Development of Software Package for Determining Protein

Titration PropertiesBy

Kaila Bennett, Amitoj Chopra, Jesse Johnson, Enrico Sagullo

OverviewThis talk will address how our group proposes to develop a stand-alone software package capable of elucidating protein titration characteristics using the thermodynamic cycle

Adapted from Morikis et al

BackgroundIt is well known that proteins are highly dependant on the pH of the environmentFunctional groups within the protein can extract or release protons This proton transfer phenomena lead to the changes in ionizable charge groups:

Aspartic acidGlutamic acidArginine LysineHistadine

Charge amino acids have titratable side chain groups These titratable groups have characteritistic pKa’s

Background (pKa)The thermodynamic cycle can be used to calculate pKa

Within each pKa resides an intrinsic and apparent pKa

The intrinsic pKa describes the ionization process of a specific ionizable group when all other ionizable groups are held constant (Morikis et al). The apparent pKa relates the intrinsic pKa and the free energies between charged residues

Cycle adapted by Morikis et al

BackgroundTo extract titration properties we will be writing scripts using the programming language, RR programming language used for statistical computing and graphicsUsing R, we will be able to integrate free energy calculations using Adaptive Poisson-Boltzmann Solver (APBS)

Purpose of the ProjectUsing R programming, we want to write a function that converts PDB files to PQR files. Once the program is complete, we will use APBS software to calculate free energies and electric static potentials. These calculations will then aid us in writing a program that will calculate intrinsic and apparent pKa values

Objectives WinterGet acquainted with R programming language

Workshops with Dr. GirkeTutorial help from Chris Kieslich

Incorporation of APBS Allows us to calculate the intrinsic pKa values

Calculates Free energies

Have software able to take any protein database files (pdb) and calculate intrinsic pKa to generate titration curvesExamples of titration curves generated in R

Objectives SpringStatistical approximation for the calculation of apparent pKa values using the intrinsic values

Clustering Monte Carlo

Add scripts to print out titration curves for each and all ionizable amino acidsCalculate protein stabilities and binding free energies Example of clustering in R

Methodology Winter

Methodology Spring

BudgetAs of now, we do not foresee any expenditures due to the fact that we are using all free software

Relevant Equations

ConclusionThe goal of this project is to create a local downloadable software package that will be able to calculate the titration properties for any proteinThe software will first calculate the intrinsic pKa values of each residue which will then be correlated into the apparent pKa values

The software will work to generate titration curves for easy to view analysisThe software will integrate already defined software such as APBS to in essence create a user-friendly convenience package. It will be a stand-alone software free and available for anyone to use

Acknowledgements

Dr. Dimitrios Morikis Chris KieslichDr. Thomas GirkeDr. Jerome SchultzHong Xu

References 1. Trylska, Joanna. "View Continuum Molecular Electrostatics, Salt

Effects, and Continuum Molecular Electrostatics, Salt Effects, and Counterion Binding—A Review of the Poisson–Boltzmann Counterion Binding—A Review." Wiley InterScience 28.2 (2007). Print

2. Antosiewicz, Jan M. "Protonation Free Energy Levels in Complex Molecular Systems." Wiley InterScience 89.4 (2007). Print

3. Gilson, Micheal K. "INTRODUCTION TO CONTINUUM ELECTROSTATICS, WITH MOLECULAR APPLICATIONS." Editorial. 13 Jan. 2006. Print

4. Morikis, Dimitrios. "Molecular thermodynamics for charged biomacromolecules." Fluid Phase Equilibria (2006). Print

5. Nielsen, Jens. "Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting." Methods in Enzymology. Print.

Questions