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

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Frostbite
 3 years ago
Best ResponseYou've already chosen the best response.0The general PoissonBoltzmann 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.

abb0t
 3 years ago
Best ResponseYou've already chosen the best response.0Is this something you really need help in biology or just something you found? Because this looks like graduate level biophysics.

Frostbite
 3 years ago
Best ResponseYou've already chosen the best response.0@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?

Frostbite
 3 years ago
Best ResponseYou've already chosen the best response.0+ I really like to learn physical biochemistry / biophysics.

abb0t
 3 years ago
Best ResponseYou've already chosen the best response.0I 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.

umarsback
 3 years ago
Best ResponseYou've already chosen the best response.3\[\huge\color{red}{i'm~~not~~that~~good~~at~~biology ~~:(}\]

agreene
 3 years ago
Best ResponseYou've already chosen the best response.1I'm not sure in what bioimportant 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/
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