Serena Donnini, Florian Tegeler, Gerrit Groenhof, and Helmut Grubmüller
Typically, in a molecular dynamics simulation, the protonation states of ionizable groups of a protein are set in the beginning of the simulation. This is not always an obvious task, in particular for histidine, as its pKa is close to the physiological pH. In contrast, in a
constant pH molecular dynamics simulation, the protonation state of an ionizable group of a protein is allowed to change during the
simulation according to the local electrostatic environment and the pH of the solution. The pKa values of the ionizable groups can then be obtained from the distributions of the protonation states.
Simulation at constant pH
The downloadable movie is a 5 ns constant pH simulation (pH=4) of turkey ovomucoid third domain in water. The acidic amino acids (aspartatic acid and glutamatic acid) are drawn with sticks. They are coloured red when they are negatively charged and blue when they are protonated. The proton is highlighted as a ball.
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