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I have been told not to vortex solution containing protein. The reason I was given is bubble formation. Here I am interested in the effect of bubble formation in general.

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A "bubble" per se would do no harm unless you have cells (without walls like mammalian cells) in the suspension. If you agitate the protein mixture vigourously then it may lead to denaturation of proteins by extensive intermolecular collisions. The "froth" formation is an indication of denaturation as denatured proteins stabilize these foams [1, 2].


References:

  1. Zayas, Joseph F. "Foaming properties of proteins." Functionality of proteins in food. Springer Berlin Heidelberg, 1997. 260-309.

  2. Schmidt, Isabelle, et al. "Foaming properties of protein/pectin electrostatic complexes and foam structure at nanoscale." Journal of colloid and interface science 345.2 (2010): 316-324.

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  • $\begingroup$ would you not agree that denaturation because of "extensive intermolecular collisions" depends on whether there is a low or high concentration? Because low concentration = few collisions and high concentrations = more collisions. So is the rate/process of denaturation (therefore creation of bubbles) depended on the solution which is agitated? $\endgroup$ – Ebbinghaus Feb 4 '16 at 10:36
  • $\begingroup$ @JordiZambrino Yes concentration of the solute and other fluid properties of the solution such as viscosity etc also have a role. You do see more froth with higher concentrations. It also depends on the molecular nature of the protein. But my point is that froth is an effect of denatured proteins and not the cause. $\endgroup$ – WYSIWYG Feb 4 '16 at 11:48
  • $\begingroup$ I want to point out about undergrad labs: People vortex SDS mixtures and small volumes, and advertently the pipettes can't get everything out of the tube reasonably sometimes due to bubbles. You could try to centrifuge it, but if there are still bubbles, trying to pipette 50µL of bubbles is annoying. I can remember one lab where we had to pellet E. coli in 4 tubes and consolidate the pellets. The resulting solution was very viscous, and if you formed bubbles while pipetting it made things a lot harder to work with. $\endgroup$ – CKM Feb 5 '16 at 1:14

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