minor groove direct measurement

[maryatx3dna]

Sir

I would like to know the concept behind measurement of minor groove so that i could directly measure the minor groove (P-P) distance. I mean from which residue no: residue no.  Its surely not a 1-1 measurement; there is some  i: i+r correspondance.
Also in the output file of 'analyze' only 5 minor groove values -> 3 refined minor groove values are given. are there only these values. in the case of ligand binding studies i would like to direclty measure all the possible values. It would be helpful if you could help me in this.

Thanking you.

[xiangjun]

The details of the algorithm implemented in 3DNA for calculating the minor and major groove widths are shown in the main output file. Given below is an example for B-DNA 355d:

****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
   which take into account the directions of the sugar-phosphate backbones

   (Subtract 5.8 Angstrom from the values to take account of the vdw radii
    of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
     Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

                  Minor Groove        Major Groove
                 P-P     Refined     P-P     Refined
   1 CG/CG       ---       ---       ---       ---
   2 GC/GC       ---       ---       ---       ---
   3 CG/CG      14.3       ---      18.2       ---
   4 GA/TC      12.0      11.9      17.3      17.3
   5 AA/TT       9.7       9.6      19.1      19.0
   6 AT/AT       9.1       9.1      16.4      16.0
   7 TT/AA       9.1       9.1      17.8      17.7
   8 TC/GA       9.6       9.6      18.6      18.6
   9 CG/CG      10.4       ---      19.0       ---
  10 GC/GC       ---       ---       ---       ---
  11 CG/CG       ---       ---       ---       ---
****************************************************************************

The two-page long appendix of the El Hassan and Calladine 1998 JMB paper is well worth reading.

Note that 3DNA also produces a file named "auxiliary.par" which contains a section of pair-wise "Phosphorus-phosphorus distance in Angstroms".

For measurements of groove widths and depths, you may also want to try Dr. Lavery's Curves+.

HTH,

Xiang-Jun

[maryatx3dna]

Sir,

I go through the auxillary.par file.
all possible P-P distances are given.
But i would like to know which P-P distance is to be taken (the least distance or is there any particular correspondance like i : i+n)?
I want to understand the difference in the minor groove due to binding of a ligand ; near and away from the region of binding.

Thanking you
Mary

[xiangjun]

3DNA is a tool to be used as users see fit. While I can provide general suggestions as I did in my previous response, how to apply the program in a specific situation is beyond my support.

That said, for your question regarding for the minor groove width, I do not think in real world structures (as in the PDB) there is a strict correspondence between the shortest P-P distance and i:i+n, where n is fixed. If you are serious on this topic, it helps to perform a survey on some representative structures (please let us know your findings).

HTH,

Xiang-Jun

[maryatx3dna]

ok sir.
thanking you

mary