Abstract
The effect on the folding/unfolding equilibrium of protonating the aspartic acid on the Trp-cage miniprotein is studied by explicit solvent moleclular dynamics simulations. Replica exchange molecular dynamics (REMD) simulations spanning the temperature range from 280K to 538K were carried out to the micro second scale using the AMBER99SB forcefield in explicit TIP3P water. The root mean square distance from the backbone of the NMR structure shows two highly populated basins close to the native state with peaks at 0.6 A and 1.6 A which are consistent with previous simulations using the same forcefield. The fraction of folded replicas shows a drastic decrease because of the breaking of the salt bridge. However, significant populations of conformations with the arginine sidechain completely exposed to the solvent, but within the folded basin. This shows the possibility to reach the folded state without formation of the ion pair contrary to the expected.
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