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I am a MSc student working in mathematical biology. In my thesis I am modelling diffusion of a protein that can bind to cell surface receptors. In order to simulate this I need some rough figures about the binding rates, degradation rates, diffusion rates etc. of components involved in this system. I have managed to find some information about these things, but they have all come from reading papers - biology papers where I only barely have enough knowledge to grasp the key concepts and (lets face facts) barely have the patience to read.

Is there a better way to find this quantitative data? Ideally I would love to come across a database that had this kind of data in it, but I'm not holding my breath.

What techniques do people in my position use to find this kind of information?(short of trawling through incredibly dense biology papers)

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I'll list the papers that I obtained these parameters from. BioNumbers is a very useful resource and some of these papers that I cite have been obtained from the reference mentioned in BioNumbers. So BioNumbers should the first place to look for things like this. If you are not satisfied then start googling around :)

You should, however, keep in mind that simulation using exact parameters may not be very helpful. You can try varying the parameters in some given range and see the effects. Some parameters actually vary a lot.

  1. Protein translation rate: 11 amino acids per second. Assume some steady state concentration of mRNA. This parameter is highly variable as there can be multiple ribosomes per mRNA [1]. Also see Schwanhäusser et al. (Supplementary excel sheet) [2]
  2. Protein degradation rate: Take an average or one of the values reported by Schwanhäusser et al. (2011) [2]
  3. Association/dissociation rates: See table shown by Zhou (2003). It lists different known interactions.[3]
  4. Protein diffusivity: This differs for cytoplasm and water. You can assume diffusivity in ECF to be same as that in water. See Arrio-Dupont et al. (2000) [4]. They report it for specific proteins. You can extrapolate for other proteins using the Stoke-Einstein relation which says that diffusivity decreases inversely with the radius of the particle.

[1] Siwiak, Marlena, and Piotr Zielenkiewicz. "Transimulation-protein biosynthesis web service." PloS one 8.9 (2013): e73943.

[2] Schwanhäusser, Björn, et al. "Global quantification of mammalian gene expression control." Nature 473.7347 (2011): 337-342.

[3] Zhou, Huan‐Xiang. "Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment." Protein science 12.10 (2003): 2379-2382.

[4] Arrio-Dupont, Martine, et al. "Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells." Biophysical journal 78.2 (2000): 901-907.

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  • $\begingroup$ Thanks for the references and +1 for bionumbers! That is exactly the kind of thing I was looking for $\endgroup$ – Phill Mar 2 '16 at 22:51

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