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 one year 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)
 one year 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
 one year 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
 one year 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
 one year 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
 one year ago
Best ResponseYou've already chosen the best response.0+ I really like to learn physical biochemistry / biophysics.

abb0t
 one year 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
 one year ago
Best ResponseYou've already chosen the best response.3\[\huge\color{red}{i'm~~not~~that~~good~~at~~biology ~~:(}\]

agreene
 one year 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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