pKa Server Documentation
Overview:
This app is the ROSIE interface to Rosetta-pH, a fast and simple physics-based method to estimate the pKa values of five types of residues with varied protonation states (Asp, Glu, His, Tyr, and Lys) based on the provided input protein structure.
In Rosetta pKa calculations, the pH is titrated from 1 to 14 with Monte Carlo (MC) sampling of protonated and deprotonated side chains with χ-angles sampled from a backbone-dependent rotamer library, irrespective of the protonation state. Each rotamer configuration is accepted or rejected using the Metropolis criterion and the Rosetta score function calibrated for pKa calculations. The conformational degeneracy in the protonated variants of Asp and Glu (with H atoms on either of the terminal Oδ and Oε atoms, respectively) is explicitly incorporated by accommodating both possible protonated versions for the residues during sampling. The χ-angles for protons in the protonated variants are sampled at their canonical angles (−60, 60, 180) and ±20°. For neutral His, both possible tautomers (with proton on either Nδ1 or Nε2 atoms) are sampled.
The protonation states of the lowest-energy conformers sampled during the side-chain conformational search are recorded during every pH step of the calculation. An initial titration is carried out in intervals of 1 pH unit, starting with pH = 1 until a change in protonation state is observed, and subsequently a finer sampling interval of 0.1 pH unit is employed in the appropriate coarse interval. The pKa is identified as the pH value at which the lowest-energy conformer of the residue shifts from the protonated to the deprotonated state.
Optional: The algorithm also allows for simultaneous sampling of the side chains and protonation states of the residues neighboring the target residue during pKa calculations. The additional sampling might improve prediction accuracy if the neighboring residues are ionizable and are involved in coupling with the target residue.
Tips:
- The algorithm repacks only the target residue side chain during pKa calculations (S: Site-Repack) and retains the input
side chains for the other residues. If a repack radius is specified, the neighboring residues are included in the sampling
during pKa calculations (N : Neighbor-Repack). Alternately, all the side chains in the input PDB can be Pre-packed before
pKa calculations (P: Pre-pack).
- If a residue does not titrate during the Site-Repack (S) mode, the algorithm tries Neighbor-Repack (N) and Pre-pack (P)
method in that order. The method used for any residue can be identified based on the entry code in the Method column of the
output file.
- Water and other hetero-atoms are removed from the input PDB before pKa calculations. So, the algorithm is not recommended
for pKa calculations for residues neighboring small-molecule ligands or other non-peptide residues.
- If the input is based on an NMR structure, only Model 1 should be included in the input file.
Input:
An input structure in the PDB format containing the required residues for pKa calculations.
Interpreting Results:
The server returns a text file with the calculated pKa values for all the ionizable residues (of the type Asp, Glu, His, Tyr or Lys) in the provided input structure along with method used for pKa calculations, the residue numbers and their theoretical intrinsic pKa values. Ionizable residues buried in the core of the protein and near enzyme catalytic sites are expected to show higher pKa shifts compared to the residues on the protein surface exposed to the solvent.
We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.
Modeling tools developed by Krishna Praneeth Kilambi at GrayLab@JHU. The Rosie implementation was developed by Sergey Lyskov.