On a molecular level, is there a method often used in the field of proteins which quantifies the hydrophobic interactions present?
I've seen Molecular Hydrophobicity Potential as an option for this. Is this a well recognised method? If not, what is the most well recognised method for carrying out these analyses?
for insilco, hydropathy plot can be used.
in wet lab condition, different solvents can be used in aqueous two phase partitioning method. or contact angle measurement can be tried
Hi Thomas,
good question!
There are several (dozens of) hydrophobicity scales like the one of Kyte & Doolittle:
Article A Simple Method for Displaying the Hydropathic Character of a Protein
There is also the option to calculate a gravy score for your protein: http://www.gravy-calculator.de/
The best you can do is to combine the protein topology and the local hydrophilicity/-phobicity. We also did that once on a quite coarse level:
Article Evidence for Water-Tuned Structural Differences in Proteins:...
I think there are some more intricate approaches like the determination of PMF (potential of mean force) or MHP (molecular hydrophobicity potential).
Just go through some of the bioinformatic tools, then you will surely find something helpful.
The topic, however, is not easy to digest at the beginning as it is generally very empiric.
Good Luck,
Joerg
Thank you both for your responses!
Joerg Reichenwallner Thanks, I found my first forays into this field to be rather overwhelming! These are very helpful starting points.
In experimental field, you can carry out 8-Anilino-1-naphthalenesulfonic acid (ANS) Displacement study of protein by fluorescence technique as ANS is best known for hydrophobic probe.
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