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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.
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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:
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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 --- --- --- ---
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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
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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
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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
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ok sir.
thanking you
mary
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University