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Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, but I didn't know if there was some estimate that could still be used to good approximation.

If this does not exist, is there still a way to approximate the diffusion constant of certain proteins. I am trying to make a rough model based on reaction-diffusion equations, and I wanted to estimate diffusion constants of certain species in the model.

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  • $\begingroup$ This great paper, Protein volumes and hydration effects, by SJ Perkins, shows how to calculate the partial specific volume from AA sequences, so you can then calculate the diffusion constant? $\endgroup$ – user1136 Sep 13 at 13:11
  • $\begingroup$ related paper to Perkins ref $\endgroup$ – user1136 Sep 13 at 13:14
  • $\begingroup$ Also, you can check PDB if the structure of the protein is available. If so you can get a reasonably close estimate of its shape in vivo. If not, then you can check out some software that predict protein structure based on homologous proteins. However, I cannot say that there is a good estimate of protein diffusivity just based on number of amino acids. Are you interested in a particular protein or you want to make a general model? $\endgroup$ – WYSIWYG Sep 13 at 15:10
  • $\begingroup$ @WYSIWYG After further reading it looks like I am looking at a cytokine that only has about 25 amino acids (49.5 kDa). I am assuming this might be easier to estimate a diffusion constant for since it is so small? $\endgroup$ – Aaron Stevens Sep 16 at 23:33
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    $\begingroup$ @AaronStevens someone could have measured diffusivity of cytokines in blood and ECF (for e.g.). If not, you can find the structure of a cytokine on PDB, obtain it's radius and estimate diffusivity using the Stokes-Einstein equation. $\endgroup$ – WYSIWYG Sep 17 at 6:34

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