AMBER Archive (2003)

Subject: Re: DNA base-step distortion

From: kbyun_at_wesleyan.edu
Date: Sun May 18 2003 - 18:43:59 CDT

Thanks for your comments, I'll look at these steps,
CpA and ApT.

The partial sequence where the MD does not agree
with crystal protein-dna complex is "ACGT". For the
free DNA, I get good agreement in terms of
base-step parameters between MD and crystal.

In the protein-bound form, xray predicts deformation
in the ACGT region, with the deformation mostly
coming from negative roll at each of these steps.
The most deformation occurs at the central CG
step. Roll is -15 degrees. In the free DNA, CG step
opens toward the major groove with roll being
approximately +10 degrees. Bending occurs
toward the minor groove in the protein-dna complex.

For the MD result, mean value roll at the CG step is
close to 0 (s.d.= 8 degrees) . A large kink appears
at the adjacent GT step of approximately -12
degrees and this is not present in the crystal. It
appears that the CG step is "straightening" out and
a kink happening at the step next to it.

The crystal structure of the protein-dna complex I
am using resolution < 2.0 A . I'm not sure why the
force field is giving me something quite different
than the crystal.

Thanks,

Suzie Byun