Development of Software Package
for Determining Protein Titration
Properties
By
Kaila Bennett, Amitoj Chopra, Jesse Johnson, Enrico Sagullo
Overview
This 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
Background
It is well known that proteins are
highly dependant on the pH of the
environment
Functional groups within the
protein can extract or release
protons
This proton transfer phenomena
lead to the changes in ionizable
charge groups:
Aspartic acid
Glutamic acid
Arginine
Lysine
Histadine
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
Background
To extract titration
properties we will be writing
scripts using the
programming language, R
R programming language
used for statistical computing
and graphics
Using R, we will be able to
integrate free energy
calculations using Adaptive
Poisson-Boltzmann Solver
(APBS)
Purpose of the Project
Using 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 Winter
Get acquainted with R
programming language
Workshops with Dr. Girke
Tutorial 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 curves
Examples of titration curves generated in R
Objectives Spring
Statistical
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
acids
Calculate protein
stabilities and binding
free energies
Example of clustering in R
Methodology Winter
Methodology Spring
Budget
As of now, we do not foresee any
expenditures due to the fact that we are
using all free software
Relevant Equations
Conclusion
The goal of this project is to create a local downloadable
software package that will be able to calculate the
titration properties for any protein
The 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 analysis
The 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 Kieslich
Dr. Thomas Girke
Dr. Jerome Schultz
Hong Xu
References
1.
2.
3.
4.
5.
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
Antosiewicz, Jan M. "Protonation Free Energy Levels in
Complex Molecular Systems." Wiley InterScience 89.4 (2007).
Print
Gilson, Micheal K. "INTRODUCTION TO CONTINUUM
ELECTROSTATICS, WITH MOLECULAR
APPLICATIONS." Editorial. 13 Jan. 2006. Print
Morikis, Dimitrios. "Molecular thermodynamics for charged
biomacromolecules." Fluid Phase Equilibria (2006). Print
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