIa.pdb"),"::",0.10);
useboundsfrom(b, m,"1:6,14:",getpdb("gg.VIa.pdb"),"::",0.10);
useboundsfrom(b, m,"1:14,18:",getpdb("gg.VIa.pdb"),"::",0.10);
useboundsfrom(b, m,"1:18,2:",getpdb("gg.VIa.pdb"),"::",0.10);
tsmooth( b, 0.0005 );
opt = "seed=-1, gdist=0, ntpr=50, k4d=2.0, randpair=5";
dg_options( b, opt );
embed(b, xyz );
ier = conjgrad( xyz, 4*m.natoms, fret, db_viol, 0.1, 10., 2000 );
[...]

Although I obtain a structure where the four Gua's are close, they are
not in plane and I already have some possible error lines of the form
below that I cannot interpret:
T2err: 434 560 158 ( 3.61 3.40)( 2.78 3.40)( 11.98
14.65)( 3.74 8.37)

I have tried adding the following command without any improvement:
setchiplane(b,m,"1:2,6,14,18:O6,N2");

2) Build single tetrad layers, assemble them using mergestr, then add
loops, merge with core, similar to program_5.nab program_6.nab in
examples. This will require a bit of an effort...

3) Read in the guanine core from an experimental structure using
getpdb and build in the missing loops along some spline and merge
them. Is it possible to merge coordinates read in and
coordinates generated within NAB?

Any pointer, example script would be appreciated.

Many thanks,
Peter 

--
Dr Peter Varnai
Department of Chemistry and Biochemistry
University of Sussex
Falmer, Brighton, BN1 9QJ, United Kingdom
T: +44 1273 873881, F: +44 1273 876687
E: p.varnai_at_sussex.ac.uk

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