mfold energies difference

Question

[nathanielsaxe]

Hi,

I have two microRNA sequences that differ by a few nucleotides. I used mfold on both sequences and they have slightly different energies -44.9 and -44.2. I was wondering what the significance of this difference is, or what sort of difference is significant. I looked at the folding prediction and the picture looks exactly the same, so I'm not too sure how to interpret this 0.7 change in binding energy.

Thanks

Answer 1

[mcc]

One thing that occurred to me is this paper by Nick Pace,

Hydrogen Bonding Stabilizes Globular Proteins
Biophysical Journal Volume 71 October 1996 2033-2039

States:

Measurements of the change in conformational stability, delta (delta G), for the mutation of a hydrogen bonded residue to one incapable of hydrogen bonding suggest a stabilization of 1.0 kcal/mol per hydrogen bond. If the delta (delta G) values are corrected for differences in side-chain hydrophobicity and conformational entropy, then the estimated stabilization becomes 2.2 kcal/mol per hydrogen bond.

So, H-bonding seems outside your range.
HTH