Question

How do we explain the electrostatic interactions that affect the acid dissociation constant, using PB (Poisson-Boltzmann) relationship for biological macromolecule
@blues (or any other relation if you deem it better)

Answer 1

The general Poisson-Boltzmann relationship for electrostatic interactions:
\[\nabla D(r) \nabla V_{e}(r)-D(r)K ^{2}\sinh[V _{e}(r)]+\frac{ 4 \pi Ze \rho(r) }{ k_{B}T }=0\]
\[K=\frac{ 8 \pi (Ze)^{2}I }{ D(r) k_{B}T }\]
\[I=\sum_{i=1}^{N}\frac{ Z_{i}^{2} c _{i}}{ 2 }\]
So much I do know.

Answer 2

Is this something you really need help in biology or just something you found? Because this looks like graduate level biophysics.

Answer 3

@abb0t
The assignment say, argue for a change in the acid dissociation constant by electrostatic interactions. I only know the equation because I have been reading Physical Biochemistry by Van Holde. He explain that the electrostatic interactions are affecting the pKa, but I don't see how he manage to say he graph the pKa change as a function of the logarithm to the ionic strength of the solution (log(I)).
But I suppose you could look at the "self energy" as Van Holde call it and then estimate the change in pKa by the change in self energy?

Answer 4

+ I really like to learn physical biochemistry / biophysics.

Answer 5

I think only a professor in that field might be able to help you best with what you're researching. And I don't think there are any physical biochemists here....that I know of.

Answer 6

\[\huge\color{red}{i'm~~not~~that~~good~~at~~biology ~~:(}\]

Answer 7

http://assets.openstudy.com/updates/attachments/514b444de4b07974555dca25-nincompoop-1363938224479-1s2.0s0006349502753757main.pdf

Answer 8

I'm not sure in what bio-important situation your question is referring to, which makes it a bit difficult to help you. But as for the general idea of a change to pKa for experimentation, due to electrostatic force interactions, any general chemistry book should be able to provide reasons for this.

I do computational molecular and structural biology / biophysics, and the specific numbers we use depend on the calculation and the algorithm we use. We normally use autodock, i suppose i could search around the documentation to see how they handle this issue, but its never really come up in any meaningful way... http://autodock.scripps.edu/