A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH

The pyrin domain is one of four subfamilies of the death domain superfamily of proteins, all members of which share a similar three-dimensional fold with a structure comprising five or six antiparallel alpha-helices. The pyrin domain of the ASC (six-helical fold) and of the NALP1 (five-helical fold) proteins were simulated at two different pH values, 3.7 and 6.5, with two different force-field parameter sets, and the molecular dynamics simulation trajectories were compared to NMR experimental data. The two force fields that were used did not show very different results. The simulations of NALP1 at pH 6.5 largely satisfied the experimental NOE atom-atom distance bounds that were measured at pH 6.5, and preserved its tertiary structure. The simulations at pH 3.7 showed a denaturation of the protein. The simulations of ASC at pH 3.7 only satisfied the experimental NOE atom-atom distance bounds that were measured at pH 3.7 if either three acidic side chains (Asp48, Glu64 and Asp75) or only two (Glu64 and Asp75) were not protonated. This indicates that the ASC tertiary structure is stabilized by salt bridges at low pH. A corresponding analysis for NALP1 at pH 3.7 only yielded one possible salt bridge, but this did not stabilize the tertiary structure at low pH. The results show that the particular protonation states of acidic side chains in the protein interior might be crucial to properly modeling these proteins at low pH.