Week 7 Progress Report
Development of Software Package for Determining Protein Titration Properties
By
Kaila Bennett, Amitoj Chopra, Jesse Johnson, Enrico Sagullo
Work completed:
As right now we have successfully completed four scripts. One to clean a PDB files, we also have written a script to convert our cleaned PDB file to a PQR file. The rational behind this script is to obtain a file that is compatible to the Adaptive Poisson-Boltzmann Solver. PQR format incorporates
van der Waals radii and partial charge. We then have successfully written a script that can successfully call to APBS to calculate free energies. It should be noted that to calculate free energies, we need to use the thermodynamic cycle, the thermodynamic cycle has four proposed states, so our scripts for the conversion to PQR has to able to generate four PQR files. Our group is working to make all scripts platform independent, but right now are script for PDB2PQR can only run on LINUX and UNIX based systems. It should also be noted that right now all calculations have been performed on PDB 1LY2. We have also successfully completed a script that can extrapolate free energies from output calculation of APBS. Our group also presented our accomplishments thus far, creating PPT the outlined our accomplishment, we worked on this from Saturday to Monday.
Future work:
As a group we are coming up with a detailed plan for a way of completing the rest of our goals for the winter quarter. First and for most we need to make all our codes platform independent. Next we need to make sure our free energies values are accurate for our PDB file 1LY2. We then to optimize all our scripts, so that we can move onto our next step. Using the thermodynamic cycles proposed by Morikis et al and Antosiewicz et al to write a input script for calculations of intrinsic pKa. We will first write the script that it will only calculate intrinsic pKa for four ionizable residues. These pKa values will then be correlated to other software. Once we are sure of our outputs values, we will then make this code capable of calculating pKa values for m ionizable residues. We will then need to create codes that are able to output calculated pKa for m residues on a titration curve. Then eventually down the road these values will then be used to calculate our ultimate goal of apparent pKa for our protein. Apparent pKa values will also be outputted on a titration curve.
Project review:
As of right now our group is slightly behind. Although we do have some codes done, we should have already completed codes that calculate intrinsic pKa’s, and should have already optimized those codes, and correlated our values to check their accuracy. To that end we know the theoretical knowledge for calculations of intrinsic pKa’s starting first with one ionizable
Amino acid residue and then moving to m ionizable amino acids. We have included in the appendix our derivations of pKa for the thermodynamic cycle. These derivations will help us in our efforts to write scripts for calculations of the pKa intrinsic.
Appendix:
Equation 1:
Equation 2:
Equation 3: Remark that this is how we will define the change in free energy
Equation 4: Follow the inner arrows of the thermodynamic cycle
Equation 5: Simplification
Equation 6: Final Form
Corollary: the next derivation will now look at on ionized amino acid while the other are neutralized. Eventually this prove will be extrapolated to account for M ionizable amino acids.
Equation 7:
Equation 8:
Remark:
Equation 9: We redefined the change in free energies
So from equation 6 we redefine the difference of free energy, to account from the neutral to charged state
Equation 9:
Equation 10:
Equation 11: This is away to calulate intrinsic pKa
Equation 12:
To be able to find intrinsic pKa follow much of the above derivation but notice the slighty modified thermodynamic cycle:
Equation 13:
Equation 14: Final form intrinsic pKa for one ionizable residue
Antosiewicz model will then be used to in the spring quarter to calculate apparent pKa value.