Geometrical and Energy Consequences of Proteolytic Event

CutTPproT finds aminoacids on the adjoining surfaces after proteolytic event in a protein. It performs calculations of the energies for the initial protein and the two fragments after the proteolytic cut. It calculates also the interaction energy between two pieces of a protein after proteolytic event. At this point no conformational changes are taken into account. They could be taken into account by employing more advanced methods such as molecular mechanics and dynamics.

Energies of the protein and its fragments before and after proteolytic event are calculated using PSQS - Protein Structure Quality Score method. According to this method the energy-like term is a sum of local, burial and contact potentials. Local potential - describes local geometry propensities of polypeptide chain. It is a function of residue types of neighbor residues: i-1, i and i+1. Burial potential - describes the tendency of hydrophobic residues to concentrate in the protein core and the tendency of hydrophilic residues to concentrate on the protein surface. Contact potential - describes the likelihood of different residue pairs to be in close contact.

Only burial and contact potentials are taken into account for rough estimation of the energy outcome of proteolytic event.

Currently the interaction energies are not well calibrated, but the general suggestion is that the more positive value of the interaction energy the more likely the protein fragments will dissociate after proteolytic event.

Server produces rasmol scripts that can be used for displaying two parts of the protein after the cut and show residues that were in contact before the cut. Server uses rasmol/chime or jmol programs.

User needs to provide the position of the cut site in the form: Res1-number (- Res2-number).

This tool performs calculations on either uploaded local PDB file or downloaded from RCSB file if PDB id code is provided.

PSQS method