Eric Martz was wondering on the Jmol mailing list if there are animations around of 3D conformational changes of protein structures due to changes in the pH?
I spent some time looking through the literature to try and answer this, because I found it pretty interesting, but I found very little. I looked through a bunch of papers on constant pH charmm simulations, but none provided movies. It seems like only one in 10 or 20 MD papers do anyway.
You can have a look at ion channels simulations and normal modes analysis. Specially acid sensing ion channels, activated by protons.