Protein Electrical Simulation
What is the role of molecular dynamics simulation?
Computer simulations are a powerful tool for analyzing complex systems consisting of a large number of particles. The assumption
underlying these simulations is that the molecular behavior and interactions in a system can be described by the fundamental law of electrostatics,
quantum mechanics, and statistical mechanics. The computer becomes a virtual laboratory, and when the simulation model agrees with expermental
results, we can better understand the physical characteristics of the measured phenomena. Listed below are some topics within Protein Electrical Simulation
that have been studied in our group.
The simulation program CHARMM (Chemistry at Harvard
Macromolecular Mechanics) is a standard molecular dynamics program and is useful
for investigating complex macromolecular systems in biology. It is based on sets of force fields
for each atom in a system. By running transient response and steady state response simulations in
CHARMM, one can obtain a protein's relaxation time and its change in permittivity.
Calculation of Protein Charge Moments
The spatial charge distribution of a protein is perhaps best indicated by its electric dipole moment.
Charge distribution, three-dimensional structures from the Protein Data Bank, covalent bonds, pKa shifts,
and partial charge values give us enough information to effectively calculate the dipole moment of a protein.
B. L. Mellor, E. Cruz Cortes, D. D. Busath, and B. A. Mazzeo.
Method for estimating the internal permittivity of proteins using dielectric spectroscopy.
Journal of Physical Chemistry B 115, 2205 (2011).
B. L. Mellor, S. Khadka, D. D. Busath, and B. A. Mazzeo.
Influence of pKa shifts on the calculated dipole moments of proteins.
The Protein Journal 30, 490-498 (2011).