Hello everyone,
I know one can calculate the theoretical pI based on the primary structure (i.e. sequence), but I also know this is slightly inaccurate due to how the protein folds (as indicated in cIEF experiments not matching theoretical calculations). The problem is while I understand that depending on the fold, some charged residues may be shielded or covered by hydrophobic groups, and their contributions to the pI will be less than say an exposed charged residue, I cannot find any literature that explicitly discusses what specific interactions are modified or affected by protein folding (i.e. tertiary structure).
Can anyone point me into the right direction here? Maybe provide some articles that explicitly state the relationship between pI and tertiary structure and what interactions are influencing the pI?
Edit:
I just wanted to add, I'm not looking to calculate a specific pI for a protein, but rather looking for some papers that address how tertiary structure (interactions such as charge-charge or steric hinderance) influence the pI.
Hi Sam, sorry but as far as I know there is no relationship between pI and tertiary structures.
All protein tertiary structures are different. Some are dependent on charge-charge interactions, hydrophobic interactions, hydrogen bonds, steric hindrance, hydration, van der Waals or most commonly a mixture of all of the above.
This is not a case of "one size fits all."
Hi Sam
It depends on what you want to do. If you're trying to purify protein using Ion exchange chromatography, in calculating pI is only useful to get you in the ballpark and after that it is a matter of trial and error until you figure out the right pH of your buffer. I can only suggest 3D protein structure prediction programs that might give you a hint of shielded aminoacids, upon which you might guesstimates pI differently. Nonetheless, I agree with Steingrimur that it is not an easy task.
Hello Sam,
maybe this article could help a bit...
Article Empirical relationships between protein structure and carbox...
To calculate the pI of a protein you need the pKa of each group, which is a function of the local electrostatic field.
A list of servers that will do electrostatic analyses based on atomic resolution structures: https://omictools.com/protein-pka-prediction-category. To calculate the pI, you would start from a first estimate of the pI, calculate the pKa of all groups at this pH, recalculate the pI using these pKa values, and do as many iterations as needed to get a sufficiently good approximation of the actual pI.
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