> 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
>
It may well be the imbalance of the force field on the
protein - DNA interface.
Perhaps try to resume the simulation of free DNA starting from the
distorted one in the complexes, to see ho the solute responds.
Resolution just below 2A should be sufficient to see
some portion of the local variations and no major errors
should be present in the structure, provided the refinement
was properly done (not always the case for the DNA part).
Best wishes, Jiri
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
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Received on Mon May 19 2003 - 11:53:02 PDT
