I am analyzing DNA minor groove width using Curve+. Can anyone please help me to know how it calculate DNA minor groove width.
Typically, major and minor grooves widths are calculated as defined in the following publication:
El Hassan MA, Calladine CR. Two distinct modes of protein-induced bending in DNA. J Mol Biol. 1998 Sep 18;282(2):331-43.
Imagine we have a dsDNA and we are situated at the phosphate at position i (i.e. P(i)). If we increase the phosphate position in the complementary strand (i.e. P'(i+1), P'(i+2) ... P'(n)) and we calculate distances from those phosphates to P(i), we will observe that as the phosphate position increases, the distance between phosphates also gets larger, up to a maximum, but later, the distance starts decreasing until a minimum, and then it increases again. If we repeat the same procedure but decrasing phosphate positions, we will obtain another minimum. The larger of the two minimums is the width of the major groove and the smaller is the width of the minor groove.
If you need a software, 3DNA is the most widelly used among structural biologists: http://x3dna.org/.
Thanks for reply Oriol. I have one confusion which will be correct method to calculate minor groove width
either calculate minor groove width for MD simulated average structure
or calculate average of calculated minor groove of snapshots of MD trajectory i.e. calculate minor groove width throughout trajectory then calculate average of them?
because I am getting different result by using two different approaches.
Well, first of all, what I told you is how to calculate the "groove width". The definition major/minor stands on which one is the largest and which one is the shortest. The i values in B-DNA +/- 4 for major groove and +/- 3 for minor groove.
But now I have a confusion, I have to analyze MD simulated trajectory of protein - DNA complex, If you are doing MD simulation.
which approach I should use for calculation of minor groove width of MD simulated trajectory
either I generate average structure of whole MD simulation trajectory and calculate minor groove width most of the papers have done like this?
or for each snapshot calculate minor groove width and then average of them?
I'm not an specialist, but if I were you I would first set at which point I want to make the calculus (e.g. from Phosphate 3 to Phosphate 6') and calculate the width at every snapshot. This way you can provide the mean of the minor groove width +/- the standard deviation.
I would calculate major and minor group for each base pair step from each frame. Then, I would take an average and SD/SE for each base pair from the trajectory. Then, I would make a plot of base pair step vs average groove (SD/SE as error bar). This plot will give the information that which base pair step was affected by the protein interactions. These type of plots are also useful for other base pair parameters. I used X3DNA for the all type of calculation.
I am doing same in addition to calculation of minor groove width of average structure and in both case I am getting different result. What I am doing exactly that, it is known that intermixing of CG bp with AT rich sequence will widen minor groove so I did MD simulation of two DNA wt and mutant. When I calculate minor groove of MD simulated average structure wt having CG bp mixed with AT rich sequence have wide minor groove compare to only AT rich DNA. When I calculate minor groove through out trajectory of both DNA average width of all snapshot, minor groove is similar in both DNA.
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