After modelling our protein through the 3 modelling methods- homology modelling,
threading and ab-initio, we compared all the models to choose the best model.
All the models obtained through threading were monomers and since the native R2-NTF
pyocin and AP22 bacteriophage structures are trimers, we discarded these monomeric
structures from our consideration. We then compared the models obtained via
homology modelling and threading to choose the best model.
- Root Mean Square Deviation (RMSD):
In bioinformatics, the root-mean-square deviation of atomic positions is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed proteins. It is a measure to study how good the alignment of two proteins is. Lower the RMSD, better is the alignment and lesser is the deviation of the backbones of the two proteins. A low RMSD usually below 3 is considered good for alignment. We calculated the RMSD of each fusion-protein model with:
- The R2-NTF tail fiber protein
- The AP-22 bacteriophage tail fiber protein
- Ramachandran Plot:
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. It gives information about the energetically allowed and disallowed regions in the protein. Having a lower number of residues in the disallowed regions and a high number of residues in the allowed energy regions indicates a good protein structure.
All these parameters were compared across models obtained via homology modelling & ab-initio methods. Higher weightage was given to the Ramachandran Plot values over the RMSD values.
RMSD with lower part (4mtm) RMSD with upper part (6cu2) Residues in disallowed regions Residues in favoured regions Ab-initio Model 1 0.435 2.648 0% 89.2% Ab-initio Model 2 0.419 6.264 0% 87.8% Ab-initio Model 3 0.375 2.335 0% 86.1% Ab-initio Model 4 0.475 4.024 0.2% 86% Ab-initio Model 5 0.427 4.631 0% 89.4% Swiss Model 4.666 1.527 0.3% 88.1%
Based on the table above, model 1 was chosen as the best model.
Ab-initio Model 1
We then performed the Energy Minimization for this chosen model using the YASARA Energy Minimization toolkit. The PDB file of Model 1 was submitted at the YASARA web server and results were obtained via email. The energy of the submitted structure was minimised from -360503.1 kJ/mol to -371201.4 kJ/mol.Energy Minimization
Energy Minimization Alignment