AMBER Archive (2009)

Subject: Re: [AMBER] building quadruplex with NAB

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed May 13 2009 - 06:48:38 CDT

On Mon, May 11, 2009, Peter Varnai wrote:
>
> 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 );

Try setting pembed=1. I haven't done much distance geometry for a while, but
that option often works better than the default. You may have to play a bit
with the rbox, riter and slearn parameters, and be prepared to have multiple
trials, saving only the best ones. No guarantees, but it's worth a try.

Also, did you try the setboundsfromdb() routine, rather than useboundsfrom()?

> 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?

One approach is to read in the core, apply useboundsfrom() to the whole core
(not just base pairs), then use distance geometry to build the missing loops.

Let us know if you get this to work...it would be great to have more examples
of building things. We're working here on some routines to build four-way
(Holliday) junction structures, but the more examples one has, the better.

...good luck...dac

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