This dataset contains results from molecular dynamics simulations of the Hsp90 chaperone, including the corresponding PDB structures. The trajectory files are provided in .xtc format. There are ten simulation files corresponding to different systems of the dimeric structure. These systems include: the dimer with both tyrosine 33 residues nitrated and protonated (dimer-nY33prot), the dimer with both tyrosine 33 residues nitrated and deprotonated (dimer-nY33deprot), the dimer with both tyrosine 56 residues nitrated and protonated (dimer-nY56prot), the dimer with both tyrosine 56 residues nitrated and deprotonated (dimer-nY56deprot), and the native dimer (dimer-native). All of these systems have ATP bound as a ligand.

Additionally, there are ten simulation files corresponding to different systems of the N-terminal domain structure, in which the ATP lid region is in the open conformation. These systems include the native N-terminal domain (NTD-native), the N-terminal domain with tyrosine 56 nitrated and protonated (NTD-nY56prot), and the N-terminal domain with tyrosine 56 nitrated and deprotonated (NTD-nY56deprot). In all these cases, ATP is bound as a ligand.

Finally, there are three additional systems of the N-terminal domain in which ATP is not bound: the native N-terminal domain (NTD-noATP-native), the domain with tyrosine 33 nitrated and protonated (NTD-noATP-nY33prot), and the domain with tyrosine 33 nitrated and deprotonated (NTD-noATP-nY33deprot).

Each simulation runs for 1 microsecond and is summarized in 1000 frames.

This dataset supports the findings of the article entitled “Nitration-driven structural changes in Hsp90 linked to gain of pathological functions”.